dnaE:Gene Product(s): Difference between revisions

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|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Domains/Motifs/Modification Sites|Domains]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Gene Product Resources|Resources]]
|{{Sub}}[[#Gene Product Resources|Resources]]
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{|{{Prettytable}}
{|  id="K46aa21fc7e37d"  class=" tableEdit Product_nomenclature_table" 
 
|-
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!{{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
|
||
DnaE product
DnaE  
|-
|-
!{{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
|
||
DNA polymerase III alpha subunit product<ref name='LIB:Riley_2006'/>, B0184 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, SdgC product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PolC product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, DnaE product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''DNA polymerase III alpha subunit<ref name='LIB:Riley_2006'/>, B0184<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, SdgC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PolC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, DnaE<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0183, JW0179, polC, sdgC, b0184''
|-
|-
!{{table heading style}} |Product description
!align=left {{table heading style}} |Product description
|
||
DNA polymerase III, &alpha; subunit<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>;  
DNA polymerase III, &alpha; subunit<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>;  


Component of ; [[:Category:Complex:DNA polymerase III, core enzyme|DNA polymerase III, core enzyme]]<ref name='LIB:EcoCyc11.1'/>; [[:Category:Complex:DNA polymerase III, holoenzyme|DNA polymerase III, holoenzyme]]<ref name='LIB:EcoCyc11.1'/>
Component of [[:Category:Complex:DNA polymerase III, core enzyme|DNA polymerase III, core enzyme]]<ref name='LIB:EcoCyc11.1'/>; [[:Category:Complex:DNA polymerase III, holoenzyme|DNA polymerase III, holoenzyme]]<ref name='LIB:EcoCyc11.1'/>


DNA polymerase III, alpha subunit; suppressor of dnaG-Ts<ref name='LIB:EcoGene'/>
|-
|-
!{{table heading style}} |EC number (for enzymes)
!align=left {{table heading style}} |EC number (for enzymes)
|
||
** [http://www.brenda.uni-koeln.de/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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<protect><!--Nomenclature_notes--></protect>
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===Notes===
===Notes===
Line 66: Line 70:
{{BacktoTop}}
{{BacktoTop}}
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<big>'''Gene Ontology'''</big>
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.19938.R46aa21fe413ca-->
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****************************************************************************************** -->{{Product_GO_help}}
{|class = 'sortable' {{Prettytable}} id='152765'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46aa21fe413ca"  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
|-
|-
|
NOT
|
GO:0008408
|
3'-5' exonuclease activity
|
PMID:2997151
|
IDA: Inferred from Direct Assay
|
 
|
F
|
 
|
complete
|-
|
 
|
GO:0003887
|
DNA-directed DNA polymerase activity
|
PMID:2997151
|
IDA: Inferred from Direct Assay
|
 
|
F
|
 
|
complete
|-
|
 
|
GO:0003676
|
nucleic acid binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR004365
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003677
|
DNA binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR003141
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003824
|
catalytic activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR004013
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003824
|
catalytic activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR016195
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003887
|
DNA-directed DNA polymerase activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR003141
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003887
|
DNA-directed DNA polymerase activity
|
GOA:spec<br />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<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0239
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0005737
|
cytoplasm
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR004805
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0005737
|
cytoplasm
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011708
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0005737
|
cytoplasm
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0963
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0005737
|
cytoplasm
|
GO_REF:0000023
|
IEA: Inferred from Electronic Annotation
|
SP_SL:SL-0086
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0006260
|
DNA replication
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR003141
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0006260
|
DNA replication
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR004805
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0006260
|
DNA replication
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011708
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
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
|-
|
 
|
GO:0008408
|
3'-5' exonuclease activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR004805
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0008408
|
3'-5' exonuclease activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011708
|
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:0005737  
GO:0005737
|
|
cytoplasm  
cytoplasm
|
|
PMID:2997151
|
|
IDA: Inferred from Direct Assay
|
|
 
|
|
C  
C
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
 
|
|
required fields missing 
complete
|-
|-  
|
|
 
|
|
GO:0006261
GO:0003887
|
|
DNA-dependent DNA replication
DNA-directed DNA polymerase activity
|
|
PMID:2997151
|
|
IDA: Inferred from Direct Assay
|
|
 
|
|
P
F
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
 
|
|
required fields missing 
complete
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<span id="Interactions"></span><big>'''Interactions'''</big>
<span id="Interactions"></span><big>'''Interactions'''</big>
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{|class = 'sortable' {{Prettytable}} id='152766'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46aa2214b5639"  class=" tableEdit Product_interactions_table dataTable" 
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!Partner Type!!Partner!!Notes
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Protein
Protein
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Subunits of [[:Category:Complex:DNA polymerase III, core enzyme|DNA polymerase III, core enzyme]]  
Subunits of [[:Category:Complex:DNA polymerase III, core enzyme|DNA polymerase III, core enzyme]]  
|
|
could be indirect   
could be indirect  
|-
|
 
|
   
|-
|
Protein
|
ssb<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-883487<br />
|-
|
Protein
|
aceE<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-883487<br />
|-
|
Protein
|
dnaX<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-883487, EBI-890781<br />
|-
|
Protein
|
holA<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-883487, EBI-890781<br />
|-
|
Protein
|
holB<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-883487, EBI-880223<br />
|-
|
Protein
|
holC<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-883487, EBI-880166, EBI-885330, EBI-890781<br />
|-
|
Protein
|
holD<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-883487, EBI-880133, EBI-890781<br />
|-
|
Protein
|
rpsB<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-883487, EBI-890781<br />
|-
|
Protein
|
tufA<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-883487, EBI-890781<br />
|-
|
Protein
|
pta<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1135853<br />
|-
|
Protein
|
helD<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1135853<br />
|-
|
Protein
|
asnB<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-890781<br />
|-
|
Protein
|
dnaK<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-890781<br />
|-
|
Protein
|
hrpB<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-890781<br />
|-
|
Protein
|
lpdA<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-890781<br />
|-
|
Protein
|
nikD<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-890781<br />
|-
|
Protein
|
rhsD<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-890781<br />
|-
|
Protein
|
rplA<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-890781<br />
|-
|
Protein
|
rplC<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-890781<br />
|-
|
Protein
|
rplD<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-890781<br />
|-
|
Protein
|
rplL<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-890781<br />
|-
|
Protein
|
rplM<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-890781<br />
|-
|
Protein
|
rplU<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-890781<br />
|-
|
Protein
|
rpsA<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-890781<br />
|-
|
Protein
|
rpsP<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-890781<br />
|-
|
Protein
|
tpiA<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-890781<br />
|-
|
Protein
|
ybdL<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-890781<br />
|-
|
Protein
|
bcsA<br />
|
 
|
PMID:15690043
|
Experiment(s):EBI-890781<br />
|-
|
Protein
|
rpsA
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
dnaN
|
 
|
PMID:19402753
|
MALDI(Z-score):26.949307
|-
|
Protein
|
rplU
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
tpiA
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
rpsP
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
rplM
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
tufB
|
 
|
PMID:19402753
|
MALDI(Z-score):19.758845
|-
|
Protein
|
rplA
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
ssb
|
 
|
PMID:19402753
|
LCMS(ID Probability):96.3 MALDI(Z-score):30.794950
|-
|
Protein
|
holA
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6 MALDI(Z-score):38.471077
|-
|
Protein
|
holC
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6 MALDI(Z-score):22.027887
|-
|
Protein
|
dnaQ
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6 MALDI(Z-score):36.181251
|-
|
Protein
|
holE
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6 MALDI(Z-score):18.880290
|-
|
Protein
|
holB
|
 
|
PMID:19402753
|
MALDI(Z-score):39.020174
|-
|
Protein
|
dnaX
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6 MALDI(Z-score):28.891532
|-
|
Protein
|
holD
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6 MALDI(Z-score):26.029135
|-
|
Protein
|
asnB
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.0
|-
|
Protein
|
rplL
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-  
|
|
Protein
Protein
Line 145: Line 1,057:
Subunits of [[:Category:Complex:DNA polymerase III, holoenzyme|DNA polymerase III, holoenzyme]]  
Subunits of [[:Category:Complex:DNA polymerase III, holoenzyme|DNA polymerase III, holoenzyme]]  
|
|
could be indirect   
could be indirect  
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<!--Function_notes--></protect>
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===Notes===
===Notes===
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<!--
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|- {{table heading style}}
|- {{table heading style}}
!Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
|-class='sortbottom'
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|
Cytoplasm
|
 
|
Purification
|
PMID:2997151
|
 
|- class="tableEdit_footer"
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{|{{Prettytable}}
{|   id="R46aa22173c2b1"  class=" tableEdit Product_phys_prop_table" 
 
|-
!align=left {{table heading style}} |Name
||
 
|-
|-
!{{table heading style}} |Sequence
!align=left {{table heading style}} |Sequence
|
||
[http://biocyc.org/ECOLI/sequence-aa?object=EG10238-MONOMER at EcoCyc]  
[http://biocyc.org/ECOLI/sequence-aa?object=EG10238-MONOMER at EcoCyc]  
<pre>MSEPRFVHLR VHSDYSMIDG LAKTAPLVKK AAALGMPALA ITDFTNLCGL VKFYGAGHGA
<pre>MSEPRFVHLR VHSDYSMIDG LAKTAPLVKK AAALGMPALA ITDFTNLCGL VKFYGAGHGA
Line 213: Line 1,147:
RLLNDLRGLI GSEQVELEFD</pre>  
RLLNDLRGLI GSEQVELEFD</pre>  
|-
|-
!{{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Length
|
||
129.9 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
1,160
|-
|-
!{{table heading style}} |pI
!align=left {{table heading style}} |Mol. Wt
|
||
129.908 kDa
|-
|-
!{{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |pI
|
||
102110 - 103610 (calc based on 39 Y, 8 W, and 12 C residues)  
5.1 (calculated)
|-
|-
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!align=left {{table heading style}} |Extinction coefficient
||
102,110 - 103,610 (calc based on 39 Y, 8 W, and 12 C residues)
 
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<big>'''Domains/Motifs/Modification Sites'''</big>
 
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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
<tr align="left" valign="top">
<td><!--box uid=421aa90e079fa326b6494f812ad13e79.19938.U46aa2217944e7-->
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|- {{table heading style}}
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!Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-class='sortbottom'
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|
Domain
|
7..192
|
[http://pfam.janelia.org/family/PF02811 PF02811  PHP domain]
|
 
|
PMID:19920124
|-
|
Domain
|
994..1073
|
[http://pfam.janelia.org/family/PF01336 PF01336  OB-fold nucleic acid binding domain]
|
 
|
PMID:19920124
|-
|
Domain
|
290..735
|
[http://pfam.janelia.org/family/PF07733 PF07733  Bacterial DNA polymerase III alpha subunit]
|
 
|
PMID:19920124
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19938.U46aa2217944e7&page=19938&pagename={{FULLPAGENAMEE}}&type=&template=Product_motif_table edit table]</span> || || || ||
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<td>
<!-- motifs column 2-->
<motif_map/>
</td>
</tr>
</table>


<span id="Structure"></span><big>'''Structure'''</big>
<table><tr valign='top'><td>
<span id='Structure'></span><big>'''Structure'''</big><br />
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{|class = 'sortable' {{Prettytable}} id='102084'
{|   id="S46a7b34b0ea48"  class=" tableEdit Product_structure_table" 
|- {{table heading style}}
 
!Structure Type!!Organism!!Accession!!Residues covered!!Notes
|-
|-class='sortbottom'
!align=left {{table heading style}} |Structures
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19938.S46a7b34b0ea48&page=19938&pagename={{FULLPAGENAMEE}} edit table] || || || ||
||
<beststructure>
gene=dnaE
taxon=562,83333
</beststructure>
|-
!align=left {{table heading style}} |Models
||
View models at:
* [http://www.proteinmodelportal.org/query/uniprot/Q9JMR9 Protein Model Portal]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P10443 PSI-PRED (P10443)]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P10443 Genomes TO Protein (P10443)] (GTOP)
 
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<!--Structure_notes--></protect>
</td><td></protect>
==== Structure figures ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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===Notes===
===Notes===


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===Notes===
===Notes===
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|- {{table_heading_style}}
|- {{table_heading_style}}
!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-
|
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/16128177 GI:16128177]
|
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_414726.1 GeneID:944877]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0000624
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P10443 UniProtKB/Swiss-Prot:P10443]
|
Escherichia coli str. K-12 substr. MG1655
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10238-MONOMER EcoCyc:EG10238-MONOMER] 
EcoCyc:EG10238
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.expasy.ch/cgi-bin/sprot-search-ac?P10443 UniProt:P10443] 
EcoGene:EG10238
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.sanger.ac.uk/Software/Pfam/ PFAM] ([[PFAM|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF02231 PFAM:PF02231]
[http://www.ncbi.nlm.nih.gov/gene?term=944877 GeneID:944877]
|
|
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=NP_414726 RefSeq:NP_414726] 
RegulonDB:ECK120000232
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://salilab.org/modbase/searchbyid?databaseID=P10443 ModBase:P10443] 
EchoBASE:EB0234
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</noinclude>
===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0006261_!_DNA-dependent DNA replication]][[Category:Complex:DNA polymerase III, core enzyme]][[Category:Complex:DNA polymerase III, holoenzyme]]

Latest revision as of 20:22, 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

DnaE

Synonyms

DNA polymerase III alpha subunit[1], B0184[2][1], SdgC[2][1], PolC[2][1], DnaE[2][1] , ECK0183, JW0179, polC, sdgC, b0184

Product description

DNA polymerase III, α subunit[2][3];

Component of DNA polymerase III, core enzyme[3]; DNA polymerase III, holoenzyme[3]

DNA polymerase III, alpha subunit; suppressor of dnaG-Ts[4]

EC number (for enzymes)
edit table


Notes

Function

[back to top]


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

NOT

GO:0008408

3'-5' exonuclease activity

PMID:2997151[5]

IDA: Inferred from Direct Assay

F

complete

GO:0003887

DNA-directed DNA polymerase activity

PMID:2997151[5]

IDA: Inferred from Direct Assay

F

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004365

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003141

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004013

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016195

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:IPR003141

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:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004805

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011708

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003141

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004805

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011708

P

Seeded from EcoCyc (v14.0)

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:0008408

3'-5' exonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004805

F

Seeded from EcoCyc (v14.0)

complete

GO:0008408

3'-5' exonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011708

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:0005737

cytoplasm

PMID:2997151[5]

IDA: Inferred from Direct Assay

C

complete

GO:0003887

DNA-directed DNA polymerase activity

PMID:2997151[5]

IDA: Inferred from Direct Assay

F

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 polymerase III, core enzyme

could be indirect

Protein

ssb

PMID:15690043[6]

Experiment(s):EBI-883487

Protein

aceE

PMID:15690043[6]

Experiment(s):EBI-883487

Protein

dnaX

PMID:15690043[6]

Experiment(s):EBI-883487, EBI-890781

Protein

holA

PMID:15690043[6]

Experiment(s):EBI-883487, EBI-890781

Protein

holB

PMID:15690043[6]

Experiment(s):EBI-883487, EBI-880223

Protein

holC

PMID:15690043[6]

Experiment(s):EBI-883487, EBI-880166, EBI-885330, EBI-890781

Protein

holD

PMID:15690043[6]

Experiment(s):EBI-883487, EBI-880133, EBI-890781

Protein

rpsB

PMID:15690043[6]

Experiment(s):EBI-883487, EBI-890781

Protein

tufA

PMID:15690043[6]

Experiment(s):EBI-883487, EBI-890781

Protein

pta

PMID:16606699[7]

Experiment(s):EBI-1135853

Protein

helD

PMID:16606699[7]

Experiment(s):EBI-1135853

Protein

asnB

PMID:15690043[6]

Experiment(s):EBI-890781

Protein

dnaK

PMID:15690043[6]

Experiment(s):EBI-890781

Protein

hrpB

PMID:15690043[6]

Experiment(s):EBI-890781

Protein

lpdA

PMID:15690043[6]

Experiment(s):EBI-890781

Protein

nikD

PMID:15690043[6]

Experiment(s):EBI-890781

Protein

rhsD

PMID:15690043[6]

Experiment(s):EBI-890781

Protein

rplA

PMID:15690043[6]

Experiment(s):EBI-890781

Protein

rplC

PMID:15690043[6]

Experiment(s):EBI-890781

Protein

rplD

PMID:15690043[6]

Experiment(s):EBI-890781

Protein

rplL

PMID:15690043[6]

Experiment(s):EBI-890781

Protein

rplM

PMID:15690043[6]

Experiment(s):EBI-890781

Protein

rplU

PMID:15690043[6]

Experiment(s):EBI-890781

Protein

rpsA

PMID:15690043[6]

Experiment(s):EBI-890781

Protein

rpsP

PMID:15690043[6]

Experiment(s):EBI-890781

Protein

tpiA

PMID:15690043[6]

Experiment(s):EBI-890781

Protein

ybdL

PMID:15690043[6]

Experiment(s):EBI-890781

Protein

bcsA

PMID:15690043[6]

Experiment(s):EBI-890781

Protein

rpsA

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

dnaN

PMID:19402753[8]

MALDI(Z-score):26.949307

Protein

rplU

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

tpiA

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rpsP

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rplM

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

tufB

PMID:19402753[8]

MALDI(Z-score):19.758845

Protein

rplA

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

ssb

PMID:19402753[8]

LCMS(ID Probability):96.3 MALDI(Z-score):30.794950

Protein

holA

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):38.471077

Protein

holC

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):22.027887

Protein

dnaQ

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):36.181251

Protein

holE

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):18.880290

Protein

holB

PMID:19402753[8]

MALDI(Z-score):39.020174

Protein

dnaX

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):28.891532

Protein

holD

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):26.029135

Protein

asnB

PMID:19402753[8]

LCMS(ID Probability):99.0

Protein

rplL

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

Subunits of DNA polymerase III, holoenzyme

could be indirect


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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

Cytoplasm

Purification

PMID:2997151[5]


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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 

MSEPRFVHLR VHSDYSMIDG LAKTAPLVKK AAALGMPALA ITDFTNLCGL VKFYGAGHGA
GIKPIVGADF NVQCDLLGDE LTHLTVLAAN NTGYQNLTLL ISKAYQRGYG AAGPIIDRDW
LIELNEGLIL LSGGRMGDVG RSLLRGNSAL VDECVAFYEE HFPDRYFLEL IRTGRPDEES
YLHAAVELAE ARGLPVVATN DVRFIDSSDF DAHEIRVAIH DGFTLDDPKR PRNYSPQQYM
RSEEEMCELF ADIPEALANT VEIAKRCNVT VRLGEYFLPQ FPTGDMSTED YLVKRAKEGL
EERLAFLFPD EEERLKRRPE YDERLETELQ VINQMGFPGY FLIVMEFIQW SKDNGVPVGP
GRGSGAGSLV AYALKITDLD PLEFDLLFER FLNPERVSMP DFDVDFCMEK RDQVIEHVAD
MYGRDAVSQI ITFGTMAAKA VIRDVGRVLG HPYGFVDRIS KLIPPDPGMT LAKAFEAEPQ
LPEIYEADEE VKALIDMARK LEGVTRNAGK HAGGVVIAPT KITDFAPLYC DEEGKHPVTQ
FDKSDVEYAG LVKFDFLGLR TLTIINWALE MINKRRAKNG EPPLDIAAIP LDDKKSFDML
QRSETTAVFQ LESRGMKDLI KRLQPDCFED MIALVALFRP GPLQSGMVDN FIDRKHGREE
ISYPDVQWQH ESLKPVLEPT YGIILYQEQV MQIAQVLSGY TLGGADMLRR AMGKKKPEEM
AKQRSVFAEG AEKNGINAEL AMKIFDLVEK FAGYGFNKSH SAAYALVSYQ TLWLKAHYPA
EFMAAVMTAD MDNTEKVVGL VDECWRMGLK ILPPDINSGL YHFHVNDDGE IVYGIGAIKG
VGEGPIEAII EARNKGGYFR ELFDLCARTD TKKLNRRVLE KLIMSGAFDR LGPHRAALMN
SLGDALKAAD QHAKAEAIGQ ADMFGVLAEE PEQIEQSYAS CQPWPEQVVL DGERETLGLY
LTGHPINQYL KEIERYVGGV RLKDMHPTER GKVITAAGLV VAARVMVTKR GNRIGICTLD
DRSGRLEVML FTDALDKYQQ LLEKDRILIV SGQVSFDDFS GGLKMTAREV MDIDEAREKY
ARGLAISLTD RQIDDQLLNR LRQSLEPHRS GTIPVHLYYQ RADARARLRF GATWRVSPSD
RLLNDLRGLI GSEQVELEFD
Length

1,160

Mol. Wt

129.908 kDa

pI

5.1 (calculated)

Extinction coefficient

102,110 - 103,610 (calc based on 39 Y, 8 W, and 12 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

7..192

PF02811 PHP domain

PMID:19920124[9]

Domain

994..1073

PF01336 OB-fold nucleic acid binding domain

PMID:19920124[9]

Domain

290..735

PF07733 Bacterial DNA polymerase III alpha subunit

PMID:19920124[9]

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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=dnaE 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:16128177

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944877

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000624

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P10443

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10238

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10238

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944877

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000232

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0234

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 1.4 1.5 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 2.4 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 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 5.2 5.3 5.4 Maki, H & Kornberg, A (1985) The polymerase subunit of DNA polymerase III of Escherichia coli. II. Purification of the alpha subunit, devoid of nuclease activities. J. Biol. Chem. 260 12987-92 PubMed
  6. ↑ 6.00 6.01 6.02 6.03 6.04 6.05 6.06 6.07 6.08 6.09 6.10 6.11 6.12 6.13 6.14 6.15 6.16 6.17 6.18 6.19 6.20 6.21 6.22 6.23 6.24 6.25 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  7. ↑ 7.0 7.1 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  8. ↑ 8.00 8.01 8.02 8.03 8.04 8.05 8.06 8.07 8.08 8.09 8.10 8.11 8.12 8.13 8.14 8.15 8.16 8.17 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  9. ↑ 9.0 9.1 9.2 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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