gyrB:Gene Product(s)
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Nomenclature
See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.
| 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] |
| Product description |
Component of DNA gyrase[3] DNA gyrase, subunit B; novobiocin, coumermycin resistance[4] |
| EC number (for enzymes) | |
| edit table |
Notes
Function
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(s) | Evidence Code | with/from | Aspect | Notes | Status |
|---|---|---|---|---|---|---|---|---|
| GO:0000166 |
nucleotide binding |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc [5] |
complete | |||
| GO:0003676 |
nucleic acid binding |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc 12.5 [6] |
complete | |||
| GO:0003916 |
DNA topoisomerase activity |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc [5] |
complete | |||
| GO:0003918 |
DNA topoisomerase (ATP-hydrolyzing) activity |
GO_REF:0000002 |
IEA: Inferred from Electronic Annotation |
InterPro:IPR001241 |
F |
Seeded from EcoCyc 12.5 [6] |
complete | |
| GO:0005524 |
ATP binding |
GO_REF:0000002 |
IEA: Inferred from Electronic Annotation |
InterPro:IPR001241 |
F |
Seeded from EcoCyc 12.5 [6] |
complete | |
| GO:0005694 |
chromosome |
GO_REF:0000002 |
IEA: Inferred from Electronic Annotation |
InterPro:IPR001241 |
C |
Seeded from EcoCyc 12.5 [6] |
complete | |
| GO:0006265 |
DNA topological change |
GO_REF:0000002 |
IEA: Inferred from Electronic Annotation |
InterPro:IPR001241 |
P |
Seeded from EcoCyc 12.5 [6] |
complete | |
| GO:0006304 |
DNA modification |
IEA: Inferred from Electronic Annotation |
P |
Seeded from EcoCyc 12.5 [6] |
complete | |||
| GO:0016853 |
isomerase activity |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc [5] |
complete | |||
| GO:0046677 |
response to antibiotic |
IEA: Inferred from Electronic Annotation |
P |
Seeded from EcoCyc [5] |
complete | |||
| GO:0005737 |
cytoplasm |
C |
Seeded from EcoCyc 11.1[3]. |
required fields missing | ||||
| GO:0000166 |
nucleotide binding |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc |
complete | |||
| GO:0003677 |
DNA binding |
GO_REF:0000002 |
IDA: Inferred from Direct Assay |
InterPro:IPR001241 |
F |
Seeded from EcoCyc |
complete | |
| GO:0003916 |
DNA topoisomerase activity |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc |
complete | |||
| GO:0003918 |
DNA topoisomerase (ATP-hydrolyzing) activity |
GO_REF:0000002 |
IDA: Inferred from Direct Assay |
InterPro:IPR001241 |
F |
Seeded from EcoCyc |
complete | |
| GO:0005524 |
ATP binding |
GO_REF:0000002 |
IDA: Inferred from Direct Assay |
InterPro:IPR001241 |
F |
Seeded from EcoCyc |
complete | |
| GO:0005694 |
chromosome |
GO_REF:0000002 |
IEA: Inferred from Electronic Annotation |
InterPro:IPR001241 |
C |
Seeded from EcoCyc |
complete | |
| GO:0006261 |
DNA-dependent DNA replication |
IMP: Inferred from Mutant Phenotype |
P |
Seeded from EcoCyc 11.1[3]. gyrB(ts) |
complete | |||
| GO:0006350 |
transcription |
P |
Seeded from EcoCyc 11.1[3]. |
required fields missing | ||||
| GO:0008094 |
DNA-dependent ATPase activity |
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:0003677 |
DNA binding |
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) |
IDA: Inferred from Direct Assay |
C |
E. coli gyrase consists of the gene products of gyrA and gyrB genes (Figures 2 & 7). |
complete | |||
| GO:0006265 |
DNA topological change |
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:0005524 |
ATP binding |
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:0042493 |
response to drug |
IDA: Inferred from Direct Assay |
P |
Coumarin antibiotic sensitivity, including clorobiocin, novobiocin, and coumermycin A1. |
complete | |||
| GO:0003918 |
DNA topoisomerase (ATP-hydrolyzing) activity |
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 |
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:0006350 |
transcription |
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. |
complete | |||
| GO:0005737 |
cytoplasm |
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:0006265 |
DNA topological change |
GO_REF:0000002 |
IEA: Inferred from Electronic Annotation |
InterPro:IPR001241 |
P |
Seeded from EcoCyc |
complete | |
| edit table |
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 |
Experiment(s):EBI-884130 | ||
|
Protein |
bglJ |
Experiment(s):EBI-884130 | ||
|
Protein |
deaD |
Experiment(s):EBI-884130 | ||
|
Protein |
glyS |
Experiment(s):EBI-884130 | ||
|
Protein |
gyrA |
Experiment(s):EBI-884130, EBI-884206, EBI-891214, EBI-891237 | ||
|
Protein |
metK |
Experiment(s):EBI-884130 | ||
|
Protein |
rplJ |
Experiment(s):EBI-884130 | ||
|
Protein |
rpsB |
Experiment(s):EBI-884130 | ||
|
Protein |
tufA |
Experiment(s):EBI-884130, EBI-891214 | ||
|
Protein |
yacG |
Experiment(s):EBI-884130, EBI-879073, EBI-882474, EBI-891214 | ||
|
Protein |
parE |
Experiment(s):EBI-891214 | ||
|
Protein |
rplW |
Experiment(s):EBI-891214 | ||
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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 | Notes |
|---|---|---|---|
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Notes
Structure and Physical Properties
Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.
| Sequence |
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 |
89.95 kDa (calc) [2] |
| pI | |
| Extinction coefficient |
71740 - 72365 (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.
|
<motif_map/> |
Structure See Help:Product_structure for help entering or editing information in this section of EcoliWiki.
| Structures |
<beststructure>gyrB 562</beststructure> |
|---|---|
| Models |
View models at: |
| edit table |
Notes
Gene Product Resources
See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.
| Resource type | Source | Notes/Reference |
|---|---|---|
| edit table |
Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
| ||
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Notes
Links
| Name | URL | Comments |
|---|---|---|
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References
- ↑ 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 2.11 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ 3.0 3.1 3.2 3.3 3.4 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.
- ↑ 5.0 5.1 5.2 5.3 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
- ↑ 6.0 6.1 6.2 6.3 6.4 6.5 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ 7.0 7.1 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
- ↑ 8.0 8.1 Higgins, NP & Cozzarelli, NR (1982) The binding of gyrase to DNA: analysis by retention by nitrocellulose filters. Nucleic Acids Res. 10 6833-47 PubMed
- ↑ 9.0 9.1 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
- ↑ 10.0 10.1 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
- ↑ 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
- ↑ Maxwell, A & Gellert, M (1984) The DNA dependence of the ATPase activity of DNA gyrase. J. Biol. Chem. 259 14472-80 PubMed
- ↑ 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
- ↑ Steck, TR et al. (1984) DNA supercoiling in gyrase mutants. J. Bacteriol. 158 397-403 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
- ↑ Peter, BJ et al. (2004) Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol. 5 R87 PubMed
- ↑ Thornton, M et al. (1994) Immunogold localization of GyrA and GyrB proteins in Escherichia coli. Microbiology (Reading, Engl.) 140 ( Pt 9) 2371-82 PubMed
- ↑ 18.00 18.01 18.02 18.03 18.04 18.05 18.06 18.07 18.08 18.09 18.10 18.11 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
Categories
- GO:0000166 ! nucleotide binding
- GO:0003676 ! nucleic acid binding
- GO:0003916 ! DNA topoisomerase activity
- GO:0003918 ! DNA topoisomerase type II (ATP-hydrolyzing) activity
- GO:0005524 ! ATP binding
- GO:0005694 ! chromosome
- GO:0006265 ! DNA topological change
- GO:0006304 ! DNA modification
- GO:0016853 ! isomerase activity
- GO:0046677 ! response to antibiotic
- GO:0005737 ! cytoplasm
- GO:0003677 ! DNA binding
- GO:0006261 ! DNA-dependent DNA replication
- GO:0006350 ! transcription
- GO:0008094 ! DNA-dependent ATPase activity
- GO:0009330 ! DNA topoisomerase complex (ATP-hydrolyzing)
- GO:0042493 ! response to drug
- Proteins
- Complex:DNA gyrase
- Products with structures in PDB