umuD:Gene Product(s)

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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

UmuD

Synonyms

DNA polymerase V, subunit D[1], B1183[2][1], UmuD[2][1] , ECK1171, JW1172, b1183

Product description

SOS mutagenesis; error-prone repair; processed to UmuD'; forms complex with UmuC[2][3];

Component of DNA polymerase V[3]

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[4]

EC number (for enzymes) 
3.4.21.-[1]
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Notes

Function

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<protect> 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
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[5]

IPI: Inferred from Physical Interaction

EcoliWiki:umuC


F

complete

GO:0006974

response to DNA damage stimulus

PMID:10760165[6]

IEP: Inferred from Expression Pattern

P

complete

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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 V

could be indirect

Protein

purE

PMID:16606699[7]

Experiment(s):EBI-1139115

Protein

fldB

PMID:16606699[7]

Experiment(s):EBI-1139115

Protein

fur

PMID:16606699[7]

Experiment(s):EBI-1139115

Protein

insO2

PMID:16606699[7]

Experiment(s):EBI-1139115

Protein

rpsE

PMID:16606699[7]

Experiment(s):EBI-1139115

Protein

ybiA

PMID:16606699[7]

Experiment(s):EBI-1139115

Protein

dnaN (beta clamp)

Protein

RecA


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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

Structure and Physical Properties

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<protect> 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 

MLFIKPADLR EIVTFPLFSD LVQCGFPSPA ADYVEQRIDL NQLLIQHPSA TYFVKASGDS
MIDGGISDGD LLIVDSAITA SHGDIVIAAV DGEFTVKKLQ LRPTVQLIPM NSAYSPITIS
SEDTLDVFGV VIHVVKAMR
Length

139

Mol. Wt

15.063 kDa

pI

4.4 (calculated)

Extinction coefficient

4,470 - 4,595 (calc based on 3 Y, 0 W, and 1 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

55..122

PF00717 Peptidase S24-like

PMID:19920124[8]

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

Structures

<beststructure> gene=umuD taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

NMR structure clarifies the dimer interface [9] from the original Xtal structure [10].
Hydrogen deuterium exchange experiments show UmuD2 and UmuD'2 to be highly dynamic proteins [11].

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:16129146

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945746

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003974

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AG11

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11057

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11057

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945746

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001046

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1050

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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 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. ↑ Woodgate, R et al. (1989) UmuC mutagenesis protein of Escherichia coli: purification and interaction with UmuD and UmuD'. Proc. Natl. Acad. Sci. U.S.A. 86 7301-5 PubMed
  6. ↑ Caramel, A & Schnetz, K (2000) Antagonistic control of the Escherichia coli bgl promoter by FIS and CAP in vitro. Mol. Microbiol. 36 85-92 PubMed
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  8. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed
  9. ↑ Ferentz, AE et al. (1997) Dimerization of the UmuD' protein in solution and its implications for regulation of SOS mutagenesis. Nat. Struct. Biol. 4 979-83 PubMed
  10. ↑ Peat, TS et al. (1996) Structure of the UmuD' protein and its regulation in response to DNA damage. Nature 380 727-30 PubMed
  11. ↑ Fang, J et al. (2010) Conformational dynamics of the Escherichia coli DNA polymerase manager proteins UmuD and UmuD'. J. Mol. Biol. 398 40-53 PubMed

Categories

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