prfB: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

prfB

Gene Synonym(s)

ECK2886, b2891, JW5847, supK[1], supK

Product Desc.

peptide chain release factor RF2[2][3]

Peptide chain release factor 2, RF-2; translation termination factor recognizes UGA and UAA.[4]

Product Synonyms(s)

peptide chain release factor RF-2[1], B2891[2][1], SupK[2][1], PrfB[2][1] , ECK2886, JW5847, supK, b2891

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): dsbC-recJ-prfB[2], prfB-lysS[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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The ribosome changes reading frame after codon 25. The very poor growth of rluD mutants can be suppressed by a point mutation in prfB and a role in translation termination for the 23S rRNA helix 69 pseudouridines has been demonstrated (Ejby, 2007).[4]

prfB in E. coli K-12 has a variation relative other bacteria including E. coli B


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

prfB

Mnemonic

Protein release factor

Synonyms

ECK2886, b2891, JW5847, supK[1], supK

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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

65.38 minutes 

MG1655: 3034304..3033206
<gbrowseImage> name=NC_000913:3033206..3034304 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2921959..2920937
<gbrowseImage> name=NC_012967:2920937..2921959 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2920354..2921452
<gbrowseImage> name=NC_012759:2920354..2921452 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3034938..3033840
<gbrowseImage> name=NC_007779:3033840..3034938 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3128098..3127076
<gbrowseImage> name=NC_010473:3127076..3128098 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

3033206

Edman degradation

PMID:3889910


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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

prfB(del) (Keio:JW5847)

deletion

deletion

PMID:16738554

Shigen

prfBT246A

T246A

(in strain: BL21 and MRE-600; increased termination efficiency)

Strain variation; seeded from UniProt:P07012

prfB11(UGAs)

UGA (opal) suppressor

CGSC:81433

prfB neg40

Resistant to

Negamycin resistance

PMID:7028032

Parental with resistance: RIB40

Experimental strain: RIB185-1


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Notes

The Keio collection[5] lists a deletion of prfB. The insertion in this strain is a duplication of the prfB region.[6]


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

JW5847

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTTTGAAATTAATCCGGTAAA

Primer 2:CCTAACCCTGCTTTCAAACTTGC

5B4

Kohara Phage

Genobase

PMID:3038334

22H4

Kohara Phage

Genobase

PMID:3038334

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[7]

est. P1 cotransduction: % [8]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[7]

est. P1 cotransduction: 8% [8]
Synonyms:zgd-210::Tn10, zgf-210::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:EG10762

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10762

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000753

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947369

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0755

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009488

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

PrfB

Synonyms

peptide chain release factor RF-2[1], B2891[2][1], SupK[2][1], PrfB[2][1] , ECK2886, JW5847, supK, b2891

Product description

peptide chain release factor RF2[2][3]

Peptide chain release factor 2, RF-2; translation termination factor recognizes UGA and UAA.[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:0003747

translation release factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000352

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00094

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004374

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005139

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020853

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:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0648

P

Seeded from EcoCyc (v14.0)

complete

GO:0006415

translational termination

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00094

P

Seeded from EcoCyc (v14.0)

complete

GO:0006415

translational termination

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000352

P

Seeded from EcoCyc (v14.0)

complete

GO:0006415

translational termination

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004374

P

Seeded from EcoCyc (v14.0)

complete

GO:0006415

translational termination

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005139

P

Seeded from EcoCyc (v14.0)

complete

GO:0006415

translational termination

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020853

P

Seeded from EcoCyc (v14.0)

complete

GO:0016149

translation release factor activity, codon specific

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00094

F

Seeded from EcoCyc (v14.0)

complete

GO:0016149

translation release factor activity, codon specific

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004374

F

Seeded from EcoCyc (v14.0)

complete

GO:0016149

translation release factor activity, codon specific

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005139

F

Seeded from EcoCyc (v14.0)

complete

GO:0016149

translation release factor activity, codon specific

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020853

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

ynfE

PMID:15690043

Experiment(s):EBI-889160

Protein

yeiT

PMID:15690043

Experiment(s):EBI-889160

Protein

ccmB

PMID:15690043

Experiment(s):EBI-889160

Protein

hupA

PMID:15690043

Experiment(s):EBI-889160

Protein

hupB

PMID:15690043

Experiment(s):EBI-889160

Protein

parE

PMID:15690043

Experiment(s):EBI-889160

Protein

polA

PMID:15690043

Experiment(s):EBI-889160

Protein

wecA

PMID:15690043

Experiment(s):EBI-889160

Protein

rplL

PMID:15690043

Experiment(s):EBI-889160

Protein

rplV

PMID:15690043

Experiment(s):EBI-889160

Protein

rpoA

PMID:15690043

Experiment(s):EBI-889160

Protein

rpsB

PMID:15690043

Experiment(s):EBI-889160

Protein

rpsE

PMID:15690043

Experiment(s):EBI-889160

Protein

ulaA

PMID:15690043

Experiment(s):EBI-889160

Protein

nagK

PMID:15690043

Experiment(s):EBI-889160

Protein

gcp

PMID:15690043

Experiment(s):EBI-889160

Protein

yjcF

PMID:15690043

Experiment(s):EBI-889160

Protein

rpsJ

PMID:15690043

Experiment(s):EBI-889160

Protein

parE

PMID:19402753

LCMS(ID Probability):99.0

Protein

yeiT

PMID:19402753

LCMS(ID Probability):99.6

Protein

ynfE

PMID:19402753

LCMS(ID Probability):99.0

Protein

nagK

PMID:19402753

LCMS(ID Probability):99.0

Protein

ygjD

PMID:19402753

LCMS(ID Probability):99.6

Protein

yjcF

PMID:19402753

LCMS(ID Probability):99.0

Protein

rfe

PMID:19402753

LCMS(ID Probability):99.0

Protein

ulaA

PMID:19402753

LCMS(ID Probability):99.0

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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 

MFEINPVNNR IQDLTERSDV LRGYLDYDAK KERLEEVNAE LEQPDVWNEP ERAQALGKER
SSLEAVVDTL DQMKQGLEDV SGLLELAVEA DDEETFNEAV AELDALEEKL AQLEFRRMFS
GEYDSADCYL DIQAGSGGTE AQDWASMLER MYLRWAESRG FKTEIIEESE GEVAGIKSVT
IKISGDYAYG WLRTETGVHR LVRKSPFDSG GRRHTSFSSA FVYPEVDDDI DIEINPADLR
IDVYRTSGAG GQHVNRTESA VRITHIPTGI VTQCQNDRSQ HKNKDQAMKQ MKAKLYELEM
QKKNAEKQAM EDNKSDIGWG SQIRSYVLDD SRIKDLRTGV ETRNTQAVLD GSLDQFIEAS
LKAGL
Length

365

Mol. Wt

41.25 kDa

pI

4.5 (calculated)

Extinction coefficient

43,890 - 44,140 (calc based on 11 Y, 5 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

85..195

PF03462 PCRF domain

PMID:19920124

Domain

225..337

PF00472 RF-1 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=prfB 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:16130793

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947369

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009488

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P07012

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10762

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10762

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947369

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000753

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0755

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

1.78E+03

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

10031

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

1732

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

5473

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)

dsbC-recJ-prfB

prfB-lysS

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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_000913:3034284..3034324 source=MG1655 flip=1 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:b2891 (EcoliWiki Page)

NCBI GEO profiles for prfB

microarray

GenExpDB:b2891 (EcoliWiki Page)

Summary of data for prfB 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 (3034233..3034467) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ09; Well:A8[9]

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Notes

Accessions Related to prfB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10762

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0755

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2891

EcoGene

EcoGene:EG10762

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000753

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009488

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

Apis mellifera

  • ENSAPMP00000031336 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT1G56350 (score: 1.000; bootstrap: 88%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00039181 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00020993 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0188136 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000051246 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

E. coli O157

PRFB

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)

PF03462 PCRF domain

Panther (EcoliWiki Page)

PTHR11075:SF6

Superfamily (EcoliWiki Page)

SUPERFAMILY:75620

Pfam (EcoliWiki Page)

PF00472 RF-1 domain

EcoCyc

EcoCyc:EG10762

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10762

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000753

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0755

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009488

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 2.9 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. ↑ Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  6. ↑ Yamamoto, N et al. (2009) Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol. Syst. Biol. 5 335 PubMed
  7. ↑ 7.0 7.1 CGSC: The Coli Genetics Stock Center
  8. ↑ 8.0 8.1 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).
  9. ↑ 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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