recD: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

RecD

Synonyms

exonuclease V (RecBCD complex), alpha chain[1], B2819[2][1], HopE[2][1], RecD[2][1] , ECK2815, hopE, JW2787, b2819

Product description

DNA helicase, ATP-dependent dsDNA/ssDNA exonuclease V subunit, ssDNA endonuclease[2][3];

Component of recBCD[2][3]

RecBCD Exonuclease V subunit, recombination and repair; recD mutants are constitutively activated for recombination; RecBCD 5'-3' fast helicase subunit; RecD alone has 5'-3' helicase activity; contains ATP-binding site; binds RecC; inhibits RecA loading[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: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:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000606

F

Seeded from EcoCyc (v14.0)

complete

GO:0003724

RNA helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000606

F

Seeded from EcoCyc (v14.0)

complete

GO:0003968

RNA-directed RNA polymerase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000606

F

Seeded from EcoCyc (v14.0)

complete

GO:0004386

helicase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0347

F

Seeded from EcoCyc (v14.0)

complete

GO:0004518

nuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0540

F

Seeded from EcoCyc (v14.0)

complete

Contributes to

GO:0004386

helicase activity

PMID:1618858[5]

IDA: Inferred from Direct Assay

F

with RecB, RecC

complete

GO:0004519

endonuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0255

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

PMID:3298248[6]

IDA: Inferred from Direct Assay

F

complete

GO:0004527

exonuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0269

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

PMID:1618858[5]

IMP: Inferred from Mutant Phenotype

F

complete

GO:0005515

protein binding

PMID:1618858[5]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0009338

exodeoxyribonuclease V complex

PMID:1618858[5]

IDA: Inferred from Direct Assay

C

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

Contributes to

GO:0008854

exodeoxyribonuclease V activity

PMID:1618858[5]

IDA: Inferred from Direct Assay

F

with RecB, RecC

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:0008854

exodeoxyribonuclease V activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006344

F

Seeded from EcoCyc (v14.0)

complete

GO:0006310

DNA recombination

PMID:1618858[5]

IDA: Inferred from Direct Assay

P

complete

GO:0008854

exodeoxyribonuclease V activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.1.11.5

F

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

PMID:1618858[5]

IDA: Inferred from Direct Assay

P

complete

GO:0009338

exodeoxyribonuclease V complex

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006344

C

Seeded from EcoCyc (v14.0)

complete

GO:0005515

protein binding

PMID:1618858[5]

IDA: Inferred from Direct Assay

F

RecB & RecC

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:0017111

nucleoside-triphosphatase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0019079

viral genome replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000606

P

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

Subunits of recBCD

could be indirect

Protein

aceE

PMID:15690043[7]

Experiment(s):EBI-882133

Protein

lpdA

PMID:15690043[7]

Experiment(s):EBI-882133

Protein

groL

PMID:15690043[7]

Experiment(s):EBI-882133

Protein

recC

PMID:15690043[7]

Experiment(s):EBI-882133

Protein

groL

PMID:16606699[8]

Experiment(s):EBI-1144053

Protein

fucI

PMID:16606699[8]

Experiment(s):EBI-1144053

Protein

htpG

PMID:16606699[8]

Experiment(s):EBI-1144053

Protein

dnaJ

PMID:16606699[8]

Experiment(s):EBI-1144053

Protein

groS

PMID:19402753[9]

MALDI(Z-score):24.578913

Protein

recC

PMID:19402753[9]

MALDI(Z-score):18.813516

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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 

MKLQKQLLEA VEHKQLRPLD VQFALTVAGD EHPAVTLAAA LLSHDAGEGH VCLPLSRLEN
NEASHPLLAT CVSEIGELQN WEECLLASQA VSRGDEPTPM ILCGDRLYLN RMWCNERTVA
RFFNEVNHAI EVDEALLAQT LDKLFPVSDE INWQKVAAAV ALTRRISVIS GGPGTGKTTT
VAKLLAALIQ MADGERCRIR LAAPTGKAAA RLTESLGKAL RQLPLTDEQK KRIPEDASTL
HRLLGAQPGS QRLRHHAGNP LHLDVLVVDE ASMIDLPMMS RLIDALPDHA RVIFLGDRDQ
LASVEAGAVL GDICAYANAG FTAERARQLS RLTGTHVPAG TGTEAASLRD SLCLLQKSYR
FGSDSGIGQL AAAINRGDKT AVKTVFQQDF TDIEKRLLQS GEDYIAMLEE ALAGYGRYLD
LLQARAEPDL IIQAFNEYQL LCALREGPFG VAGLNERIEQ FMQQKRKIHR HPHSRWYEGR
PVMIARNDSA LGLFNGDIGI ALDRGQGTRV WFAMPDGNIK SVQPSRLPEH ETTWAMTVHK
SQGSEFDHAA LILPSQRTPV VTRELVYTAV TRARRRLSLY ADERILSAAI ATRTERRSGL
AALFSSRE
Length

608

Mol. Wt

66.903 kDa

pI

7.0 (calculated)

Extinction coefficient

47,900 - 49,025 (calc based on 10 Y, 6 W, and 9 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

168..355

PF05127 Putative ATPase (DUF699)

PMID:19920124[10]

Domain

517..581

PF01443 Viral (Superfamily 1) RNA helicase

PMID:19920124[10]

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

Structures

<beststructure> gene=recD 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:16130723

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947287

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009247

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P04993

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10826

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10826

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947287

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000817

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0819

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 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 5.5 5.6 5.7 Masterson, C et al. (1992) Reconstitution of the activities of the RecBCD holoenzyme of Escherichia coli from the purified subunits. J. Biol. Chem. 267 13564-72 PubMed
  6. ↑ Julin, DA & Lehman, IR (1987) Photoaffinity labeling of the recBCD enzyme of Escherichia coli with 8-azidoadenosine 5'-triphosphate. J. Biol. Chem. 262 9044-51 PubMed
  7. ↑ 7.0 7.1 7.2 7.3 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  8. ↑ 8.0 8.1 8.2 8.3 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  9. ↑ 9.0 9.1 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  10. ↑ 10.0 10.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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