rdgB: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

YggV

Synonyms

dITP/XTP pyrophosphatase[1], B2954[2][1], YggV[2][1], RdgB[2][1] , ECK2949, JW2921, yggV, b2954

Product description

G7530[2][3]

dITP/XTP pyrophosphatase, synthetic lethal with recA; mutant is hyper-recombinogenic[4]

EC number (for enzymes)
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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:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0000287

magnesium ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

F

Seeded from EcoCyc (v14.0)

complete

GO:0000287

magnesium ion binding

PMID:12297000[5]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0009143

nucleoside triphosphate catabolic process

PMID:12297000[5]

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0009143

nucleoside triphosphate catabolic process

PMID:19943897[6]

IGI: Inferred from Genetic Interaction

P

Seeded from EcoCyc (v14.0)

Missing: with/from

GO:0016151

nickel ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0533

F

Seeded from EcoCyc (v14.0)

complete

GO:0017111

nucleoside-triphosphatase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01405

F

Seeded from EcoCyc (v14.0)

complete

GO:0017111

nucleoside-triphosphatase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020922

F

Seeded from EcoCyc (v14.0)

complete

GO:0017111

nucleoside-triphosphatase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.6.1.15

F

Seeded from EcoCyc (v14.0)

complete

GO:0030145

manganese ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0464

F

Seeded from EcoCyc (v14.0)

complete

GO:0047429

nucleoside-triphosphate diphosphatase activity

PMID:12297000[5]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

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

visC

PMID:16606699[7]

Experiment(s):EBI-1144430

Protein

nusG

PMID:16606699[7]

Experiment(s):EBI-1144430

Protein

pepB

PMID:16606699[7]

Experiment(s):EBI-1144430
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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 

MQKVVLATGN VGKVRELASL LSDFGLDIVA QTDLGVDSAE ETGLTFIENA ILKARHAAKV
TALPAIADDS GLAVDVLGGA PGIYSARYSG EDATDQKNLQ KLLETMKDVP DDQRQARFHC
VLVYLRHAED PTPLVCHGSW PGVITREPAG TGGFGYDPIF FVPSEGKTAA ELTREEKSAI
SHRGQALKLL LDALRNG
Length

197

Mol. Wt

21.038 kDa

pI

5.2 (calculated)

Extinction coefficient

11,460 - 11,710 (calc based on 4 Y, 1 W, and 2 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

4..194

PF01725 Ham1 family

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=rdgB taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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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:16130855

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947429

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009692

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P52061

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7530

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12982

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947429

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004091

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2807

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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 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 Chung, JH et al. (2002) Identification of the dITP- and XTP-hydrolyzing protein from Escherichia coli. J. Biochem. Mol. Biol. 35 403-8 PubMed
  6. ↑ Budke, B & Kuzminov, A (2010) Production of clastogenic DNA precursors by the nucleotide metabolism in Escherichia coli. Mol. Microbiol. 75 230-45 PubMed
  7. ↑ 7.0 7.1 7.2 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

Categories

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