EcoliWiki - User contributions [en]

umuD:Quickview

2011-02-21T22:46:36Z

Beuning: /* Notes */

umuD:Quickview

2011-02-21T22:45:25Z

Beuning: /* Notes */

umuD:Quickview

2011-02-21T22:42:39Z

Beuning: /* Notes */

umuD:Gene Product(s)

2011-02-21T21:26:27Z

Beuning: /* Notes */

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|umuD}}{{Tab|Gene|umuD}}{{Tab On|Gene Product(s)|umuD}}{{Tab|Expression|umuD}}{{Tab|Evolution|umuD}}{{Tab|On One Page|umuD}}{{TabsBottom}}
{|
|-
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Function |Function]]
|{{Sub}}[[#Interactions |Interactions]]
|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Domains/Motifs/Modification Sites|Domains]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Gene Product Resources|Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References| References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude>
==Nomenclature==

{{Product_nomenclature_help}}
{| {{Prettytable}} id="F46aa5aa9a562a" class=" tableEdit Product_nomenclature_table"

|-
!align=left {{table heading style}} |Standard name
||
UmuD
|-
!align=left {{table heading style}} |Synonyms
||
DNA polymerase V, subunit D<ref name='LIB:Riley_2006'/>, B1183<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, UmuD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>
|-
!align=left {{table heading style}} |Product description
||
SOS mutagenesis; error-prone repair; processed to UmuD'; forms complex with UmuC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>;

Component of [[:Category:Complex:DNA polymerase V|DNA polymerase V]]<ref name='LIB:EcoCyc11.1'/>

DNA polymerase V subunit, capable of translesion synthesis; inducible mutagenesis; error-prone repair; UmuDC single-stranded binding protein with RecA-coated DNA; intrinsic AP lyase activity<ref name='LIB:EcoGene'/>
|-
!align=left {{table heading style}} |EC number (for enzymes)
||
[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.- 3.4.21.-]<ref name='LIB:Riley_2006'/>

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|}


<protect></protect>
===Notes===

==Function==
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<protect>
<big>'''Gene Ontology'''</big> 
{{Product_GO_help}}
{| id="M46aa5aab0abcf" class=" tableEdit GO_table_product dataTable"
|- {{table_heading_style}}
!|Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-
|

|
GO:0003677
|
DNA binding
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR006197
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0006281
|
DNA repair
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0234
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0006974
|
response to DNA damage stimulus
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0227
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0008233
|
peptidase activity
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0645
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0008236
|
serine-type peptidase activity
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0720
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0009432
|
SOS response
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0742
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0016787
|
hydrolase activity
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0378
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0045449
|
regulation of transcription
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR006197
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0005515
|
protein binding
|
PMID:2552436
|
IPI: Inferred from Physical Interaction
|
EcoliWiki:umuC

|
F
|

|
complete
|-
|

|
GO:0006974
|
response to DNA damage stimulus
|
PMID:10760165
|
IEP: Inferred from Expression Pattern
|

|
P
|

|
complete

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|}


<big>'''Interactions'''</big>

{{Product_interactions_help}}
{| {{Prettytable}} id="J46aa5acba3518" class=" tableEdit Product_interactions_table dataTable"
|- {{table heading style}}
!|Partner Type!!Partner!!Notes!!References!!Evidence
|-
|
Protein
|
Subunits of [[:Category:Complex:DNA polymerase V|DNA polymerase V]]
|
could be indirect
|

|

|-
|
Protein
|
purE 
|

|
PMID:16606699
|
Experiment(s):EBI-1139115 
|-
|
Protein
|
fldB 
|

|
PMID:16606699
|
Experiment(s):EBI-1139115 
|-
|
Protein
|
fur 
|

|
PMID:16606699
|
Experiment(s):EBI-1139115 
|-
|
Protein
|
insO2 
|

|
PMID:16606699
|
Experiment(s):EBI-1139115 
|-
|
Protein
|
rpsE 
|

|
PMID:16606699
|
Experiment(s):EBI-1139115 
|-
|
Protein
|
ybiA 
|

|
PMID:16606699
|
Experiment(s):EBI-1139115 
|-
|
Protein
|
[[dnaN:Gene_Product(s)|dnaN]] (beta clamp)
|

|

|

|-
|
Protein
|
[[recA:Gene_Product(s)|RecA]]
|

|

|

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</protect>
===Notes===

==Localization==

{{Product_localization_help}}
{| id="B46a7eda9681ac" class=" tableEdit Product_localization_table"
|- {{table heading style}}
!|Compartment!!Description!!Evidence!!Source!!Notes

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.22284.B46a7eda9681ac&page=22284&pagename={{FULLPAGENAMEE}}&type=&template=Product_localization_table edit table] || || || ||
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<protect></protect>

===Notes===

==Structure and Physical Properties==
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<protect>
<big>'''Physical Properties'''</big>

{{Product_physical_properties_help}}
{| id="W46aa5acdc747d" class=" tableEdit Product_phys_prop_table"

|-
!align=left {{table heading style}} |Sequence
||
[http://biocyc.org/ECOLI/sequence-aa?object=EG11057-MONOMER at EcoCyc]
<pre>MLFIKPADLR EIVTFPLFSD LVQCGFPSPA ADYVEQRIDL NQLLIQHPSA TYFVKASGDS
MIDGGISDGD LLIVDSAITA SHGDIVIAAV DGEFTVKKLQ LRPTVQLIPM NSAYSPITIS
SEDTLDVFGV VIHVVKAMR</pre>
|-
!align=left {{table heading style}} |Length
||
139
|-
!align=left {{table heading style}} |Mol. Wt
||
15.063 kDa
|-
!align=left {{table heading style}} |pI
||
4.4 (calculated)
|-
!align=left {{table heading style}} |Extinction coefficient
||
4,470 - 4,595 (calc based on 3 Y, W, and 1 C residues)

|- class="tableEdit_footer"
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|}


<big>'''Domains/Motifs/Modification Sites'''</big><table>
<tr align="left" valign="top">
<td>
{{Product_domains_motifs_help}}
{| id="N46aa5ace30349" class=" tableEdit Product_motif_table dataTable"
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
55..122
|
[http://pfam.janelia.org/family/PF00717 PF00717 Peptidase S24-like]
|

|
PMID:19920124

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|}
</td>
<td>


<motif_map/>
</td>
</tr>
</table>

<table><tr valign='top'><td>
<big>'''Structure'''</big> 

{{Product_structure_help}}
{| id="D46aa5ace7d033" class=" tableEdit Product_structure_table"

|-
!align=left {{table heading style}} |Structures
||
<beststructure>
gene=umuD
taxon=562,83333
</beststructure>
|-
!align=left {{table heading style}} |Models
||
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
* [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/psipred/ PSI-PRED]
* [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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|}


</td><td></protect>
==== Structure figures ====

<protect>
</td><tr><table></protect>
===Notes===
NMR structure clarifies the dimer interface <ref name='PMID:9406544'/> from the original Xtal structure <ref name='PMID:8614470'/>. 
Hydrogen deuterium exchange experiments show UmuD2 and UmuD'2 to be highly dynamic proteins <ref name='PMID:20206636'/>.

==Gene Product Resources==
{{BacktoTop}}

{{Product_resources_help}}
{| id="W46aa5ad052ee6" class=" tableEdit Product_resource_table"
|- {{table_heading_style}}
!|Resource type!!Source!!Notes/Reference

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.22284.W46aa5ad052ee6&page=22284&pagename={{FULLPAGENAMEE}}&type=&template=Product_resource_table edit table] || ||
|}


<protect></protect>
===Notes===

==Accessions in Other Databases==
{{BacktoTop}}

{{Gene_accessions_help}}
{| id="W46aa5ad0a04fa" class=" tableEdit Gene_accessions_table"
|- {{table_heading_style}}
!|Database!!Accession!!Notes
|-
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11057-MONOMER EcoCyc:EG11057-MONOMER]
|

|-
|
[http://swissmodel.expasy.org/repository/ SwissModel] ([[SwissModel|EcoliWiki Page]])
|
[http://swissmodel.expasy.org/repository/smr.php?job=2&sptr_ac=P0AG11 SwissModel:P0AG11]
|

|-
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[[uniprot:P0AG11|UniProt:P0AG11]]
|

|-
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
|
[http://pfam.janelia.org/protein/P0AG11 Pfam:P0AG11]
|

|-
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_415701 RefSeq:NP_415701]
|

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|}


<protect></protect>
===Notes===

==Links==
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{| id="P46a7edb1872d3" class=" tableEdit Links_table"
|- {{table_heading_style}}
!|Name!!URL!!Comments

|- class="tableEdit_footer"
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|}


<noinclude>
==References==
{{BacktoTop}}
{{RefHelp}}
<references />
__NOTOC__
===Categories===
{{BacktoTop}}
[[Category:Proteins]]

umuD:Expression

2011-02-21T21:09:25Z

Beuning: /* Notes */