rnhB: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

rnhB

Gene Synonym(s)

ECK0182, b0183, JW0178[1], JW0178

Product Desc.

RNAse HII, degrades RNA of DNA-RNA hybrids[2][3]

Degrades RNA of DNA-RNA hybrids; RNase HII; nicks DNA 5' to misincorporated ribonucleotides[4]

Product Synonyms(s)

ribonuclease HII, degrades RNA of DNA-RNA hybrids[1], B0183[2][1], RnhB[2][1] , ECK0182, JW0178, b0183

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yaeT-hlpA-lpxD-fabZ-lpxAB-rnhB-dnaE[2], ecfK-skp-lpxD-fabZ-lpxAB-rnhB-dnaE

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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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

rnhB

Mnemonic

RNase H

Synonyms

ECK0182, b0183, JW0178[1], JW0178

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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

4.41 minutes 

MG1655: 204493..205089
<gbrowseImage> name=NC_000913:204493..205089 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 207335..207931
<gbrowseImage> name=NC_012967:207335..207931 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 204492..205088
<gbrowseImage> name=NC_012759:204492..205088 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 204493..205089
<gbrowseImage> name=NC_007779:204493..205089 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 178597..179193
<gbrowseImage> name=NC_010473:178597..179193 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

204493

Edman degradation

PMID:2172991


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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

rnhB(del) (Keio:JW0178)

deletion

deletion

PMID:16738554

Shigen
CGSC8427[5]

rnhB782(del)::kan

PMID:16738554

CGSC:102752


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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

JW0178

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCATCGAATTTGTTTATCCGCA

Primer 2:CCGGACGCAAGTCCCAGTGCGCG

E2B8

Kohara Phage

Genobase

PMID:3038334

6F5

Kohara Phage

Genobase

PMID:3038334

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[5]

est. P1 cotransduction: 6% [6]

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[5]

est. P1 cotransduction: 35% [6]
Synonyms:zae-502::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:EG10861

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10861

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000852

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944852

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0854

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000622

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

RnhB

Synonyms

ribonuclease HII, degrades RNA of DNA-RNA hybrids[1], B0183[2][1], RnhB[2][1] , ECK0182, JW0178, b0183

Product description

RNAse HII, degrades RNA of DNA-RNA hybrids[2][3]

Degrades RNA of DNA-RNA hybrids; RNase HII; nicks DNA 5' to misincorporated ribonucleotides[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:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012337

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001352

F

Seeded from EcoCyc (v14.0)

complete

GO:0004518

nuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0540

F

Seeded from EcoCyc (v14.0)

complete

GO:0004519

endonuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0255

F

Seeded from EcoCyc (v14.0)

complete

GO:0004523

ribonuclease H activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00052

F

Seeded from EcoCyc (v14.0)

complete

GO:0004523

ribonuclease H activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001352

F

Seeded from EcoCyc (v14.0)

complete

GO:0004523

ribonuclease H activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.1.26.4

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00052

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:0006401

RNA catabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00052

P

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc (v14.0)

complete

GO:0030145

manganese ion binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00052

F

Seeded from EcoCyc (v14.0)

complete

GO:0030145

manganese ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0464

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

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

lpxA

PMID:16606699

Experiment(s):EBI-1135846

Protein

thiD

PMID:16606699

Experiment(s):EBI-1135846

Protein

btuE

PMID:16606699

Experiment(s):EBI-1135846

Protein

cysH

PMID:16606699

Experiment(s):EBI-1135846

Protein

sdhA

PMID:16606699

Experiment(s):EBI-1135846
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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 

MIEFVYPHTQ LVAGVDEVGR GPLVGAVVTA AVILDPARPI AGLNDSKKLS EKRRLALYEE
IKEKALSWSL GRAEPHEIDE LNILHATMLA MQRAVAGLHI APEYVLIDGN RCPKLPMPAM
AVVKGDSRVP EISAASILAK VTRDAEMAAL DIVFPQYGFA QHKGYPTAFH LEKLAEHGAT
EHHRRSFGPV KRALGLAS
Length

198

Mol. Wt

21.525 kDa

pI

7.7 (calculated)

Extinction coefficient

12,950 - 13,075 (calc based on 5 Y, 1 W, and 1 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

13..190

PF01351 Ribonuclease HII

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=rnhB 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:16128176

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944852

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000622

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P10442

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10861

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10861

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944852

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000852

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0854

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 MG1655

604

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

131

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

233

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)

yaeT-hlpA-lpxD-fabZ-lpxAB-rnhB-dnaE

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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_000913:204473..204513 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:b0183 (EcoliWiki Page)

NCBI GEO profiles for rnhB

microarray

GenExpDB:b0183 (EcoliWiki Page)

Summary of data for rnhB 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
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Notes

Accessions Related to rnhB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10861

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0854

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0183

EcoGene

EcoGene:EG10861

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000852

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000622

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

  • ENSANGP00000022231 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000017696 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT2G25100 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000012731 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00027367 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00004383 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000012778 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0218016 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0031252 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA12461-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:1916974 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q53QG3 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000004667 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000142676 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

RNHB

From SHIGELLACYC

E. coli O157

RNHB

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)

PF01351 Ribonuclease HII

Superfamily (EcoliWiki Page)

SUPERFAMILY:53098

Panther (EcoliWiki Page)

PTHR10954:SF7

EcoCyc

EcoCyc:EG10861

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10861

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000852

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0854

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000622

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 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 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 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).

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