srmB:On One Page

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

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Standard Name

srmB

Gene Synonym(s)

ECK2574, b2576, JW2560, rbaB, rhlA[1], rhlA

Product Desc.

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]

Product Synonyms(s)

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

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): srmB[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

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

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Notes

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SrmB binds RNaseE. Deletion mutant has slow growth phenotype at low temperature.[4]



Gene

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Nomenclature

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

Standard name

srmB

Mnemonic

Suppressor ribosomal mutant

Synonyms

ECK2574, b2576, JW2560, rbaB, rhlA[1], rhlA

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Notes

Location(s) and DNA Sequence

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<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

58.43 minutes 

MG1655: 2710918..2712252
<gbrowseImage> name=NC_000913:2710918..2712252 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2634389..2635723
<gbrowseImage> name=NC_012967:2634389..2635723 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2596723..2598057
<gbrowseImage> name=NC_012759:2596723..2598057 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2711552..2712886
<gbrowseImage> name=NC_007779:2711552..2712886 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2802683..2804017
<gbrowseImage> name=NC_010473:2802683..2804017 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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

Feature Type Strain Genomic Location Evidence Reference Notes
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Notes

Alleles and Phenotypes

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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

ΔsrmB (Keio:JW2560)

deletion

deletion

PMID:16738554

Shigen
CGSC10035[5]

ΔsrmB744::kan

PMID:16738554

CGSC:103020


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Notes

Genetic Interactions

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

Genetic Resources

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

Resource Resource Type Source Notes/Reference

JW2560

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACTGTAACGACTTTTTCCGA

Primer 2:CCtTCTTCTGTCGTTTGCGGTGG

4A12

Kohara Phage

Genobase

PMID:3038334

nadB51::Tn10

Linked marker

CAG18480 = CGSC7419[5]

est. P1 cotransduction: 96% [6]

pheA18::Tn10

Linked marker

CAG12158 = CGSC7421[5]

est. P1 cotransduction: 36% [6]

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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

EcoCyc

EcoCyc:EG10975

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10975

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000964

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947055

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0968

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008478

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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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

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

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0005515

protein binding

PMID:10361280

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

Experiment(s):EBI-889906

Protein

rpsC

PMID:15690043

Experiment(s):EBI-889906

Protein

tufA

PMID:15690043

Experiment(s):EBI-889906

Protein

ycbY

PMID:15690043

Experiment(s):EBI-889906

Protein

rplA

PMID:15690043

Experiment(s):EBI-889906

Protein

rplB

PMID:15690043

Experiment(s):EBI-889906

Protein

rplV

PMID:15690043

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

Protein

rplX

PMID:15690043

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

Protein

rplL

PMID:15690043

Experiment(s):EBI-894853

Protein

rplW

PMID:15690043

Experiment(s):EBI-894853

Protein

dnaB

PMID:16606699

Experiment(s):EBI-1143343

Protein

rpsI

PMID:16606699

Experiment(s):EBI-1143343

Protein

rplB

PMID:16606699

Experiment(s):EBI-1143343

Protein

tnaA

PMID:19402753

MALDI(Z-score):19.674947

Protein

tufB

PMID:19402753

MALDI(Z-score):18.610686

Protein

dnaJ

PMID:19402753

MALDI(Z-score):32.128737

Protein

rplW

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplA

PMID:19402753

MALDI(Z-score):23.226981

Protein

rplX

PMID:19402753

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

Protein

rplB

PMID:19402753

MALDI(Z-score):35.322013

Protein

rplD

PMID:19402753

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

Domain

266..343

PF00271 Helicase conserved C-terminal domain

PMID:19920124

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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=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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Expression

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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

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See Help:Cellular levels

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

Protein

E. coli K-12 MC4100

1.57E+02

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

E. coli K-12 MG1655

2324

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

559

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

842

molecules/cell/generation

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

Ribosome Profiling

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation

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<protect>

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

Transcription unit(s)

srmB

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Figure courtesy of RegulonDB

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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

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<protect><gbrowseImage> name=NC_000913:2710898..2710938 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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

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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

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

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b2576 (EcoliWiki Page)

NCBI GEO profiles for srmB

microarray

GenExpDB:b2576 (EcoliWiki Page)

Summary of data for srmB from multiple microarray studies

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

Resource Name Resource Type Description Source Notes

GFP Fusion

Intergenic region (2710816..2710949) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ08; Well:B2[7]

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Notes

Accessions Related to srmB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10975

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0968

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2576

EcoGene

EcoGene:EG10975

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000964

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008478

Escherichia coli str. K-12 substr. MG1655

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Notes

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Evolution

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Homologs in Other Organisms

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

Organism Homologs (Statistics) Comments

Anopheles gambiae

  • ENSANGP00000003952 (score: 1.000; bootstrap: 86%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00031298 (score: 1.000; bootstrap: 72%)
  • WBGene00036557 (score: 0.085)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00008119 (score: 1.000; bootstrap: 53%)
  • WBGene00018776 (score: 0.093)
  • WBGene00010260 (score: 0.054)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0021995 (score: 1.000; bootstrap: 83%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA15282-PA (score: 1.000; bootstrap: 90%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YLL008W (score: 1.000; bootstrap: 74%)

From Inparanoid:20070104

Shigella flexneri

SRMB

From SHIGELLACYC

E. coli O157

SRMB

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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

Database Accession Notes

Pfam (EcoliWiki Page)

PF00271 Helicase conserved C-terminal domain

Pfam (EcoliWiki Page)

PF00270 DEAD/DEAH box helicase

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Panther (EcoliWiki Page)

PTHR24031:SF52

EcoCyc

EcoCyc:EG10975

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10975

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

ASAP

ASAP:ABE-0008478

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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 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 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 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 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).
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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