dnaX:Gene Product(s): Difference between revisions

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*  
*  
****************************************************************************************** -->{{Product_nomenclature_help}}
****************************************************************************************** -->{{Product_nomenclature_help}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{|   id="D46aa31de68d41" class=" tableEdit Product_nomenclature_table"


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!align=left {{table heading style}} |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'/>  
''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'/> , dnaZ, ECK0464, JW0459, b0470''
|-
|-
!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
||
||
* DNA polymerase III, γ subunit<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
* DNA polymerase III, gamma subunit<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
* DNA polymerase III, τ subunit<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
* DNA polymerase III, tau subunit<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
* Component of  
* Component of  
** [[:Category:Complex:DNA polymerase III, preinitiation complex|DNA polymerase III, preinitiation complex]]<ref name='LIB:EcoCyc11.1'/>;  
** [[:Category:Complex:DNA polymerase III, preinitiation complex|DNA polymerase III, preinitiation complex]]<ref name='LIB:EcoCyc11.1'/>;  
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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'/>
[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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*  
*  
****************************************************************************************** -->{{Product_GO_help}}
****************************************************************************************** -->{{Product_GO_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="A46aa31e02b0a3"  class=" tableEdit GO_table_product dataTable" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-  
|-  
|
|


|
|
GO:0017111
GO:0043846
|
DNA polymerase III, DnaX complex
|
 
|
 
|
 
|
C
|
 
|
Missing: evidence, reference
|-
|
 
|
GO:0003689
|
DNA clamp loader activity
|
 
|
 
|
 
|
F
|
 
|
Missing: evidence, reference
|-
|
 
|
GO:0000166
|
nucleotide binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR003593
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0000166
|
nucleotide binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR003593
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0000166
|
|
nucleoside-triphosphatase activity
nucleotide binding
|
|
GO_REF:0000002<br />GO_REF:0000002
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR003593<br />InterPro:IPR003593
SP_KW:KW-0547
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 110: Line 186:


|
|
GO:0016779
GO:0000166
|
|
nucleotidyltransferase activity
nucleotide binding
|
|
GO_REF:0000004<br />GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0548<br />SP_KW:KW-0548
SP_KW:KW-0547
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 129: Line 205:


|
|
GO:0016740
GO:0003677
|
|
transferase activity
DNA binding
|
|
GO_REF:0000004<br />GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0808<br />SP_KW:KW-0808
InterPro:IPR008921
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 148: Line 224:


|
|
GO:0009360
GO:0003677
|
|
DNA polymerase III complex
DNA binding
|
|
GO_REF:0000002<br />GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR012763<br />InterPro:IPR012763
InterPro:IPR008921
|
|
C
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 167: Line 243:


|
|
GO:0006260
GO:0003887
|
|
DNA replication
DNA-directed DNA polymerase activity
|
|
GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000004<br />GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR008921<br />InterPro:IPR008921<br />InterPro:IPR012763<br />InterPro:IPR012763<br />SP_KW:KW-0235<br />SP_KW:KW-0235
InterPro:IPR012763
|
|
P
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 186: Line 262:


|
|
GO:0005634
GO:0003887
|
|
nucleus
DNA-directed DNA polymerase activity
|
|
GO_REF:0000002<br />GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR008921<br />InterPro:IPR008921
InterPro:IPR012763
|
|
C
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 205: Line 281:


|
|
GO:0005524
GO:0003887
|
|
ATP binding
DNA-directed DNA polymerase 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:0000004<br />GO_REF:0000004
GOA:spec<br />GO_REF:0000003
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR001270<br />InterPro:IPR001270<br />InterPro:IPR003959<br />InterPro:IPR003959<br />InterPro:IPR012763<br />InterPro:IPR012763<br />SP_KW:KW-0067<br />SP_KW:KW-0067
EC:2.7.7.7
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 228: Line 304:
DNA-directed DNA polymerase activity
DNA-directed DNA polymerase activity
|
|
GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000003<br />GO_REF:0000003<br />GO_REF:0000004<br />GO_REF:0000004
GOA:spec<br />GO_REF:0000003
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR012763<br />InterPro:IPR012763<br />EC:2.7.7.7<br />EC:2.7.7.7<br />SP_KW:KW-0239<br />SP_KW:KW-0239
EC:2.7.7.7
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 243: Line 319:


|
|
GO:0003677
GO:0003887
|
|
DNA binding
DNA-directed DNA polymerase activity
|
|
GO_REF:0000002<br />GO_REF:0000002
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR008921<br />InterPro:IPR008921
SP_KW:KW-0239
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 262: Line 338:


|
|
GO:0000166
GO:0003887
|
|
nucleotide binding
DNA-directed DNA polymerase activity
|
|
GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000004<br />GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR003593<br />InterPro:IPR003593<br />SP_KW:KW-0547<br />SP_KW:KW-0547
SP_KW:KW-0239
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 285: Line 361:
protein binding
protein binding
|
|
PMID:15690043
PMID:19703395
|
|
IPI: Inferred from Physical Interaction
IPI: Inferred from Physical Interaction
|
|
UniProtKB:P0A7L0
UniProtKB:P0A988
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 304: Line 380:
protein binding
protein binding
|
|
PMID:15690043
PMID:19703395
|
|
IPI: Inferred from Physical Interaction
IPI: Inferred from Physical Interaction
|
|
UniProtKB:P0A7L0
UniProtKB:P0A988
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-  
|-  
|
|
 
|
|
GO:0005737
GO:0005524
|
|
cytoplasm
ATP binding
|
|
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR001270
|
|
C
F
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|
 
|
|
GO:0006261
GO:0005524
|
|
DNA-dependent DNA replication
ATP binding
|
|
PMID:10748120
GOA:interpro<br />GO_REF:0000002
|
|
IDA: Inferred from Direct Assay
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR001270
|
|
P
F
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-  
|-  
|
|
 
|
GO:0005524
|
ATP binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR003959
|
F
|
|
GO:0043846
Seeded from [[EcoCyc]] (v14.0)
|
|
DNA polymerase III, DnaX complex
complete
|-
|
|


|
|
GO:0005524
|
ATP binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR003959
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
|


|
|
C
GO:0005524
|
ATP binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR012763
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
|


|
|
required field missing
GO:0005524
|
ATP binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR012763
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-  
|-  
|
|
 
|
GO:0005524
|
ATP binding
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0067
|
F
|
|
GO:0003689
Seeded from [[EcoCyc]] (v14.0)
|
|
DNA clamp loader activity
complete
|-
|
|


|
|
GO:0005524
|
ATP binding
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
|
 
SP_KW:KW-0067
|
|
F
F
|
|
 
Seeded from [[EcoCyc]] (v14.0)
|
|
required field missing
complete
|-  
|-  
|
|
Line 408: Line 560:
|
|


|
complete
|-
|
|
GO:0006260
|
DNA replication
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR008921
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 419: Line 590:
|
|
PMID:11029431
PMID:11029431
|
|
IDA: Inferred from Direct Assay
IDA: Inferred from Direct Assay
Line 447: Line 617:
|
|


|
complete
|-
|
|
GO:0006260
|
DNA replication
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR012763
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 466: Line 655:
|
|


|
complete
|-
|
|
GO:0006260
|
DNA replication
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0235
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 485: Line 693:
|
|


|
complete
|-
|
|
GO:0009360
|
DNA polymerase III complex
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR012763
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 504: Line 731:
|
|


|
complete
|-
|
|
GO:0009360
|
DNA polymerase III complex
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR012763
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
|
GO:0016740
|
transferase activity
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0808
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
|
GO:0016740
|
transferase activity
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0808
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
|
GO:0016779
|
nucleotidyltransferase activity
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0548
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
|
GO:0016779
|
nucleotidyltransferase activity
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0548
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
|
GO:0017111
|
nucleoside-triphosphatase activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR003593
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
|
GO:0017111
|
nucleoside-triphosphatase activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR003593
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  


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*  
****************************************************************************************** -->{{Product_interactions_help}}
****************************************************************************************** -->{{Product_interactions_help}}
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="G46aa31eb0e561"  class=" tableEdit Product_interactions_table dataTable" 
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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
Line 658: Line 1,018:
|
|
Experiment(s):EBI-1136784<br />  
Experiment(s):EBI-1136784<br />  
|-
|
Protein
|
ugpB
|
|
PMID:19402753
|
LCMS(ID Probability):99.0
|-
|
Protein
|
fecB
|
|
PMID:19402753
|
LCMS(ID Probability):99.0
|-  
|-  
|
|
Line 717: Line 1,099:
   
   


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*  
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!|Compartment!!Description!!Evidence!!Source!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


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===Notes===
===Notes===
 
Quantitation of DnaX products in replisomes shows three molecules of Tau and no Gamma at the replication fork <ref name='PMID:20413500'/>.


==Structure and Physical Properties==
==Structure and Physical Properties==
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46,410 - 47,160 (calc based on 9 Y, 6 W, and 6 C residues)
46,410 - 47,160 (calc based on 9 Y, 6 W, and 6 C residues)


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|- {{table heading style}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
41..177
|
[http://pfam.janelia.org/family/PF00004 PF00004  ATPase family associated with various cellular activities (AAA)]
|
 
|
PMID:19920124
|-
|
Domain
|
416..498
|
[http://pfam.janelia.org/family/PF12168 PF12168  DNA polymerase III subunits tau domain IV DnaB-binding]
|
 
|
PMID:19920124
|-
|
Domain
|
232..372
|
[http://pfam.janelia.org/family/PF12169 PF12169  DNA polymerase III subunits gamma and tau domain III]
|
 
|
PMID:19920124
|-
|
Domain
|
499..640
|
[http://pfam.janelia.org/family/PF12170 PF12170  DNA polymerase III tau subunit V interacting with alpha]
|
 
|
PMID:19920124


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||
||
View models at:
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P06710 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=recA&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P06710 PSI-PRED (P06710)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P06710 Genomes TO Protein (P06710)] (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)


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|- {{table_heading_style}}
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!|Database!!Accession!!Notes
!|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/16128454 GI:16128454]
|
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/NP_415003.1 GeneID:945105]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10245-MONOMER EcoCyc:EG10245-MONOMER]
[[ASAP]]
|
|
ASAP:ABE-0001633
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P06710 UniProtKB/Swiss-Prot:P06710]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:EG10245
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG10245
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[[uniprot:P06710|UniProt:P06710]]
[http://www.ncbi.nlm.nih.gov/gene?term=945105 GeneID:945105]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://pfam.sanger.ac.uk/family?acc=PF00004 PFAM:PF00004]
RegulonDB:ECK120000239
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_415003 RefSeq:NP_415003]
EchoBASE:EB0241
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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<noinclude>
<noinclude>
==References==
==References==
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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0006261_!_DNA-dependent DNA replication]][[Category:Complex:DNA polymerase III, preinitiation complex]][[Category:Complex:DNA polymerase III, holoenzyme]][[Category:Complex:DNA polymerase III, &tau; subunit dimer]][[Category:Products with structures in PDB]]

Latest revision as of 20:26, 17 February 2015

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

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

Standard name

DnaX

Synonyms

DNA polymerase III/DNA elongation factor III, tau and gamma subunits[1], DnaZ[2][1], B0470[2][1] , dnaZ, ECK0464, JW0459, b0470

Product description


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]

edit table


Notes

Function

[back to top]


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 Evidence Code with/from Aspect Notes Status
GO:0043846

DNA polymerase III, DnaX complex

C

Missing: evidence, reference

GO:0003689

DNA clamp loader activity

F

Missing: evidence, reference

GO:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008921

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008921

F

Seeded from EcoCyc (v14.0)

complete

GO:0003887

DNA-directed DNA polymerase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012763

F

Seeded from EcoCyc (v14.0)

complete

GO:0003887

DNA-directed DNA polymerase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012763

F

Seeded from EcoCyc (v14.0)

complete

GO:0003887

DNA-directed DNA polymerase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.7.7.7

F

Seeded from EcoCyc (v14.0)

complete

GO:0003887

DNA-directed DNA polymerase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.7.7.7

F

Seeded from EcoCyc (v14.0)

complete

GO:0003887

DNA-directed DNA polymerase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0239

F

Seeded from EcoCyc (v14.0)

complete

GO:0003887

DNA-directed DNA polymerase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0239

F

Seeded from EcoCyc (v14.0)

complete

GO:0005515

protein binding

PMID:19703395[5]

IPI: Inferred from Physical Interaction

UniProtKB:P0A988

F

Seeded from EcoCyc (v14.0)

complete

GO:0005515

protein binding

PMID:19703395[5]

IPI: Inferred from Physical Interaction

UniProtKB:P0A988

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001270

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001270

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003959

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003959

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012763

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012763

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: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:0006260

DNA replication

PMID:391641[6]

IMP: Inferred from Mutant Phenotype

P

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008921

P

Seeded from EcoCyc (v14.0)

complete

GO:0017111

nucleoside-triphosphatase activity

PMID:11029431[7]

IDA: Inferred from Direct Assay

F

complete

GO:0043846

DNA polymerase III, DnaX complex

PMID:8376347[8]

IDA: Inferred from Direct Assay

C

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012763

P

Seeded from EcoCyc (v14.0)

complete

GO:0016887

ATPase activity

PMID:2681183[9]

IDA: Inferred from Direct Assay

F

complete

GO:0006260

DNA replication

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0235

P

Seeded from EcoCyc (v14.0)

complete

GO:0030337

DNA polymerase processivity factor activity

PMID:11525729[10]

IDA: Inferred from Direct Assay

F

complete

GO:0009360

DNA polymerase III complex

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012763

C

Seeded from EcoCyc (v14.0)

complete

GO:0030337

DNA polymerase processivity factor activity

PMID:7494000[11]

IDA: Inferred from Direct Assay

F

complete

GO:0009360

DNA polymerase III complex

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012763

C

Seeded from EcoCyc (v14.0)

complete

GO:0016740

transferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

Seeded from EcoCyc (v14.0)

complete

GO:0016740

transferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

Seeded from EcoCyc (v14.0)

complete

GO:0016779

nucleotidyltransferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0548

F

Seeded from EcoCyc (v14.0)

complete

GO:0016779

nucleotidyltransferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0548

F

Seeded from EcoCyc (v14.0)

complete

GO:0017111

nucleoside-triphosphatase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0017111

nucleoside-triphosphatase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

edit table


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[12]

Experiment(s):EBI-883400

Protein

fecB

PMID:15690043[12]

Experiment(s):EBI-890677

Protein

nusG

PMID:15690043[12]

Experiment(s):EBI-890677

Protein

rplL

PMID:15690043[12]

Experiment(s):EBI-890677

Protein

rpmC

PMID:15690043[12]

Experiment(s):EBI-890677

Protein

rpsF

PMID:15690043[12]

Experiment(s):EBI-890677

Protein

ugpB

PMID:15690043[12]

Experiment(s):EBI-890677

Protein

yfiF

PMID:15690043[12]

Experiment(s):EBI-890677

Protein

yjgD

PMID:15690043[12]

Experiment(s):EBI-890677

Protein

rhsD

PMID:16606699[13]

Experiment(s):EBI-1136784

Protein

rpoC

PMID:16606699[13]

Experiment(s):EBI-1136784

Protein

ugpB

PMID:19402753[14]

LCMS(ID Probability):99.0

Protein

fecB

PMID:19402753[14]

LCMS(ID Probability):99.0

Protein

Subunits of DNA polymerase III, holoenzyme

could be indirect

Protein

ParC from Topo IV


PMID:12535532[15]

Microscopy- colocalization at the fork lost in dnaX mutant


Protein

subunits of the clamp loader

PMID:11525729[10]

Protein

DnaB (Helicase)-Interacts with tau

PMID:10748120[16]

Protein

alpha subunit of DNA Polymerase III- interacts with tau

PMID:10748120[16]


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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

Quantitation of DnaX products in replisomes shows three molecules of Tau and no Gamma at the replication fork [17].

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 

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

Domain

41..177

PF00004 ATPase family associated with various cellular activities (AAA)

PMID:19920124[18]

Domain

416..498

PF12168 DNA polymerase III subunits tau domain IV DnaB-binding

PMID:19920124[18]

Domain

232..372

PF12169 DNA polymerase III subunits gamma and tau domain III

PMID:19920124[18]

Domain

499..640

PF12170 DNA polymerase III tau subunit V interacting with alpha

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=dnaX taxon=562,83333 </beststructure>

Models

View models at:

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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:16128454

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945105

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001633

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P06710

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10245

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10245

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945105

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000239

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0241

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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

  1. ↑ 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. ↑ 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. ↑ 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
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 Parks, AR et al. (2009) Transposition into replicating DNA occurs through interaction with the processivity factor. Cell 138 685-95 PubMed
  6. ↑ Henson, JM et al. (1979) Isolation and characterization of dnaX and dnaY temperature-sensitive mutants of Escherichia coli. Genetics 92 1041-59 PubMed
  7. ↑ 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
  8. ↑ 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
  9. ↑ 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
  10. ↑ 10.0 10.1 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
  11. ↑ 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
  12. ↑ 12.0 12.1 12.2 12.3 12.4 12.5 12.6 12.7 12.8 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  13. ↑ 13.0 13.1 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  14. ↑ 14.0 14.1 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  15. ↑ Espeli, O et al. (2003) Temporal regulation of topoisomerase IV activity in E. coli. Mol. Cell 11 189-201 PubMed
  16. ↑ 16.0 16.1 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
  17. ↑ Reyes-Lamothe, R et al. (2010) Stoichiometry and architecture of active DNA replication machinery in Escherichia coli. Science 328 498-501 PubMed
  18. ↑ 18.0 18.1 18.2 18.3 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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