recQ:Gene Product(s): Difference between revisions

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Added to the category for various RefGenome genes.
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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
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ATP-dependent DNA helicase<ref name='LIB:Riley_2006'/>, B3822<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, RecQ<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''ATP-dependent DNA helicase<ref name='LIB:Riley_2006'/>, B3822<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, RecQ<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK3816, JW5855, b3822''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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!|Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Experiment(s):EBI-889737<br />  
Experiment(s):EBI-889737<br />  
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Protein
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rpmB
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PMID:19402753
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LCMS(ID Probability):99.6
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Protein
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topA
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PMID:19402753
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LCMS(ID Probability):98.5 MALDI(Z-score):28.250265
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Protein
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ssb
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PMID:19402753
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LCMS(ID Probability):99.6 MALDI(Z-score):35.825787


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!|Compartment!!Description!!Evidence!!Source!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


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!align=left {{table heading style}} |Name
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46ab063f2c471"  class=" tableEdit Product_motif_table dataTable"   
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!|Type!!Residues!!Description!!Notes!!References
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View models at:
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P15043 Protein Model Portal]
* [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/genome3d/read?uniprot_id=P15043 PSI-PRED (P15043)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P15043 Genomes TO Protein (P15043)] (GTOP)
* [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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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/protein/162135918 GI:162135918]
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Escherichia coli str. K-12 substr. MG1655
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10833-MONOMER EcoCyc:EG10833-MONOMER]
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/protein/YP_026263.3 GeneID:948318]
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Escherichia coli str. K-12 substr. MG1655
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[[ASAP]]
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ASAP:ABE-0012483
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
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[http://www.uniprot.org/uniprot/P15043 UniProtKB/Swiss-Prot:P15043]
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Escherichia coli str. K-12 substr. MG1655
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[[EcoCyc]]
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EcoCyc:EG10833
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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EcoGene:EG10833
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
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[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
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[[uniprot:P15043|UniProt:P15043]]
[http://www.ncbi.nlm.nih.gov/gene?term=948318 GeneID:948318]
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Escherichia coli str. K-12 substr. MG1655
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[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
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[http://pfam.janelia.org/protein/P15043 Pfam:P15043]
RegulonDB:ECK120000824
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[EchoBASE]]
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[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=YP_026263 RefSeq:YP_026263]
EchoBASE:EB0826
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Latest revision as of 21:08, 17 February 2015

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

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

RecQ

Synonyms

ATP-dependent DNA helicase[1], B3822[2][1], RecQ[2][1] , ECK3816, JW5855, b3822

Product description

ATP-dependent DNA helicase[2][3]

DNA helicase involved in recombination, replication, repair; ATP-dependent; monomeric[4]

EC number (for enzymes)
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Notes

  • A mutant of the human homolog of RecQ, known as BLM, is responsible for Bloom syndrome. See BLM on GONUTS.

Function

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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:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010997

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:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002121

F

Seeded from EcoCyc (v14.0)

complete

GO:0046914

transition metal ion binding

PMID:2164680[5]

IDA: Inferred from Direct Assay

F

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011545

F

Seeded from EcoCyc (v14.0)

complete

GO:0016887

ATPase activity

PMID:2164680[5]

IDA: Inferred from Direct Assay

F

complete

GO:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0008094

DNA-dependent ATPase activity

PMID:2164680[5]

IDA: Inferred from Direct Assay

F

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010997

F

Seeded from EcoCyc (v14.0)

complete

GO:0004003

ATP-dependent DNA helicase activity

PMID:2164680[5]

IDA: Inferred from Direct Assay

F

complete

GO:0004003

ATP-dependent DNA helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006293

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

PMID:2164680[5]

IDA: Inferred from Direct Assay

C

complete

GO:0005515

protein binding

PMID:19150358[6]

IPI: Inferred from Physical Interaction

UniProtKB:P0AGE0

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

PMID:14665634[7]

IDA: Inferred from Direct Assay

F

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

PMID:15292213[8]

IMP: Inferred from Mutant Phenotype

F

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011545

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

PMID:15292213[8]

IPI: Inferred from Physical Interaction

F

Missing: with/from

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

GO:0017116

single-stranded DNA-dependent ATP-dependent DNA helicase activity

PMID:12805371[9]

IDA: Inferred from Direct Assay

F

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002121

C

Seeded from EcoCyc (v14.0)

complete

GO:0017117

single-stranded DNA-dependent ATP-dependent DNA helicase complex

PMID:12805371[9]

IDA: Inferred from Direct Assay

C

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018982

P

Seeded from EcoCyc (v14.0)

complete

GO:0006310

DNA recombination

PMID:7868608[10]

IMP: Inferred from Mutant Phenotype

P

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018982

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

PMID:7868608[10]

IGI: Inferred from Genetic Interaction

EcoliWiki:recB|EcoliWiki:recC|EcoliWiki:sbcB|EcoliWiki:sbcC

P

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

PMID:7868608[10]

IGI: Inferred from Genetic Interaction

EcoliWiki:recB|EcoliWiki:recC|EcoliWiki:sbcB|EcoliWiki:sbcC

P

complete

GO:0006281

DNA repair

PMID:7868608[10]

IGI: Inferred from Genetic Interaction

P

Seeded from EcoCyc (v14.0)

Missing: with/from

GO:0006310

DNA recombination

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004589

P

Seeded from EcoCyc (v14.0)

complete

GO:0006310

DNA recombination

PMID:9553043[11]

IDA: Inferred from Direct Assay

P

With RecA & SSB.

complete

GO:0005515

protein binding

PMID:19150358[6]

IPI: Inferred from Physical Interaction

UniProtKB:P0AGE0

F

SSB (Single-stranded DNA-binding protein)

complete

GO:0006310

DNA recombination

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006293

P

Seeded from EcoCyc (v14.0)

complete

GO:0006310

DNA recombination

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018329

P

Seeded from EcoCyc (v14.0)

complete

GO:0006310

DNA recombination

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0233

P

Seeded from EcoCyc (v14.0)

complete

GO:0006310

DNA recombination

PMID:9553043[11]

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0009432

SOS response

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006293

P

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:0030894

replisome

PMID:16385024[12]

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0043140

ATP-dependent 3'-5' DNA helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018982

F

Seeded from EcoCyc (v14.0)

complete

GO:0043590

bacterial nucleoid

PMID:16385024[12]

IDA: Inferred from Direct Assay

C

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

ssb

PMID:15690043[13]

Experiment(s):EBI-882208, EBI-885071, EBI-889737

Protein

aceE

PMID:15690043[13]

Experiment(s):EBI-882208

Protein

aceF

PMID:15690043[13]

Experiment(s):EBI-882208, EBI-889737

Protein

lpdA

PMID:15690043[13]

Experiment(s):EBI-882208, EBI-889737

Protein

topA

PMID:15690043[13]

Experiment(s):EBI-882208, EBI-888130

Protein

rpmB

PMID:15690043[13]

Experiment(s):EBI-889737

Protein

rpsN

PMID:15690043[13]

Experiment(s):EBI-889737

Protein

rpmB

PMID:19402753[14]

LCMS(ID Probability):99.6

Protein

topA

PMID:19402753[14]

LCMS(ID Probability):98.5 MALDI(Z-score):28.250265

Protein

ssb

PMID:19402753[14]

LCMS(ID Probability):99.6 MALDI(Z-score):35.825787

edit table


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


Notes

Structure and Physical Properties

[back to top]


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 

MAQAEVLNLE SGAKQVLQET FGYQQFRPGQ EEIIDTVLSG RDCLVVMPTG GGKSLCYQIP
ALLLNGLTVV VSPLISLMKD QVDQLQANGV AAACLNSTQT REQQLEVMTG CRTGQIRLLY
IAPERLMLDN FLEHLAHWNP VLLAVDEAHC ISQWGHDFRP EYAALGQLRQ RFPTLPFMAL
TATADDTTRQ DIVRLLGLND PLIQISSFDR PNIRYMLMEK FKPLDQLMRY VQEQRGKSGI
IYCNSRAKVE DTAARLQSKG ISAAAYHAGL ENNVRADVQE KFQRDDLQIV VATVAFGMGI
NKPNVRFVVH FDIPRNIESY YQETGRAGRD GLPAEAMLFY DPADMAWLRR CLEEKPQGQL
QDIERHKLNA MGAFAEAQTC RRLVLLNYFG EGRQEPCGNC DICLDPPKQY DGSTDAQIAL
STIGRVNQRF GMGYVVEVIR GANNQRIRDY GHDKLKVYGM GRDKSHEHWV SVIRQLIHLG
LVTQNIAQHS ALQLTEAARP VLRGESSLQL AVPRIVALKP KAMQKSFGGN YDRKLFAKLR
KLRKSIADES NVPPYVVFND ATLIEMAEQM PITASEMLSV NGVGMRKLER FGKPFMALIR
AHVDGDDEE
Length

609

Mol. Wt

68.364 kDa

pI

7.3 (calculated)

Extinction coefficient

48,820 - 50,195 (calc based on 18 Y, 4 W, and 11 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

Initiator Methionine

1

Removed

UniProt:P15043

Domain

27..192

PF00270 DEAD/DEAH box helicase

PMID:19920124[15]

Domain

254..331

PF00271 Helicase conserved C-terminal domain

PMID:19920124[15]

Domain

532..599

PF00570 HRDC domain

PMID:19920124[15]

Domain

411..514

PF09382 RQC domain

PMID:19920124[15]

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<motif_map/>

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

Structures

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

Models

View models at:

edit table

Structure figures

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


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:162135918

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948318

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012483

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P15043

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10833

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10833

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948318

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000824

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0826

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

[back to top]




References

[back to top]


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. ↑ 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 Umezu, K et al. (1990) Escherichia coli RecQ protein is a DNA helicase. Proc. Natl. Acad. Sci. U.S.A. 87 5363-7 PubMed
  6. ↑ 6.0 6.1 Shereda, RD et al. (2009) Identification of the SSB binding site on E. coli RecQ reveals a conserved surface for binding SSB's C terminus. J. Mol. Biol. 386 612-25 PubMed
  7. ↑ Dou, SX et al. (2004) The DNA binding properties of the Escherichia coli RecQ helicase. J. Biol. Chem. 279 6354-63 PubMed
  8. ↑ 8.0 8.1 Liu, JL et al. (2004) The zinc finger motif of Escherichia coli RecQ is implicated in both DNA binding and protein folding. J. Biol. Chem. 279 42794-802 PubMed
  9. ↑ 9.0 9.1 Xu, HQ et al. (2003) The Escherichia coli RecQ helicase functions as a monomer. J. Biol. Chem. 278 34925-33 PubMed
  10. ↑ 10.0 10.1 10.2 10.3 Mendonca, VM et al. (1995) DNA helicases in recombination and repair: construction of a delta uvrD delta helD delta recQ mutant deficient in recombination and repair. J. Bacteriol. 177 1326-35 PubMed
  11. ↑ 11.0 11.1 Harmon, FG & Kowalczykowski, SC (1998) RecQ helicase, in concert with RecA and SSB proteins, initiates and disrupts DNA recombination. Genes Dev. 12 1134-44 PubMed
  12. ↑ 12.0 12.1 Sanchez, H et al. (2006) Recruitment of Bacillus subtilis RecN to DNA double-strand breaks in the absence of DNA end processing. J. Bacteriol. 188 353-60 PubMed
  13. ↑ 13.0 13.1 13.2 13.3 13.4 13.5 13.6 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  14. ↑ 14.0 14.1 14.2 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  15. ↑ 15.0 15.1 15.2 15.3 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

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