dnaX:Gene Product(s): Difference between revisions

Standard name	DnaX
Synonyms	DNA polymerase III/DNA elongation factor III, tau and gamma subunits^[1], DnaZ^[2]^[1], B0470^[2]^[1]
Product description	DNA polymerase III, γ subunit^[2]^[3] DNA polymerase III, τ subunit^[2]^[3] Component of DNA polymerase III, preinitiation complex^[3]; DNA polymerase III, τ subunit dimer^[3] DNA polymerase III, holoenzyme^[3] DNA polymerase III holoenzyme, tau and gamma ATPase subunits; gamma chain (aa 1-431) is main subunit of the clamp loader complex^[4]
EC number (for enzymes)	2.7.7.7^[1]
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Notes

Function

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Gene Ontology

DNA polymerase III

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:0017111	nucleoside-triphosphatase activity	GO_REF:0000002 GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003593 InterPro:IPR003593	F	Seeded from EcoCyc ^[5]	complete
	GO:0016779	nucleotidyltransferase activity	GO_REF:0000004 GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0548 SP_KW:KW-0548	F	Seeded from EcoCyc ^[5]	complete
	GO:0016740	transferase activity	GO_REF:0000004 GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808 SP_KW:KW-0808	F	Seeded from EcoCyc ^[5]	complete
	GO:0009360	DNA polymerase III complex	GO_REF:0000002 GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012763 InterPro:IPR012763	C	Seeded from EcoCyc ^[5]	complete
	GO:0006260	DNA replication	GO_REF:0000002 GO_REF:0000002 GO_REF:0000002 GO_REF:0000002 GO_REF:0000004 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR008921 InterPro:IPR008921 InterPro:IPR012763 InterPro:IPR012763 SP_KW:KW-0235 SP_KW:KW-0235	P	Seeded from EcoCyc ^[5]	complete
	GO:0005634	nucleus	GO_REF:0000002 GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008921 InterPro:IPR008921	C	Seeded from EcoCyc ^[5]	complete
	GO:0005524	ATP binding	GO_REF:0000002 GO_REF:0000002 GO_REF:0000002 GO_REF:0000002 GO_REF:0000002 GO_REF:0000002 GO_REF:0000004 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR001270 InterPro:IPR001270 InterPro:IPR003959 InterPro:IPR003959 InterPro:IPR012763 InterPro:IPR012763 SP_KW:KW-0067 SP_KW:KW-0067	F	Seeded from EcoCyc ^[5]	complete
	GO:0003887	DNA-directed DNA polymerase activity	GO_REF:0000002 GO_REF:0000002 GO_REF:0000003 GO_REF:0000003 GO_REF:0000004 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR012763 InterPro:IPR012763 EC:2.7.7.7 EC:2.7.7.7 SP_KW:KW-0239 SP_KW:KW-0239	F	Seeded from EcoCyc ^[5]	complete
	GO:0003677	DNA binding	GO_REF:0000002 GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008921 InterPro:IPR008921	F	Seeded from EcoCyc ^[5]	complete
	GO:0000166	nucleotide binding	GO_REF:0000002 GO_REF:0000002 GO_REF:0000004 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR003593 InterPro:IPR003593 SP_KW:KW-0547 SP_KW:KW-0547	F	Seeded from EcoCyc ^[5]	complete
	GO:0005515	protein binding	PMID:15690043^[6]	IPI: Inferred from Physical Interaction	UniProtKB:P0A7L0	F	Seeded from EcoCyc 12.5 ^[7]	complete
	GO:0005515	protein binding	PMID:15690043^[6]	IPI: Inferred from Physical Interaction	UniProtKB:P0A7L0	F	Seeded from EcoCyc 12.5 ^[7]	complete
	GO:0005737	cytoplasm				C	Seeded from EcoCyc 11.1^[3].	required fields missing
	GO:0006261	DNA-dependent DNA replication	PMID:10748120^[8]	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc 11.1^[3].	complete
	GO:0043846	DNA polymerase III, DnaX complex				C		required field missing
	GO:0003689	DNA clamp loader activity				F		required field missing
	GO:0006260	DNA replication	PMID:391641^[9]	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0017111	nucleoside-triphosphatase activity	PMID:11029431^[10]	IDA: Inferred from Direct Assay		F		complete
	GO:0043846	DNA polymerase III, DnaX complex	PMID:8376347^[11]	IDA: Inferred from Direct Assay		C		complete
	GO:0016887	ATPase activity	PMID:2681183^[12]	IDA: Inferred from Direct Assay		F		complete
	GO:0030337	DNA polymerase processivity factor activity	PMID:11525729^[13]	IDA: Inferred from Direct Assay		F		complete
	GO:0030337	DNA polymerase processivity factor activity	PMID:7494000^[14]	IDA: Inferred from Direct Assay		F		complete
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Interactions

DNA polymerase III

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 polymerase III, preinitiation complex	could be indirect
Protein	rplA		PMID:15690043^[6]	Experiment(s):EBI-883400
Protein	fecB		PMID:15690043^[6]	Experiment(s):EBI-890677
Protein	nusG		PMID:15690043^[6]	Experiment(s):EBI-890677
Protein	rplL		PMID:15690043^[6]	Experiment(s):EBI-890677
Protein	rpmC		PMID:15690043^[6]	Experiment(s):EBI-890677
Protein	rpsF		PMID:15690043^[6]	Experiment(s):EBI-890677
Protein	ugpB		PMID:15690043^[6]	Experiment(s):EBI-890677
Protein	yfiF		PMID:15690043^[6]	Experiment(s):EBI-890677
Protein	yjgD		PMID:15690043^[6]	Experiment(s):EBI-890677
Protein	rhsD		PMID:16606699^[15]	Experiment(s):EBI-1136784
Protein	rpoC		PMID:16606699^[15]	Experiment(s):EBI-1136784
Protein	Subunits of DNA polymerase III, holoenzyme	could be indirect
Protein	ParC from Topo IV		PMID:12535532^[16]	Microscopy- colocalization at the fork lost in dnaX mutant
Protein	subunits of the clamp loader		PMID:11525729^[13]
Protein	DnaB (Helicase)-Interacts with tau		PMID:10748120^[8]
Protein	alpha subunit of DNA Polymerase III- interacts with tau		PMID:10748120^[8]
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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	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.

Sequence	at EcoCyc MSYQVLARKW RPQTFADVVG QEHVLTALAN GLSLGRIHHA YLFSGTRGVG KTSIARLLAK GLNCETGITA TPCGVCDNCR EIEQGRFVDL IEIDAASRTK VEDTRDLLDN VQYAPARGRF KVYLIDEVHM LSRHSFNALL KTLEEPPEHV KFLLATTDPQ KLPVTILSRC LQFHLKALDV EQIRHQLEHI LNEEHIAHEP RALQLLARAA EGSLRDALSL TDQAIASGDG QVSTQAVSAM LGTLDDDQAL SLVEAMVEAN GERVMALINE AAARGIEWEA LLVEMLGLLH RIAMVQLSPA ALGNDMAAIE LRMRELARTI PPTDIQLYYQ TLLIGRKELP YAPDRRMGVE MTLLRALAFH PRMPLPEPEV PRQSFAPVAP TAVMTPTQVP PQPQSAPQQA PTVPLPETTS QVLAARQQLQ RVQGATKAKK SEPAAATRAR PVNNAALERL ASVTDRVQAR PVPSALEKAP AKKEAYRWKA TTPVMQQKEV VATPKALKKA LEHEKTPELA AKLAAEAIER DPWAAQVSQL SLPKLVEQVA LNAWKEESDN AVCLHLRSSQ RHLNNRGAQQ KLAEALSMLK GSTVELTIVE DDNPAVRTPL EWRQAIYEEK LAQARESIIA DNNIQTLRRF FDAELDEESI RPI
Length	643
Mol. Wt	71.138 kDa
pI	6.8 (calculated)
Extinction coefficient	46,410 - 47,160 (calc based on 9 Y, 6 W, and 6 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
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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=dnaX 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
EcoCyc (EcoliWiki Page)	EcoCyc:EG10245-MONOMER
UniProt (EcoliWiki Page)	UniProt:P06710
PFAM (EcoliWiki Page)	PFAM:PF00004
RefSeq (EcoliWiki Page)	RefSeq:NP_415003
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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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 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 ^3.5 ^3.6 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.
↑ ^5.00 ^5.01 ^5.02 ^5.03 ^5.04 ^5.05 ^5.06 ^5.07 ^5.08 ^5.09 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
↑ ^6.00 ^6.01 ^6.02 ^6.03 ^6.04 ^6.05 ^6.06 ^6.07 ^6.08 ^6.09 ^6.10 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
↑ ^7.0 ^7.1 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^8.0 ^8.1 ^8.2 Dallmann, HG et al. (2000) Characterization of the unique C terminus of the Escherichia coli tau DnaX protein. Monomeric C-tau binds alpha AND DnaB and can partially replace tau in reconstituted replication forks. J. Biol. Chem. 275 15512-9 PubMed
↑ Henson, JM et al. (1979) Isolation and characterization of dnaX and dnaY temperature-sensitive mutants of Escherichia coli. Genetics 92 1041-59 PubMed
↑ Walker, JR et al. (2000) Escherichia coli DNA polymerase III tau- and gamma-subunit conserved residues required for activity in vivo and in vitro. J. Bacteriol. 182 6106-13 PubMed
↑ Blinkova, A et al. (1993) The Escherichia coli DNA polymerase III holoenzyme contains both products of the dnaX gene, tau and gamma, but only tau is essential. J. Bacteriol. 175 6018-27 PubMed
↑ Tsuchihashi, Z & Kornberg, A (1989) ATP interactions of the tau and gamma subunits of DNA polymerase III holoenzyme of Escherichia coli. J. Biol. Chem. 264 17790-5 PubMed
↑ ^13.0 ^13.1 Jeruzalmi, D et al. (2001) Crystal structure of the processivity clamp loader gamma (gamma) complex of E. coli DNA polymerase III. Cell 106 429-41 PubMed
↑ Olson, MW et al. (1995) DnaX complex of Escherichia coli DNA polymerase III holoenzyme. The chi psi complex functions by increasing the affinity of tau and gamma for delta.delta' to a physiologically relevant range. J. Biol. Chem. 270 29570-7 PubMed
↑ ^15.0 ^15.1 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
↑ Espeli, O et al. (2003) Temporal regulation of topoisomerase IV activity in E. coli. Mol. Cell 11 189-201 PubMed

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-!align=left  |Standard name
+!align=left {{table heading style}} |Standard name
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 DnaX
 |-
-!align=left  |Synonyms
+!align=left {{table heading style}} |Synonyms
 ||
 DNA polymerase III/DNA elongation factor III, tau and gamma subunits<ref name='LIB:Riley_2006'/>, DnaZ<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B0470<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>
 |-
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 * DNA polymerase III, γ subunit<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
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 DNA polymerase III holoenzyme, tau and gamma ATPase subunits; gamma chain (aa 1-431) is main subunit of the clamp loader complex<ref name='LIB:EcoGene'/>
 |-
-!align=left  |EC number (for enzymes)
+!align=left {{table heading style}} |EC number (for enzymes)
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 [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7]<ref name='LIB:Riley_2006'/>
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 !|Partner Type!!Partner!!Notes!!References!!Evidence
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-!align=left  |Sequence
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 [http://biocyc.org/ECOLI/sequence-aa?object= at EcoCyc]
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 EWRQAIYEEK LAQARESIIA DNNIQTLRRF FDAELDEESI RPI</pre>
 |-
-!align=left  |Length
+!align=left {{table heading style}} |Length
 ||
 |-
-!align=left  |Mol. Wt
+!align=left {{table heading style}} |Mol. Wt
 ||
 .138 kDa
 |-
-!align=left  |pI
+!align=left {{table heading style}} |pI
 ||
 .8 (calculated)
 |-
-!align=left  |Extinction coefficient
+!align=left {{table heading style}} |Extinction coefficient
 ||
 ,410 - 47,160 (calc based on 9 Y, 6 W, and 6 C residues)
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 ****************************************************************************************** -->{{Product_domains_motifs_help}}
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 <beststructure>
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 </beststructure>
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 View models at:
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dnaX:Gene Product(s): Difference between revisions

Revision as of 19:42, 23 February 2010

Nomenclature

Notes

Function

DNA polymerase III

DNA polymerase III

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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dnaX:Gene Product(s): Difference between revisions

Revision as of 19:42, 23 February 2010

Nomenclature

Notes

Function

DNA polymerase III

DNA polymerase III

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

Navigation menu

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