gyrB:Gene Product(s): Difference between revisions

Standard name	GyrB
Synonyms	DNA gyrase, subunit B^[1], B3699^[2]^[1], NalC^[2]^[1], ParA^[2]^[1], PcbA^[2]^[1], PcpA^[2]^[1], HopA^[2]^[1], Cou^[2]^[1], HisU^[2]^[1], HimB^[2]^[1], GyrB^[2]^[1] , acrB, Cou, ECK3691, himB, hisU, hopA, JW5625, nalC, parA, pcbA, pcpA, b3699
Product description	DNA gyrase, subunit B^[2]^[3]; Component of DNA gyrase^[3] DNA gyrase, subunit B; novobiocin, coumermycin resistance^[4]
EC number (for enzymes)	5.99.1.3^[1]
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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0003918	DNA topoisomerase (ATP-hydrolyzing) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000565	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003918	DNA topoisomerase (ATP-hydrolyzing) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001241	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003918	DNA topoisomerase (ATP-hydrolyzing) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002288	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008094	DNA-dependent ATPase activity	PMID:6094559^[5]	IDA: Inferred from Direct Assay		F	ATPase activity of the GyrB subunit was followed by measuring the release of 32P-labeled phosphate from reactions containing [y-32P]-ATP in the presence of GyrA and DNA (Figure 1). Omission of DNA or GyrA (which binds DNA) resulted in dramatically reduced ATPase activity of GyrB.	complete
	GO:0003918	DNA topoisomerase (ATP-hydrolyzing) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011557	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003918	DNA topoisomerase (ATP-hydrolyzing) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013506	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	PMID:10764756^[6]	IMP: Inferred from Mutant Phenotype		F	A truncated mutant of GyrB that lacks the C-terminal 160 residues has a reduced ability to retard the movement of DNA through a 5% polyacrylamide gel indicating a deficiency in DNA binding (Figure 5).	complete
	GO:0009330	DNA topoisomerase complex (ATP-hydrolyzing)	PMID:347446^[7]	IDA: Inferred from Direct Assay		C	E. coli gyrase consists of the gene products of gyrA and gyrB genes (Figures 2 & 7).	complete
	GO:0003918	DNA topoisomerase (ATP-hydrolyzing) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013759	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006265	DNA topological change	PMID:6327603^[8]	IMP: Inferred from Mutant Phenotype		P	Nucleoids from E. coli cells containing DNA labeled with [methyl-3H]thymidine were isolated and separated using an ethidium bromide-containing sucrose density gradient. The sedimentation profiles were reported for gyrA and gyrB temperature-sensitive mutants at the permissive and non-permissive temperatures (Figure 1 & 2). The ethidium bromide concentration is proportional to superhelical density, meaning that less supercoiled DNA from a gyrase mutant grown at the non-permissive temperature requires a lower concentration of ethidium bromide.	complete
	GO:0003918	DNA topoisomerase (ATP-hydrolyzing) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013760	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003918	DNA topoisomerase (ATP-hydrolyzing) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018522	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	PMID:9756859^[9]	IDA: Inferred from Direct Assay		F	Using gel filtration and equilibrium ultracentrifugation, the authors showed that the 43kDa N-terminal fragment of GyrB binds to ADPNP, or [32-P]ADPNP, and ATP (Figure 7 and Table 1).	complete
	GO:0003918	DNA topoisomerase (ATP-hydrolyzing) activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:5.99.1.3	F	Seeded from EcoCyc (v14.0)	complete
	GO:0042493	response to drug	PMID:9144789^[10]	IDA: Inferred from Direct Assay		P	Coumarin antibiotic sensitivity, including clorobiocin, novobiocin, and coumermycin A1.	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000565	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003918	DNA topoisomerase (ATP-hydrolyzing) activity	PMID:368801^[11]	IDA: Inferred from Direct Assay		F	Purified E. coli gyrase was shown to induce cleavage and supercoiling in ColE1 DNA in the presence of ATP, but not after the addition of novobiocin or coumermycin A1 (Figure 2). Supercoiling of DNA was monitored by agarose gel electrophoresis (Figure 2A), while the hydrolysis of ATP was measured by following the release of 32-Pi measured by thin layer chromatography (Figure 2B).	complete
	GO:0003677	DNA binding	PMID:6294616^[12]	IDA: Inferred from Direct Assay		F	E. coli gyrase incubated with radiolabeled ColE1 DNA and passed over nitrocellulose filters. The complexes were retained on the filters and radioactivity of the filters was measured and reported in Figure 1.	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001241	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006351	transcription, DNA-dependent	PMID:15535863^[13]	IMP: Inferred from Mutant Phenotype		P	The authors used 3 conditions (treatment with either a quinolone or coumarin anitbiotic or growth of a gyrAts mutant at non-permissive temperature) to alter negative supercoiling of DNA and measured the changes in gene expression by microarray analysis. More than 300 SSGs (supercoiling sensitive genes) were identified that responded rapidly to the experimental conditions. GO replaced obsolete GO:0006350	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002288	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003594	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	PMID:7952188^[14]	IDA: Inferred from Direct Assay		C	Immunogold labeling of cells with anti-GyrB antibodies indicated the presence of GyrB in the cytoplasm of E. coli.	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011557	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013506	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013759	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013760	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018522	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0067	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005694	chromosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000565	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005694	chromosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001241	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005694	chromosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002288	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005694	chromosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011557	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005694	chromosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013506	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005694	chromosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013759	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005694	chromosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013760	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	PMID:7952188^[14]	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0006261	DNA-dependent DNA replication	PMID:6194415^[15]	IMP: Inferred from Mutant Phenotype		P	Seeded from EcoCyc (v14.0)	complete
	GO:0006265	DNA topological change	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000565	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006265	DNA topological change	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001241	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006265	DNA topological change	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002288	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006265	DNA topological change	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011557	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006265	DNA topological change	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013506	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006265	DNA topological change	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013759	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006265	DNA topological change	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013760	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006265	DNA topological change	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018522	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006265	DNA topological change	PMID:6327603^[8]	IMP: Inferred from Mutant Phenotype		P	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	PMID:15535863^[13]	IMP: Inferred from Mutant Phenotype		P	Seeded from EcoCyc (v14.0)	complete
	GO:0009330	DNA topoisomerase complex (ATP-hydrolyzing)	PMID:347446^[7]	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0046677	response to antibiotic	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0046	P	Seeded from EcoCyc (v14.0)	complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	Notes	References	Evidence
Protein	Subunits of DNA gyrase	could be indirect
Protein	prsA		PMID:15690043^[16]	Experiment(s):EBI-884130
Protein	bglJ		PMID:15690043^[16]	Experiment(s):EBI-884130
Protein	deaD		PMID:15690043^[16]	Experiment(s):EBI-884130
Protein	glyS		PMID:15690043^[16]	Experiment(s):EBI-884130
Protein	gyrA		PMID:15690043^[16]	Experiment(s):EBI-884130, EBI-884206, EBI-891214, EBI-891237
Protein	metK		PMID:15690043^[16]	Experiment(s):EBI-884130
Protein	rplJ		PMID:15690043^[16]	Experiment(s):EBI-884130
Protein	rpsB		PMID:15690043^[16]	Experiment(s):EBI-884130
Protein	tufA		PMID:15690043^[16]	Experiment(s):EBI-884130, EBI-891214
Protein	yacG		PMID:15690043^[16]	Experiment(s):EBI-884130, EBI-879073, EBI-882474, EBI-891214
Protein	parE		PMID:15690043^[16]	Experiment(s):EBI-891214
Protein	rplW		PMID:15690043^[16]	Experiment(s):EBI-891214
Protein	parE		PMID:19402753^[17]	LCMS(ID Probability):99.6
Protein	deaD		PMID:19402753^[17]	MALDI(Z-score):18.677074
Protein	metK		PMID:19402753^[17]	MALDI(Z-score):33.839565
Protein	tufB		PMID:19402753^[17]	MALDI(Z-score):21.335822
Protein	gyrA		PMID:19402753^[17]	LCMS(ID Probability):99.6 MALDI(Z-score):28.518798
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MSNSYDSSSI KVLKGLDAVR KRPGMYIGDT DDGTGLHHMV FEVVDNAIDE ALAGHCKEII VTIHADNSVS VQDDGRGIPT GIHPEEGVSA AEVIMTVLHA GGKFDDNSYK VSGGLHGVGV SVVNALSQKL ELVIQREGKI HRQIYEHGVP QAPLAVTGET EKTGTMVRFW PSLETFTNVT EFEYEILAKR LRELSFLNSG VSIRLRDKRD GKEDHFHYEG GIKAFVEYLN KNKTPIHPNI FYFSTEKDGI GVEVALQWND GFQENIYCFT NNIPQRDGGT HLAGFRAAMT RTLNAYMDKE GYSKKAKVSA TGDDAREGLI AVVSVKVPDP KFSSQTKDKL VSSEVKSAVE QQMNELLAEY LLENPTDAKI VVGKIIDAAR AREAARRARE MTRRKGALDL AGLPGKLADC QERDPALSEL YLVEGDSAGG SAKQGRNRKN QAILPLKGKI LNVEKARFDK MLSSQEVATL ITALGCGIGR DEYNPDKLRY HSIIIMTDAD VDGSHIRTLL LTFFYRQMPE IVERGHVYIA QPPLYKVKKG KQEQYIKDDE AMDQYQISIA LDGATLHTNA SAPALAGEAL EKLVSEYNAT QKMINRMERR YPKAMLKELI YQPTLTEADL SDEQTVTRWV NALVSELNDK EQHGSQWKFD VHTNAEQNLF EPIVRVRTHG VDTDYPLDHE FITGGEYRRI CTLGEKLRGL LEEDAFIERG ERRQPVASFE QALDWLVKES RRGLSIQRYK GLGEMNPEQL WETTMDPESR RMLRVTVKDA IAADQLFTTL MGDAVEPRRA FIEENALKAA NIDI
Length	804
Mol. Wt	89.951 kDa
pI	6.0 (calculated)
Extinction coefficient	71,740 - 72,365 (calc based on 26 Y, 6 W, and 5 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	Notes	References
Initiator Methionine	1	Removed	UniProt:P0AES6
Domain	31..174	PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase		PMID:19920124^[18]
Domain	221..391	PF00204 DNA gyrase B		PMID:19920124^[18]
Domain	729..793	PF00986 DNA gyrase B subunit, carboxyl terminus		PMID:19920124^[18]
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=gyrB taxon=562,83333 </beststructure>

Models

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Structure figures

Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:49176395	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948211	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012093	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AES6	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10424	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10424	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948211	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000417	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0419	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ Maxwell, A & Gellert, M (1984) The DNA dependence of the ATPase activity of DNA gyrase. J. Biol. Chem. 259 14472-80 PubMed
↑ Chatterji, M et al. (2000) The additional 165 amino acids in the B protein of Escherichia coli DNA gyrase have an important role in DNA binding. J. Biol. Chem. 275 22888-94 PubMed
↑ ^7.0 ^7.1 Higgins, NP et al. (1978) Purification of subunits of Escherichia coli DNA gyrase and reconstitution of enzymatic activity. Proc. Natl. Acad. Sci. U.S.A. 75 1773-7 PubMed
↑ ^8.0 ^8.1 Steck, TR et al. (1984) DNA supercoiling in gyrase mutants. J. Bacteriol. 158 397-403 PubMed
↑ Kampranis, SC & Maxwell, A (1998) Hydrolysis of ATP at only one GyrB subunit is sufficient to promote supercoiling by DNA gyrase. J. Biol. Chem. 273 26305-9 PubMed
↑ Tsai, FT et al. (1997) The high-resolution crystal structure of a 24-kDa gyrase B fragment from E. coli complexed with one of the most potent coumarin inhibitors, clorobiocin. Proteins 28 41-52 PubMed
↑ Sugino, A et al. (1978) Energy coupling in DNA gyrase and the mechanism of action of novobiocin. Proc. Natl. Acad. Sci. U.S.A. 75 4838-42 PubMed
↑ Higgins, NP & Cozzarelli, NR (1982) The binding of gyrase to DNA: analysis by retention by nitrocellulose filters. Nucleic Acids Res. 10 6833-47 PubMed
↑ ^13.0 ^13.1 Peter, BJ et al. (2004) Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol. 5 R87 PubMed
↑ ^14.0 ^14.1 Thornton, M et al. (1994) Immunogold localization of GyrA and GyrB proteins in Escherichia coli. Microbiology (Reading, Engl.) 140 ( Pt 9) 2371-82 PubMed
↑ Filutowicz, M & Jonczyk, P (1983) The gyrB gene product functions in both initiation and chain polymerization of Escherichia coli chromosome replication: suppression of the initiation deficiency in gyrB-ts mutants by a class of rpoB mutations. Mol. Gen. Genet. 191 282-7 PubMed
↑ ^16.00 ^16.01 ^16.02 ^16.03 ^16.04 ^16.05 ^16.06 ^16.07 ^16.08 ^16.09 ^16.10 ^16.11 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
↑ ^17.0 ^17.1 ^17.2 ^17.3 ^17.4 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
↑ ^18.0 ^18.1 ^18.2 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

gyrB:Gene Product(s): Difference between revisions

Latest revision as of 21:07, 17 February 2015

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

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-DNA gyrase, subunit B<ref name='LIB:Riley_2006'/>, B3699<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, NalC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, ParA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PcbA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PcpA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, HopA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Cou<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, HisU<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, HimB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, GyrB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>
+''DNA gyrase, subunit B<ref name='LIB:Riley_2006'/>, B3699<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, NalC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, ParA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PcbA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PcpA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, HopA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Cou<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, HisU<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, HimB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, GyrB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , acrB, Cou, ECK3691, himB, hisU, hopA, JW5625, nalC, parA, pcbA, pcpA, b3699''
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-!|Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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 |
-nucleotide binding
+DNA topoisomerase (ATP-hydrolyzing) activity
 |
-GO_REF:0000004
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
 |
-SP_KW:KW-0547
+InterPro:IPR000565
 |
 F
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 103: / Line 103: @@
 |
-GO:0003676
+GO:0003918
 |
-nucleic acid binding
+DNA topoisomerase (ATP-hydrolyzing) activity
 |
-GO_REF:0000002
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
 |
-InterPro:IPR006171
+InterPro:IPR001241
 |
 F
 |
-Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 122: / Line 122: @@
 |
-GO:0003916
+GO:0003918
 |
-DNA topoisomerase activity
+DNA topoisomerase (ATP-hydrolyzing) activity
 |
-GO_REF:0000004
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
 |
-SP_KW:KW-0799
+InterPro:IPR002288
 |
 F
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Seeded from [[EcoCyc]] (v14.0)
+|
+complete
+|-
+|
+|
+GO:0008094
+|
+DNA-dependent ATPase activity
+|
+PMID:6094559
+|
+IDA: Inferred from Direct Assay
+|
+|
+F
+|
+ATPase activity of the GyrB subunit was followed by measuring the release of  32P-labeled phosphate from reactions containing [y-32P]-ATP in the presence of GyrA and DNA (Figure 1).  Omission of DNA or GyrA (which binds DNA) resulted in dramatically reduced ATPase activity of GyrB.
 |
 complete
@@ Line 145: / Line 164: @@
 DNA topoisomerase (ATP-hydrolyzing) activity
 |
-GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000003
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
 |
-InterPro:IPR001241<br />InterPro:IPR002288<br />InterPro:IPR011557<br />InterPro:IPR011558<br />InterPro:IPR013506<br />InterPro:IPR013759<br />InterPro:IPR013760<br />EC:5.99.1.3
+InterPro:IPR011557
 |
 F
 |
-Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 160: / Line 179: @@
 |
-GO:0005524
+GO:0003918
 |
-ATP binding
+DNA topoisomerase (ATP-hydrolyzing) activity
 |
-GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000004
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
 |
-InterPro:IPR001241<br />InterPro:IPR002288<br />InterPro:IPR003594<br />InterPro:IPR011557<br />InterPro:IPR011558<br />InterPro:IPR013506<br />InterPro:IPR013759<br />InterPro:IPR013760<br />SP_KW:KW-0067
+InterPro:IPR013506
+|
+F
+|
+Seeded from [[EcoCyc]] (v14.0)
+|
+complete
+|-
+|
+|
+GO:0003677
+|
+DNA binding
+|
+PMID:10764756
+|
+IMP: Inferred from Mutant Phenotype
+|
 |
 F
 |
-Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
+A truncated mutant of GyrB that lacks the C-terminal 160 residues has a reduced ability to retard the movement of DNA through a 5% polyacrylamide gel indicating a deficiency in DNA binding (Figure 5).
 |
 complete
@@ Line 179: / Line 217: @@
 |
-GO:0005694
+GO:0009330
+|
+DNA topoisomerase complex (ATP-hydrolyzing)
+|
+PMID:347446
+|
+IDA: Inferred from Direct Assay
+|
+|
+C
+|
+<i>E. coli</i> gyrase consists of the gene products of gyrA and gyrB genes (Figures 2 & 7).
+|
+complete
+|-
+|
+|
+GO:0003918
 |
-chromosome
+DNA topoisomerase (ATP-hydrolyzing) activity
 |
-GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
 |
-InterPro:IPR001241<br />InterPro:IPR002288<br />InterPro:IPR011557<br />InterPro:IPR011558<br />InterPro:IPR013506<br />InterPro:IPR013759<br />InterPro:IPR013760
+InterPro:IPR013759
 |
-C
+F
 |
-Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 202: / Line 259: @@
 DNA topological change
 |
-GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002
+PMID:6327603
 |
-IEA: Inferred from Electronic Annotation
+IMP: Inferred from Mutant Phenotype
 |
-InterPro:IPR001241<br />InterPro:IPR002288<br />InterPro:IPR011557<br />InterPro:IPR011558<br />InterPro:IPR013506<br />InterPro:IPR013759<br />InterPro:IPR013760
 |
 P
 |
-Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
+Nucleoids from <i>E. coli</i> cells containing DNA labeled with [methyl-3H]thymidine were isolated and separated using an ethidium bromide-containing sucrose density gradient.  The sedimentation profiles were reported for gyrA and gyrB temperature-sensitive mutants at the permissive and non-permissive temperatures (Figure 1 & 2).  The ethidium bromide concentration is proportional to superhelical density, meaning that less supercoiled DNA from a gyrase mutant grown at the non-permissive temperature requires a lower concentration of ethidium bromide.
 |
 complete
@@ Line 217: / Line 274: @@
 |
-GO:0006304
+GO:0003918
 |
-DNA modification
+DNA topoisomerase (ATP-hydrolyzing) activity
 |
-GO_REF:0000002
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
 |
-InterPro:IPR006171
+InterPro:IPR013760
 |
-P
+F
 |
-Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 236: / Line 293: @@
 |
-GO:0016853
+GO:0003918
 |
-isomerase activity
+DNA topoisomerase (ATP-hydrolyzing) activity
 |
-GO_REF:0000004
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
 |
-SP_KW:KW-0413
+InterPro:IPR018522
 |
 F
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 255: / Line 312: @@
 |
-GO:0046677
+GO:0005524
+|
+ATP binding
+|
+PMID:9756859
+|
+IDA: Inferred from Direct Assay
+|
+|
+F
+|
+Using gel filtration and equilibrium ultracentrifugation, the authors showed that the 43kDa N-terminal fragment of GyrB binds to ADPNP, or [32-P]ADPNP, and ATP (Figure 7 and Table 1).
+|
+complete
+|-
+|
+|
+GO:0003918
 |
-response to antibiotic
+DNA topoisomerase (ATP-hydrolyzing) activity
 |
-GO_REF:0000004
+GOA:spec<br />GO_REF:0000003
 |
 IEA: Inferred from Electronic Annotation
 |
-SP_KW:KW-0046
+EC:5.99.1.3
+|
+F
+|
+Seeded from [[EcoCyc]] (v14.0)
+|
+complete
+|-
+|
+|
+GO:0042493
+|
+response to drug
+|
+PMID:9144789
+|
+IDA: Inferred from Direct Assay
+|
 |
 P
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Coumarin antibiotic sensitivity, including clorobiocin, novobiocin, and coumermycin A1.
 |
 complete
 |-
 |
 |
-GO:0005737
+GO:0005524
 |
-cytoplasm
+ATP binding
 |
+GOA:interpro<br />GO_REF:0000002
 |
+IEA: Inferred from Electronic Annotation
 |
+InterPro:IPR000565
 |
-C
+F
 |
-Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
+Seeded from [[EcoCyc]] (v14.0)
 |
-required fields missing
+complete
 |-
 |
 |
-GO:0000166
+GO:0003918
 |
-nucleotide binding
+DNA topoisomerase (ATP-hydrolyzing) activity
 |
-GO_REF:0000004
+PMID:368801
 |
-IEA: Inferred from Electronic Annotation
+IDA: Inferred from Direct Assay
 |
-SP_KW:KW-0547
 |
 F
 |
-Seeded from EcoCyc
+Purified E. coli gyrase was shown to induce cleavage and supercoiling in ColE1 DNA in the presence of ATP, but not after the addition of novobiocin or coumermycin A1 (Figure 2). Supercoiling of DNA was monitored by agarose gel electrophoresis (Figure 2A), while the hydrolysis of ATP was measured by following the release of 32-Pi measured by thin layer chromatography (Figure 2B).
 |
 complete
@@ Line 316: / Line 411: @@
 DNA binding
 |
-GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />PMID:10764756<br />PMID:6294616
+PMID:6294616
 |
 IDA: Inferred from Direct Assay
 |
-InterPro:IPR001241<br />InterPro:IPR002288<br />InterPro:IPR011557<br />InterPro:IPR013506<br />InterPro:IPR013759<br />InterPro:IPR013760<br /><br />
 |
 F
 |
-Seeded from EcoCyc
+E. coli gyrase incubated with radiolabeled ColE1 DNA and passed over nitrocellulose filters. The complexes were retained on the filters and radioactivity of the filters was measured and reported in Figure 1.
 |
 complete
@@ Line 331: / Line 426: @@
 |
-GO:0003916
+GO:0005524
 |
-DNA topoisomerase activity
+ATP binding
 |
-GO_REF:0000004
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
 |
-SP_KW:KW-0799
+InterPro:IPR001241
 |
 F
 |
-Seeded from EcoCyc
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 350: / Line 445: @@
 |
-GO:0003918
+GO:0006351
+|
+transcription, DNA-dependent
+|
+PMID:15535863
+|
+IMP: Inferred from Mutant Phenotype
+|
+|
+P
+|
+The authors used 3 conditions (treatment with either a quinolone or coumarin anitbiotic or growth of a gyrAts mutant at non-permissive temperature) to alter negative supercoiling of DNA and measured the changes in gene expression by microarray analysis. More than 300 SSGs (supercoiling sensitive genes) were identified that responded rapidly to the experimental conditions.
+GO replaced obsolete GO:0006350
+|
+complete
+|-
+|
+|
+GO:0005524
 |
-DNA topoisomerase (ATP-hydrolyzing) activity
+ATP binding
 |
-GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000003<br />PMID:368801
+GOA:interpro<br />GO_REF:0000002
 |
-IDA: Inferred from Direct Assay
+IEA: Inferred from Electronic Annotation
 |
-InterPro:IPR001241<br />InterPro:IPR002288<br />InterPro:IPR011557<br />InterPro:IPR013506<br />InterPro:IPR013759<br />InterPro:IPR013760<br />EC:5.99.1.3<br />
+InterPro:IPR002288
 |
 F
 |
-Seeded from EcoCyc
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 373: / Line 489: @@
 ATP binding
 |
-GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000004<br />PMID:9756859
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR003594
+|
+F
+|
+Seeded from [[EcoCyc]] (v14.0)
+|
+complete
+|-
+|
+|
+GO:0005737
+|
+cytoplasm
+|
+PMID:7952188
 |
 IDA: Inferred from Direct Assay
 |
-InterPro:IPR001241<br />InterPro:IPR002288<br />InterPro:IPR003594<br />InterPro:IPR011557<br />InterPro:IPR013506<br />InterPro:IPR013759<br />InterPro:IPR013760<br />SP_KW:KW-0067<br />
+|
+C
+|
+Immunogold labeling of cells with anti-GyrB antibodies indicated the presence of GyrB in the cytoplasm of E. coli.
+|
+complete
+|-
+|
+|
+GO:0005524
+|
+ATP binding
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR011557
 |
 F
 |
-Seeded from EcoCyc
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 388: / Line 542: @@
 |
-GO:0005694
+GO:0005524
 |
-chromosome
+ATP binding
 |
-GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
 |
-InterPro:IPR001241<br />InterPro:IPR002288<br />InterPro:IPR011557<br />InterPro:IPR013506<br />InterPro:IPR013759<br />InterPro:IPR013760
+InterPro:IPR013506
 |
-C
+F
 |
-Seeded from EcoCyc
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 407: / Line 561: @@
 |
-GO:0006265
+GO:0005524
 |
-DNA topological change
+ATP binding
 |
-GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
 |
-InterPro:IPR001241<br />InterPro:IPR002288<br />InterPro:IPR011557<br />InterPro:IPR013506<br />InterPro:IPR013759<br />InterPro:IPR013760
+InterPro:IPR013759
 |
-P
+F
 |
-Seeded from EcoCyc
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 426: / Line 580: @@
 |
-GO:0008094
+GO:0005524
+|
+ATP binding
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR013760
 |
-DNA-dependent ATPase activity
+F
 |
-PMID:6094559
+Seeded from [[EcoCyc]] (v14.0)
 |
-IDA: Inferred from Direct Assay
+complete
+|-
 |
+|
+GO:0005524
+|
+ATP binding
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR018522
 |
 F
 |
-Seeded from EcoCyc
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 445: / Line 618: @@
 |
-GO:0006261
+GO:0005524
 |
-DNA-dependent DNA replication
+ATP binding
+|
+GOA:spkw<br />SP_KW:GO_REF:0000004
+|
+IEA: Inferred from Electronic Annotation
+|
+SP_KW:KW-0067
+|
+F
 |
-PMID:6194415
+Seeded from [[EcoCyc]] (v14.0)
 |
-IMP: Inferred from Mutant Phenotype
+complete
+|-
 |
 |
-P
+GO:0005694
+|
+chromosome
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR000565
+|
+C
+|
+Seeded from [[EcoCyc]] (v14.0)
+|
+complete
+|-
 |
-Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
-''gyrB(ts)''
+|
+GO:0005694
+|
+chromosome
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR001241
+|
+C
+|
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
 |-
 |
 |
-GO:0006350
+GO:0005694
 |
-transcription
+chromosome
 |
+GOA:interpro<br />GO_REF:0000002
 |
+IEA: Inferred from Electronic Annotation
 |
+InterPro:IPR002288
 |
-P
+C
 |
-Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
+Seeded from [[EcoCyc]] (v14.0)
 |
-required fields missing
+complete
 |-
 |
 |
-GO:0008094
+GO:0005694
+|
+chromosome
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR011557
 |
-DNA-dependent ATPase activity
+C
 |
-PMID:6094559
+Seeded from [[EcoCyc]] (v14.0)
 |
-IDA: Inferred from Direct Assay
+complete
+|-
 |
 |
-F
+GO:0005694
+|
+chromosome
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR013506
+|
+C
 |
-ATPase activity of the GyrB subunit was followed by measuring the release of  32P-labeled phosphate from reactions containing [y-32P]-ATP in the presence of GyrA and DNA (Figure 1).  Omission of DNA or GyrA (which binds DNA) resulted in dramatically reduced ATPase activity of GyrB.
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 504: / Line 732: @@
 |
-GO:0003677
+GO:0005694
+|
+chromosome
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR013759
 |
-DNA binding
+C
 |
-PMID:10764756
+Seeded from [[EcoCyc]] (v14.0)
 |
-IMP: Inferred from Mutant Phenotype
+complete
+|-
 |
 |
-F
+GO:0005694
+|
+chromosome
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR013760
+|
+C
 |
-A truncated mutant of GyrB that lacks the C-terminal 160 residues has a reduced ability to retard the movement of DNA through a 5% polyacrylamide gel indicating a deficiency in DNA binding (Figure 5).
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 523: / Line 770: @@
 |
-GO:0009330
+GO:0005737
 |
-DNA topoisomerase complex (ATP-hydrolyzing)
+cytoplasm
 |
-PMID:347446
+PMID:7952188
 |
 IDA: Inferred from Direct Assay
@@ Line 535: / Line 782: @@
 C
 |
-<i>E. coli</i> gyrase consists of the gene products of gyrA and gyrB genes (Figures 2 & 7).
+Seeded from [[EcoCyc]] (v14.0)
+|
+complete
+|-
+|
+|
+GO:0006261
+|
+DNA-dependent DNA replication
+|
+PMID:6194415
+|
+IMP: Inferred from Mutant Phenotype
+|
+|
+P
+|
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 546: / Line 812: @@
 DNA topological change
 |
-PMID:6327603
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR000565
+|
+P
+|
+Seeded from [[EcoCyc]] (v14.0)
 |
-IMP: Inferred from Mutant Phenotype
+complete
+|-
 |
+|
+GO:0006265
+|
+DNA topological change
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR001241
 |
 P
 |
-Nucleoids from <i>E. coli</i> cells containing DNA labeled with [methyl-3H]thymidine were isolated and separated using an ethidium bromide-containing sucrose density gradient.  The sedimentation profiles were reported for gyrA and gyrB temperature-sensitive mutants at the permissive and non-permissive temperatures (Figure 1 & 2).  The ethidium bromide concentration is proportional to superhelical density, meaning that less supercoiled DNA from a gyrase mutant grown at the non-permissive temperature requires a lower concentration of ethidium bromide.
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 561: / Line 846: @@
 |
-GO:0005524
+GO:0006265
+|
+DNA topological change
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR002288
 |
-ATP binding
+P
 |
-PMID:9756859
+Seeded from [[EcoCyc]] (v14.0)
 |
-IDA: Inferred from Direct Assay
+complete
+|-
 |
 |
-F
+GO:0006265
+|
+DNA topological change
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR011557
+|
+P
 |
-Using gel filtration and equilibrium ultracentrifugation, the authors showed that the 43kDa N-terminal fragment of GyrB binds to ADPNP, or [32-P]ADPNP, and ATP (Figure 7 and Table 1).
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 580: / Line 884: @@
 |
-GO:0042493
+GO:0006265
+|
+DNA topological change
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR013506
 |
-response to drug
+P
 |
-PMID:9144789
+Seeded from [[EcoCyc]] (v14.0)
 |
-IDA: Inferred from Direct Assay
+complete
+|-
 |
+|
+GO:0006265
+|
+DNA topological change
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR013759
 |
 P
 |
-Coumarin antibiotic sensitivity, including clorobiocin, novobiocin, and coumermycin A1.
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 599: / Line 922: @@
 |
-GO:0003918
+GO:0006265
+|
+DNA topological change
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR013760
 |
-DNA topoisomerase (ATP-hydrolyzing) activity
+P
 |
-PMID:368801
+Seeded from [[EcoCyc]] (v14.0)
 |
-IDA: Inferred from Direct Assay
+complete
+|-
 |
 |
-F
+GO:0006265
+|
+DNA topological change
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR018522
+|
+P
 |
-Purified E. coli gyrase was shown to induce cleavage and supercoiling in ColE1 DNA in the presence of ATP, but not after the addition of novobiocin or coumermycin A1 (Figure 2). Supercoiling of DNA was monitored by agarose gel electrophoresis (Figure 2A), while the hydrolysis of ATP was measured by following the release of 32-Pi measured by thin layer chromatography (Figure 2B).
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 618: / Line 960: @@
 |
-GO:0003677
+GO:0006265
 |
-DNA binding
+DNA topological change
 |
-PMID:6294616
+PMID:6327603
 |
-IDA: Inferred from Direct Assay
+IMP: Inferred from Mutant Phenotype
 |
 |
-F
+P
 |
-E. coli gyrase incubated with radiolabeled ColE1 DNA and passed over nitrocellulose filters. The complexes were retained on the filters and radioactivity of the filters was measured and reported in Figure 1.
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 649: / Line 991: @@
 P
 |
-The authors used 3 conditions (treatment with either a quinolone or coumarin anitbiotic or growth of a gyrAts mutant at non-permissive temperature) to alter negative supercoiling of DNA and measured the changes in gene expression by microarray analysis. More than 300 SSGs (supercoiling sensitive genes) were identified that responded rapidly to the experimental conditions.
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 656: / Line 998: @@
 |
-GO:0005737
+GO:0009330
 |
-cytoplasm
+DNA topoisomerase complex (ATP-hydrolyzing)
 |
-PMID:7952188
+PMID:347446
 |
 IDA: Inferred from Direct Assay
@@ Line 668: / Line 1,010: @@
 C
 |
-Immunogold labeling of cells with anti-GyrB antibodies indicated the presence of GyrB in the cytoplasm of E. coli.
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 675: / Line 1,017: @@
 |
-GO:0016853
+GO:0046677
 |
-isomerase activity
+response to antibiotic
 |
-GO_REF:0000004
+GOA:spkw<br />SP_KW:GO_REF:0000004
 |
 IEA: Inferred from Electronic Annotation
 |
-SP_KW:KW-0413
+SP_KW:KW-0046
 |
-F
+P
 |
-Seeded from EcoCyc
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
-|-class='sortbottom'
+|- class="tableEdit_footer"
-|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.P46aafc6cd64f9&page=27976&pagename={{FULLPAGENAMEE}}&type=&template=GO_table_product edit table] || || || || || || || ||
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.P46aafc6cd64f9&page=27976&pagename={{FULLPAGENAMEE}}&type=&template=GO_table_product edit table]</span> || || || || || || || ||
 |}
 <!--box uid=421aa90e079fa326b6494f812ad13e79.27976.P46aafc6cd64f9-->
@@ Line 704: / Line 1,046: @@
 *
 ****************************************************************************************** -->{{Product_interactions_help}}
-{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y46aafc828890f"  class=" tableEdit Product_interactions_table dataTable"
 |- {{table heading style}}
 !|Partner Type!!Partner!!Notes!!References!!Evidence
@@ Line 850: / Line 1,192: @@
 |
 Experiment(s):EBI-891214<br />
+|-
+|
+Protein
+|
+parE
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+deaD
+|
+|
+PMID:19402753
+|
+MALDI(Z-score):18.677074
+|-
+|
+Protein
+|
+metK
+|
+|
+PMID:19402753
+|
+MALDI(Z-score):33.839565
+|-
+|
+Protein
+|
+tufB
+|
+|
+PMID:19402753
+|
+MALDI(Z-score):21.335822
+|-
+|
+Protein
+|
+gyrA
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6 MALDI(Z-score):28.518798
-|-class='sortbottom'
+|- class="tableEdit_footer"
-|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.Y46aafc828890f&page=27976&pagename={{FULLPAGENAMEE}}&type=&template=Product_interactions_table edit table] || || || ||
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.Y46aafc828890f&page=27976&pagename={{FULLPAGENAMEE}}&type=&template=Product_interactions_table edit table]</span> || || || ||
 |}
 <!--box uid=421aa90e079fa326b6494f812ad13e79.27976.Y46aafc828890f-->
@@ Line 868: / Line 1,265: @@
 *
 ****************************************************************************************** -->{{Product_localization_help}}
-{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D46a8886fa565f"  class=" tableEdit Product_localization_table"
 |- {{table heading style}}
-!|Compartment!!Description!!Evidence!!Notes
+!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
-|-class='sortbottom'
+|- class="tableEdit_footer"
-|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.D46a8886fa565f&page=27976&pagename={{FULLPAGENAMEE}}&type=&template=Product_localization_table edit table] || || ||
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.D46a8886fa565f&page=27976&pagename={{FULLPAGENAMEE}}&type=&template=Product_localization_table edit table]</span> || || || ||
 |}
 <!--box uid=421aa90e079fa326b6494f812ad13e79.27976.D46a8886fa565f-->
@@ Line 893: / Line 1,290: @@
 *
 ****************************************************************************************** -->{{Product_physical_properties_help}}
-{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
+{|   id="S46aafc8560656"  class=" tableEdit Product_phys_prop_table"
+|-
+!align=left {{table heading style}} |Name
+||
 |-
@@ Line 920: / Line 1,321: @@
 !align=left {{table heading style}} |Mol. Wt
 ||
-.95 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
+.951 kDa
 |-
 !align=left {{table heading style}} |pI
 ||
+.0 (calculated)
 |-
 !align=left {{table heading style}} |Extinction coefficient
 ||
-- 72365 (calc based on 26 Y, 6 W, and 5 C residues)
+,740 - 72,365 (calc based on 26 Y, 6 W, and 5 C residues)
-|-class='sortbottom'
+|- class="tableEdit_footer"
-|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.S46aafc8560656&page=27976&pagename={{FULLPAGENAMEE}}&type=1&template=Product_phys_prop_table edit table] ||
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.S46aafc8560656&page=27976&pagename={{FULLPAGENAMEE}}&type=1&template=Product_phys_prop_table edit table]</span> ||
 |}
 <!--box uid=421aa90e079fa326b6494f812ad13e79.27976.S46aafc8560656-->
@@ Line 945: / Line 1,346: @@
 *
 ****************************************************************************************** -->{{Product_domains_motifs_help}}
-{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A46aafc85dcb1e"  class=" tableEdit Product_motif_table dataTable"
 |- {{table heading style}}
-!|Type!!Residues!!Description!!Notes
+!|Type!!Residues!!Description!!Notes!!References
+|-
+|
+Initiator Methionine
+|
+|
+Removed
+|
+[http://www.uniprot.org/uniprot/P0AES6#section_features UniProt:P0AES6]
+|
+|-
+|
+Domain
+|
+..174
+|
+[http://pfam.janelia.org/family/PF02518 PF02518  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase]
+|
-|-class='sortbottom'
+|
-|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.A46aafc85dcb1e&page=27976&pagename={{FULLPAGENAMEE}}&type=&template=Product_motif_table edit table] || || ||
+PMID:19920124
+|-
+|
+Domain
+|
+..391
+|
+[http://pfam.janelia.org/family/PF00204 PF00204  DNA gyrase B]
+|
+|
+PMID:19920124
+|-
+|
+Domain
+|
+..793
+|
+[http://pfam.janelia.org/family/PF00986 PF00986  DNA gyrase B subunit, carboxyl terminus]
+|
+|
+PMID:19920124
+|- class="tableEdit_footer"
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.A46aafc85dcb1e&page=27976&pagename={{FULLPAGENAMEE}}&type=&template=Product_motif_table edit table]</span> || || || ||
 |}
 <!--box uid=421aa90e079fa326b6494f812ad13e79.27976.A46aafc85dcb1e--></td>
@@ Line 961: / Line 1,406: @@
 </table>
-<span id="Structure"></span><big>'''Structure'''</big>
+<table><tr valign='top'><td>
+<span id='Structure'></span><big>'''Structure'''</big><br />
 <!--box uid=421aa90e079fa326b6494f812ad13e79.27976.V46aafc8652430-->
 <!--
@@ Line 969: / Line 1,415: @@
 *
 ****************************************************************************************** -->{{Product_structure_help}}
-{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
+{|   id="V46aafc8652430"  class=" tableEdit Product_structure_table"
 |-
 !align=left {{table heading style}} |Structures
 ||
-<beststructure>gyrB
+<beststructure>
-</beststructure>
+gene=gyrB
+taxon=562,83333
+</beststructure>
 |-
 !align=left {{table heading style}} |Models
 ||
 View models at:
-* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=gyrB&sub=keywordSearc EcoliPredict]
+* [http://www.proteinmodelportal.org/query/uniprot/P0AES6 Protein Model Portal]
-* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=gyrB&organism=562&organismtext= ModBase]
+* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0AES6 PSI-PRED (P0AES6)]
-* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
+* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0AES6 Genomes TO Protein (P0AES6)] (GTOP)
-* [http://www.ebi.ac.uk/msd-srv/pqs/ Protein Quaternary Structure] (PQS)
-* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)
-|-class='sortbottom'
+|- class="tableEdit_footer"
-|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.V46aafc8652430&page=27976&pagename={{FULLPAGENAMEE}}&type=1&template=Product_structure_table edit table] ||
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.V46aafc8652430&page=27976&pagename={{FULLPAGENAMEE}}&type=1&template=Product_structure_table edit table]</span> ||
 |}
 <!--box uid=421aa90e079fa326b6494f812ad13e79.27976.V46aafc8652430-->
-<!--Structure_notes--></protect>
+</td><td></protect>
+==== Structure figures ====
+<protect><!--          ***** PLEASE DO NOT EDIT BELOW THIS LINE *****         -->
+</td><tr><table><!--Structure_notes--></protect>
 ===Notes===
@@ Line 1,006: / Line 1,471: @@
 *
 ****************************************************************************************** -->{{Product_resources_help}}
-{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="F46aafc889e2f8"  class=" tableEdit Product_resource_table"
 |- {{table_heading_style}}
 !|Resource type!!Source!!Notes/Reference
-|-class='sortbottom'
+|- class="tableEdit_footer"
-|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.F46aafc889e2f8&page=27976&pagename={{FULLPAGENAMEE}}&type=&template=Product_resource_table edit table] || ||
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.F46aafc889e2f8&page=27976&pagename={{FULLPAGENAMEE}}&type=&template=Product_resource_table edit table]</span> || ||
 |}
 <!--box uid=421aa90e079fa326b6494f812ad13e79.27976.F46aafc889e2f8-->
@@ Line 1,028: / Line 1,493: @@
 *
 ****************************************************************************************** -->{{Gene_accessions_help}}
-{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K46aafc890f82b"  class=" tableEdit Gene_accessions_table"
 |- {{table_heading_style}}
 !|Database!!Accession!!Notes
 |-
 |
-[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
+[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
+|
+[http://www.ncbi.nlm.nih.gov/protein/49176395 GI:49176395]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
+|
+[http://www.ncbi.nlm.nih.gov/protein/YP_026241.1 GeneID:948211]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[[ASAP]]
+|
+ASAP:ABE-0012093
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
 |
-[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10424-MONOMER EcoCyc:EG10424-MONOMER]
+[http://www.uniprot.org/uniprot/P0AES6 UniProtKB/Swiss-Prot:P0AES6]
 |
+Escherichia coli str. K-12 substr. MG1655
 |-
 |
-[http://swissmodel.expasy.org/repository/ SwissModel] ([[SwissModel|EcoliWiki Page]])
+[[EcoCyc]]
 |
-[http://swissmodel.expasy.org/repository/smr.php?job=2&sptr_ac=P0AES6 SwissModel:P0AES6]
+EcoCyc:EG10424
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |-
 |
-[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
+[[EcoGene]]
 |
-[[uniprot:P0AES6|UniProt:P0AES6]]
+EcoGene:EG10424
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |-
 |
-[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
+[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
 |
-[http://pfam.sanger.ac.uk/family?acc=PF02518 PFAM:PF02518]
+[http://www.ncbi.nlm.nih.gov/gene?term=948211 GeneID:948211]
 |
+Escherichia coli str. K-12 substr. MG1655
 |-
 |
-[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
+[[RegulonDB]]
 |
-[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=YP_026241 RefSeq:YP_026241]
+RegulonDB:ECK120000417
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |-
 |
-[http://www.rcsb.org/pdb PDB] ([[PDB|EcoliWiki Page]])
+[[EchoBASE]]
 |
-[http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1AJ6 PDB:1AJ6]
+EchoBASE:EB0419
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
-|-class='sortbottom'
+|- class="tableEdit_footer"
-|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.K46aafc890f82b&page=27976&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table] || ||
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.K46aafc890f82b&page=27976&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
 |}
 <!--box uid=421aa90e079fa326b6494f812ad13e79.27976.K46aafc890f82b-->
@@ Line 1,092: / Line 1,578: @@
 *
 ****************************************************************************************** -->
-{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J46a888770be7d"  class=" tableEdit Links_table"
 |- {{table_heading_style}}
 !|Name!!URL!!Comments
-|-class='sortbottom'
+|- class="tableEdit_footer"
-|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.J46a888770be7d&page=27976&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.J46a888770be7d&page=27976&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table]</span> || ||
 |}
 <!--box uid=421aa90e079fa326b6494f812ad13e79.27976.J46a888770be7d-->
@@ Line 1,107: / Line 1,593: @@
 ==References==
 {{BacktoTop}}
+{{RefHelp}}
-<references/>
+<references />
 __NOTOC__
-</noinclude>
 ===Categories===
 {{BacktoTop}}
 [[Category:Proteins]]
-[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0006261_!_DNA-dependent DNA replication]][[Category:GO:0006350_!_transcription]][[Category:Complex:DNA gyrase]][[Category:Products with structures in PDB]]

gyrB:Gene Product(s): Difference between revisions

Latest revision as of 21:07, 17 February 2015

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

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