srmB: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

SrmB

Synonyms

ATP-dependent RNA helicase[1], B2576[2][1], RhlA[2][1], RbaB[2][1], SrmB[2][1] , ECK2574, JW2560, rbaB, rhlA, b2576

Product description

SrmB, DEAD-box RNA helicase[2][3]

Putative ATP-dependent RNA helicase; suppresses 50S ribosome assembly defect of rplX(ts); required for effiicient ribosomal 50S subunit assembly; stabilizes exposed mRNA, possibly by protecting or destabilizing secondary structure of RNase E sites[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:0000027

ribosomal large subunit assembly

PMID:2461520[5]

IGI: Inferred from Genetic Interaction

P

Seeded from EcoCyc (v14.0)

Missing: with/from

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:IPR000629

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:IPR011545

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0694

F

Seeded from EcoCyc (v14.0)

complete

GO:0004004

ATP-dependent RNA helicase activity

PMID:15196029[6]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0005515

protein binding

PMID:10361280[7]

IPI: Inferred from Physical Interaction

UniProtKB:P0ABF1

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000629

F

Seeded from EcoCyc (v14.0)

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: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

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

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

rpsB

PMID:15690043[8]

Experiment(s):EBI-889906

Protein

rpsC

PMID:15690043[8]

Experiment(s):EBI-889906

Protein

tufA

PMID:15690043[8]

Experiment(s):EBI-889906

Protein

ycbY

PMID:15690043[8]

Experiment(s):EBI-889906

Protein

rplA

PMID:15690043[8]

Experiment(s):EBI-889906

Protein

rplB

PMID:15690043[8]

Experiment(s):EBI-889906

Protein

rplV

PMID:15690043[8]

Experiment(s):EBI-889906, EBI-894853

Protein

rplX

PMID:15690043[8]

Experiment(s):EBI-889906, EBI-894853

Protein

rplL

PMID:15690043[8]

Experiment(s):EBI-894853

Protein

rplW

PMID:15690043[8]

Experiment(s):EBI-894853

Protein

dnaB

PMID:16606699[9]

Experiment(s):EBI-1143343

Protein

rpsI

PMID:16606699[9]

Experiment(s):EBI-1143343

Protein

rplB

PMID:16606699[9]

Experiment(s):EBI-1143343

Protein

tnaA

PMID:19402753[10]

MALDI(Z-score):19.674947

Protein

tufB

PMID:19402753[10]

MALDI(Z-score):18.610686

Protein

dnaJ

PMID:19402753[10]

MALDI(Z-score):32.128737

Protein

rplW

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

rplA

PMID:19402753[10]

MALDI(Z-score):23.226981

Protein

rplX

PMID:19402753[10]

LCMS(ID Probability):99.6 MALDI(Z-score):11.337805

Protein

rplB

PMID:19402753[10]

MALDI(Z-score):35.322013

Protein

rplD

PMID:19402753[10]

LCMS(ID Probability):99.0 MALDI(Z-score):23.942796

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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

cytoplasm

From EcoCyc[3]


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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 

MTVTTFSELE LDESLLEALQ DKGFTRPTAI QAAAIPPALD GRDVLGSAPT GTGKTAAYLL
PALQHLLDFP RKKSGPPRIL ILTPTRELAM QVSDHARELA KHTHLDIATI TGGVAYMNHA
EVFSENQDIV VATTGRLLQY IKEENFDCRA VETLILDEAD RMLDMGFAQD IEHIAGETRW
RKQTLLFSAT LEGDAIQDFA ERLLEDPVEV SANPSTRERK KIHQWYYRAD DLEHKTALLV
HLLKQPEATR SIVFVRKRER VHELANWLRE AGINNCYLEG EMVQGKRNEA IKRLTEGRVN
VLVATDVAAR GIDIPDVSHV FNFDMPRSGD TYLHRIGRTA RAGRKGTAIS LVEAHDHLLL
GKVGRYIEEP IKARVIDELR PKTRAPSEKQ TGKPSKKVLA KRAEKKKAKE KEKPRVKKRH
RDTKNIGKRR KPSGTGVPPQ TTEE
Length

444

Mol. Wt

49.915 kDa

pI

9.6 (calculated)

Extinction coefficient

28,420 - 28,670 (calc based on 8 Y, 3 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

28..199

PF00270 DEAD/DEAH box helicase

PMID:19920124[11]

Domain

266..343

PF00271 Helicase conserved C-terminal domain

PMID:19920124[11]

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

Structures

<beststructure> gene=srmB 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:16130501

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947055

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008478

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P21507

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10975

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10975

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947055

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000964

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0968

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. ↑ Nishi, K et al. (1988) An eIF-4A-like protein is a suppressor of an Escherichia coli mutant defective in 50S ribosomal subunit assembly. Nature 336 496-8 PubMed
  6. ↑ Bizebard, T et al. (2004) Studies on three E. coli DEAD-box helicases point to an unwinding mechanism different from that of model DNA helicases. Biochemistry 43 7857-66 PubMed
  7. ↑ Raynal, LC & Carpousis, AJ (1999) Poly(A) polymerase I of Escherichia coli: characterization of the catalytic domain, an RNA binding site and regions for the interaction with proteins involved in mRNA degradation. Mol. Microbiol. 32 765-75 PubMed
  8. ↑ 8.0 8.1 8.2 8.3 8.4 8.5 8.6 8.7 8.8 8.9 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  9. ↑ 9.0 9.1 9.2 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  10. ↑ 10.0 10.1 10.2 10.3 10.4 10.5 10.6 10.7 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  11. ↑ 11.0 11.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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