recD:On One Page

From EcoliWiki
Jump to: navigation, search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

<protect>

Standard Name

recD

Gene Synonym(s)

ECK2815, b2819, JW2787, hopE[1], hopE

Product Desc.

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]

Product Synonyms(s)

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

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): recD[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]


RecBCD is a bipolar helicase.[4]



Gene

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

recD

Mnemonic

Recombination

Synonyms

ECK2815, b2819, JW2787, hopE[1], hopE

edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]


<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

63.55 minutes 

MG1655: 2950483..2948657
<gbrowseImage> name=NC_000913:2948657..2950483 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2847080..2845254
<gbrowseImage> name=NC_012967:2845254..2847080 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2835805..2837631
<gbrowseImage> name=NC_012759:2835805..2837631 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2951117..2949291
<gbrowseImage> name=NC_007779:2949291..2951117 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3044353..3042527
<gbrowseImage> name=NC_010473:3042527..3044353 source=DH10B preset=GeneLocation </gbrowseImage>

edit table

</protect>

Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

2948657

Edman degradation

PMID:1618858


edit table

<protect></protect>

Notes

Alleles and Phenotypes

[back to top]


See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔrecD (Keio:JW2787)

deletion

deletion

PMID:16738554

Shigen

recD1901::Tn10

Insertion at 2,948,961 bp in MG1655 (NC_000913)

adapted from Nichols et al.[5]

CAG12135 = CGSC7429[6]

Synonyms:

recD1014(Nuc-)

ds DNA exonuclease-minus

CGSC:4990

recD1009(Nuc-)

ds DNA exonuclease-minus

CGSC:10471

recD1901::Tn10

PMID:2540407

CGSC:40104

recD1903::Tn10d(Tet)

PMID:11532156

CGSC:71972


edit table

<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table

</protect>

Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW2787

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAATTGCAAAAGCAATTACT

Primer 2:CCTTCCCGTGAACTAAACAACGC

10B6

Kohara Phage

Genobase

PMID:3038334

3G11

Kohara Phage

Genobase

PMID:3038334

fucP3072::Tn10

Linked marker

CAG12079 = CGSC7427[6]

est. P1 cotransduction: 56% [5]
Synonyms:fuc-3072::Tn10

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[6]

est. P1 cotransduction: % [5]
Synonyms:zgd-210::Tn10, zgf-210::Tn10

edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG10826

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10826

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000817

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947287

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0819

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009247

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



Product(s)

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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)
edit table

<protect></protect>

Notes

Function

[back to top]


<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

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

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

IMP: Inferred from Mutant Phenotype

F

complete

GO:0005515

protein binding

PMID:1618858

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0009338

exodeoxyribonuclease V complex

PMID:1618858

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

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

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

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

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

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 recBCD

could be indirect

Protein

aceE

PMID:15690043

Experiment(s):EBI-882133

Protein

lpdA

PMID:15690043

Experiment(s):EBI-882133

Protein

groL

PMID:15690043

Experiment(s):EBI-882133

Protein

recC

PMID:15690043

Experiment(s):EBI-882133

Protein

groL

PMID:16606699

Experiment(s):EBI-1144053

Protein

fucI

PMID:16606699

Experiment(s):EBI-1144053

Protein

htpG

PMID:16606699

Experiment(s):EBI-1144053

Protein

dnaJ

PMID:16606699

Experiment(s):EBI-1144053

Protein

groS

PMID:19402753

MALDI(Z-score):24.578913

Protein

recC

PMID:19402753

MALDI(Z-score):18.813516

edit table

</protect>

Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
edit table

<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<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)

edit table


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

Domain

517..581

PF01443 Viral (Superfamily 1) RNA helicase

PMID:19920124

edit table

<motif_map/>

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:

edit table
</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

edit table

<protect></protect>

Notes

Links

[back to top]




Expression

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

[back to top]


See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

Ecoli K-12

4.761+/-0.033

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.018346112

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

113

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

46

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

47

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

edit table

Notes

Transcription and Transcriptional Regulation

[back to top]


<protect>

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

Transcription unit(s)

recD

edit table
Figure courtesy of RegulonDB

</protect>

Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

[back to top]


<protect><gbrowseImage> name=NC_000913:2950463..2950503 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

</protect>

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

[back to top]


<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
edit table


Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b2819 (EcoliWiki Page)

NCBI GEO profiles for recD

microarray

GenExpDB:b2819 (EcoliWiki Page)

Summary of data for recD from multiple microarray studies

edit table


Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes
edit table

<protect></protect>

Notes

Accessions Related to recD Expression

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG10826

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0819

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2819

EcoGene

EcoGene:EG10826

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000817

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009247

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



Evolution

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]


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

Organism Homologs (Statistics) Comments

Apis mellifera

  • ENSAPMP00000019670 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:2152895 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

RECD

From SHIGELLACYC

E. coli O157

RECD

From ECOO157CYC

edit table

<protect></protect>

Notes

Families

[back to top]


<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database Accession Notes

Pfam (EcoliWiki Page)

PF05127 Putative ATPase (DUF699)

Pfam (EcoliWiki Page)

PF01443 Viral (Superfamily 1) RNA helicase


edit table

</protect> <protect></protect>

Notes

Links

[back to top]



References

[back to top]


See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 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 3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 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 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
  6. ↑ 6.0 6.1 6.2 CGSC: The Coli Genetics Stock Center

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=recD:On_One_Page&oldid=221214"