smpB: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

smpB

Gene Synonym(s)

ECK2616, b2620, JW2601, smqB[1], smqB

Product Desc.

small protein B[2][3]

tmRNA RNA-binding protein; required for peptide-tagging trans-translation and association of tmRNA(SsrA) with ribosomes[4]

Product Synonyms(s)

trans-translation protein[1], B2620[2][1], SmqB[2][1], SmpB[2][1] , ECK2616, JW2601, smqB, b2620

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): smpB[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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otherPDB (A. aeolicus): 1P6V; 1K8H. otherPDB (T. thermophilus): 2OB7; 1J1H.[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

smpB

Mnemonic

Small protein

Synonyms

ECK2616, b2620, JW2601, smqB[1], smqB

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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

59.33 minutes 

MG1655: 2752918..2753400
<gbrowseImage> name=NC_000913:2752918..2753400 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2676191..2676673
<gbrowseImage> name=NC_012967:2676191..2676673 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2638730..2639212
<gbrowseImage> name=NC_012759:2638730..2639212 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2753552..2754034
<gbrowseImage> name=NC_007779:2753552..2754034 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2844683..2845165
<gbrowseImage> name=NC_010473:2844683..2845165 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

Coding Start (SO:0000323)

MG1655

2752921

Edman degradation

PMID:2045357
PMID:10393194


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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

ΔsmpB (Keio:JW2601)

deletion

deletion

PMID:16738554

Shigen
CGSC10058[5]

smpB::Tn5KAN-I-SceI (FB20867)

Insertion at nt 256 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20867

does not contain pKD46

smpB::Tn5KAN-I-SceI (FB20868)

Insertion at nt 256 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20868

contains pKD46

ΔsmpB776::kan

PMID:16738554

CGSC:102976


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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

JW2601

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACGAAGAAAAAAGCACATAA

Primer 2:CCACGGTGGGCGTTTTTCATGAT

E8F2

Kohara Phage

Genobase

PMID:3038334

22D7

Kohara Phage

Genobase

PMID:3038334

24G1

Kohara Phage

Genobase

PMID:3038334

pheA18::Tn10

Linked marker

CAG12158 = CGSC7421[5]

est. P1 cotransduction: 58% [6]

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[5]

est. P1 cotransduction: 1% [6]
Synonyms:zfh-3131::Tn10, zfi-3131::Tn10

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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:EG11782

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11782

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001716

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947296

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1730

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008622

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

SmpB

Synonyms

trans-translation protein[1], B2620[2][1], SmqB[2][1], SmpB[2][1] , ECK2616, JW2601, smqB, b2620

Product description

small protein B[2][3]

tmRNA RNA-binding protein; required for peptide-tagging trans-translation and association of tmRNA(SsrA) with ribosomes[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:0003723

RNA binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00023

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000037

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:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00023

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000037

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

aidB

PMID:15690043

Experiment(s):EBI-882920

Protein

clpA

PMID:15690043

Experiment(s):EBI-882920

Protein

infB

PMID:15690043

Experiment(s):EBI-882920

Protein

malP

PMID:15690043

Experiment(s):EBI-882920

Protein

parC

PMID:15690043

Experiment(s):EBI-882920

Protein

rplF

PMID:15690043

Experiment(s):EBI-882920, EBI-890426

Protein

rpsA

PMID:15690043

Experiment(s):EBI-882920, EBI-890426

Protein

rpsB

PMID:15690043

Experiment(s):EBI-882920, EBI-890426

Protein

rpsC

PMID:15690043

Experiment(s):EBI-882920

Protein

secA

PMID:15690043

Experiment(s):EBI-882920

Protein

selB

PMID:15690043

Experiment(s):EBI-882920

Protein

ycbB

PMID:15690043

Experiment(s):EBI-882920

Protein

yfiF

PMID:15690043

Experiment(s):EBI-882920

Protein

gyrA

PMID:15690043

Experiment(s):EBI-890426

Protein

gyrB

PMID:15690043

Experiment(s):EBI-890426

Protein

skp

PMID:15690043

Experiment(s):EBI-890426

Protein

hupA

PMID:15690043

Experiment(s):EBI-890426

Protein

hupB

PMID:15690043

Experiment(s):EBI-890426

Protein

rplM

PMID:15690043

Experiment(s):EBI-890426

Protein

rplX

PMID:15690043

Experiment(s):EBI-890426

Protein

rpmB

PMID:15690043

Experiment(s):EBI-890426

Protein

rpsE

PMID:15690043

Experiment(s):EBI-890426

Protein

rpsN

PMID:15690043

Experiment(s):EBI-890426

Protein

yeeX

PMID:15690043

Experiment(s):EBI-890426

Protein

vsr

PMID:16606699

Experiment(s):EBI-1143521

Protein

yibK

PMID:16606699

Experiment(s):EBI-1143521

Protein

rplA

PMID:16606699

Experiment(s):EBI-1143521

Protein

ycgE

PMID:16606699

Experiment(s):EBI-1143521

Protein

ycfJ

PMID:16606699

Experiment(s):EBI-1143521

Protein

secA

PMID:19402753

MALDI(Z-score):18.851547

Protein

aidB

PMID:19402753

LCMS(ID Probability):98.3 MALDI(Z-score):27.388524

Protein

rplF

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):35.816231

Protein

skp

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):26.098127

Protein

gyrA

PMID:19402753

LCMS(ID Probability):99.6

Protein

parC

PMID:19402753

MALDI(Z-score):37.105392

Protein

malP

PMID:19402753

MALDI(Z-score):28.886498

Protein

clpA

PMID:19402753

MALDI(Z-score):25.712309

Protein

hupB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753

LCMS(ID Probability):99.6

Protein

gyrB

PMID:19402753

LCMS(ID Probability):99.6

Protein

hupA

PMID:19402753

LCMS(ID Probability):99.6

Protein

yfiF

PMID:19402753

MALDI(Z-score):36.128347

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6

Protein

yeeX

PMID:19402753

LCMS(ID Probability):99.6

Protein

ycbB

PMID:19402753

MALDI(Z-score):24.925478

RNA

SsrA RNA


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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 

MTKKKAHKPG SATIALNKRA RHEYFIEEEF EAGLALQGWE VKSLRAGKAN ISDSYVLLRD
GEAFLFGANI TPMAVASTHV VCDPTRTRKL LLNQRELDSL YGRVNREGYT VVALSLYWKN
AWCKVKIGVA KGKKQHDKRS DIKEREWQVD KARIMKNAHR
Length

160

Mol. Wt

18.269 kDa

pI

10.4 (calculated)

Extinction coefficient

29,450 - 29,700 (calc based on 5 Y, 4 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

Initiator Methionine

1

Removed

UniProt:P0A832

Domain

12..80

PF01668 SmpB protein

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=smpB 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:16130539

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947296

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008622

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A832

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11782

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11782

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947296

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001716

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1730

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

7.63E+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

Ecoli K-12

14.608+/-0.098

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.079875519

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

4934

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

1537

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

2942

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)

smpB

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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_000913:2752898..2752938 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:b2620 (EcoliWiki Page)

NCBI GEO profiles for smpB

microarray

GenExpDB:b2620 (EcoliWiki Page)

Summary of data for smpB 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 (2752705..2752941) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ19; Well:D10[7]

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Notes

Accessions Related to smpB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11782

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1730

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2620

EcoGene

EcoGene:EG11782

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001716

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008622

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

Xenopus tropicalis

  • ENSXETP00000015164 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

SMPB

From SHIGELLACYC

E. coli O157

SMPB

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

Superfamily (EcoliWiki Page)

SUPERFAMILY:74982

Pfam (EcoliWiki Page)

PF01668 SmpB protein

PFAM (EcoliWiki Page)

PFAM:PF01668

EcoCyc

EcoCyc:EG11782

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11782

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001716

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1730

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008622

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 1.6 1.7 1.8 1.9 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 2.5 2.6 2.7 2.8 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. ↑ 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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