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rpoZ:On One Page

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See Help:Quickview for help with entering information in the Quickview table.

Standard Name

rpoZ

Gene Synonym(s)

ECK3639, b3649, JW3624, spoS[1]

Product Desc.

RNA polymerase, ω subunit[2][3]

RNA polymerase subunit, omega subunit; assembly factor; chaperone-like function stabilizes RNAP[4]

Product Synonyms(s)

RNA polymerase, omega subunit[1], B3649[2][1], SpoS[2][1], RpoZ[2][1]

Function from GO
Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rpoZ-spoT-trmH-recG[2], rpoZ-spoTU-recG

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(rpoZ)    Textpresso(rpoZ)

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Notes

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Stimulates ppGpp responsiveness of RNAP in vitro. Binds TrxA (Kumar, 2004).[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

rpoZ

Mnemonic

RNA polymerase

Synonyms

ECK3639, b3649, JW3624, spoS[1]

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

82.34 minutes 

MG1655: 3820129..3820404
gbrowse_img.php?coord=3820129..3820404&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 3760463..3760738
gbrowse_img.php?coord=3760463..3760738&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 3818309..3818034
gbrowse_img.php?coord=3818034..3818309&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 3917707..3917982
gbrowse_img.php?coord=3917707..3917982&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 3708456..3708731
gbrowse_img.php?coord=3708456..3708731&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

ΔrpoZ (Keio:JW3624)

deletion

deletion

PMID:16738554

Shigen
CGSC10664[5]

ΔrpoZ754::kan

PMID:16738554

CGSC:102796


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Notes

Genetic Resources

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

ResourceResource TypeSourceNotes/Reference

JW3624

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCACGCGTAACTGTTCAGGA

Primer 2:CCACGACGACCTTCAGCAATAGC

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[5]

est. P1 cotransduction: % [6]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[5]

est. P1 cotransduction: 77% [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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10899

EchoBASE (EcoliWiki Page)

EchoBASE:EB0892

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3649

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4474

EcoGene (EcoliWiki Page)

EcoGene:EG10899

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:RPOZ

CGSC (EcoliWiki Page)

CGSC:28445

ASAP (EcoliWikiPage)

ASAP:ABE-0011933


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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

RpoZ

Synonyms

RNA polymerase, omega subunit[1], B3649[2][1], SpoS[2][1], RpoZ[2][1]

Product description

RNA polymerase, ω subunit[2][3]

RNA polymerase subunit, omega subunit; assembly factor; chaperone-like function stabilizes RNAP[4]

EC number (for enzymes)
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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0016779

nucleotidyltransferase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0548

F

Seeded from EcoCyc [7]

complete

GO:0016740

transferase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

Seeded from EcoCyc [7]

complete

GO:0006351

transcription, DNA-dependent

GO_REF:0000002
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR006110
HAMAP:MF_00366

P

Seeded from EcoCyc 12.5 [8]

complete

GO:0006350

transcription

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR003716
SP_KW:KW-0804

P

Seeded from EcoCyc [7]

complete

GO:0003899

DNA-directed RNA polymerase activity

GO_REF:0000002
GO_REF:0000002
GO_REF:0000003
GO_REF:0000004
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR003716
InterPro:IPR006110
EC:2.7.7.6
SP_KW:KW-0240
HAMAP:MF_00366

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0003677

DNA binding

GO_REF:0000002
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR006110
HAMAP:MF_00366

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0005737

cytoplasm

C

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0006457

protein folding

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0006461

protein complex assembly

P

Seeded from EcoCyc 11.1[3].

required fields missing

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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 TypePartnerNotesReferencesEvidence

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1146407

Protein

rpoB

PMID:16606699

Experiment(s):EBI-1146407

Protein

rhsA

PMID:16606699

Experiment(s):EBI-1146407

Protein

nusA

PMID:15690043

Experiment(s):EBI-879161, EBI-893117

Protein

nusG

PMID:15690043

Experiment(s):EBI-879161, EBI-882858

Protein

rplB

PMID:15690043

Experiment(s):EBI-879161

Protein

dnaK

PMID:15690043

Experiment(s):EBI-879161

Protein

rpoA

PMID:15690043

Experiment(s):EBI-879161, EBI-879354, EBI-883271

Protein

rpoB

PMID:15690043

Experiment(s):EBI-879161, EBI-879304, EBI-882858, EBI-883170

Protein

rpoC

PMID:15690043

Experiment(s):EBI-879161, EBI-879261, EBI-882858, EBI-883046

Protein

rpsB

PMID:15690043

Experiment(s):EBI-879161

Protein

rpsG

PMID:15690043

Experiment(s):EBI-879161

Protein

rpsJ

PMID:15690043

Experiment(s):EBI-879161

Protein

rpsM

PMID:15690043

Experiment(s):EBI-879161

Protein

spoT

PMID:15690043

Experiment(s):EBI-879161

Protein

tig

PMID:15690043

Experiment(s):EBI-879161

Protein

rapA

PMID:15690043

Experiment(s):EBI-879161

Protein

rplL

PMID:15690043

Experiment(s):EBI-882858

Protein

rplW

PMID:15690043

Experiment(s):EBI-882858

Protein

rpsT

PMID:15690043

Experiment(s):EBI-882858

Protein

thiG

PMID:15690043

Experiment(s):EBI-882858

Protein

ygjI

PMID:15690043

Experiment(s):EBI-882858

Protein

ykgC

PMID:15690043

Experiment(s):EBI-882858

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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

CompartmentDescriptionEvidenceSourceNotes
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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Sequence

at EcoCyc 

MARVTVQDAV EKIGNRFDLV LVAARRARQM QVGGKDPLVP EENDKTTVIA LREIEEGLIN
NQILDVRERQ EQQEQEAAEL QAVTAIAEGR R
Length

91

Mol. Wt

10.235 kDa

pI

4.7 (calculated)

Extinction coefficient

0 (calc based on Y, W, and 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.

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

Structures
Models

View models at:

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Structure figures

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 typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10899-MONOMER

UniProt (EcoliWiki Page)

UniProt:P0A800

PFAM (EcoliWiki Page)

PFAM:PF01192

RefSeq (EcoliWiki Page)

RefSeq:NP_418106


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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

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)

rpoZ-spoT-trmH-recG

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Figure courtesy of RegulonDB

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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gbrowse_img.php?coord=3820109..3820149&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

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

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

Allele NameMutationPhenotypeReference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

TypeReferenceNotes

microarray

GEO Profiles:b3649 (EcoliWiki Page)

NCBI GEO profiles for rpoZ

microarray

GenExpDB:b3649 (EcoliWiki Page)

Summary of data for rpoZ 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 NameResource TypeDescriptionSourceNotes
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Notes

Accessions Related to rpoZ Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10899

EchoBASE (EcoliWiki Page)

EchoBASE:EB0892

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3649

EcoGene (EcoliWiki Page)

EcoGene:EG10899


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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.

OrganismHomologs (Statistics)Comments

Shigella flexneri

RPOZ

From SHIGELLACYC

E. coli O157

RPOZ

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF01192


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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 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 3.2 3.3 3.4 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. ↑ 7.0 7.1 7.2 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  8. ↑ 8.0 8.1 8.2 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

Categories

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