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Protein

Ribonuclease HI

Gene

rnhA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. RNase H participates in DNA replication; it helps to specify the origin of genomic replication by suppressing initiation at origins other than the oriC locus; along with the 5'-3' exonuclease of pol1, it removes RNA primers from the Okazaki fragments of lagging strand synthesis; and it defines the origin of replication for ColE1-type plasmids by specific cleavage of an RNA preprimer.

Catalytic activityi

Endonucleolytic cleavage to 5'-phosphomonoester.

Cofactori

Mg2+1 PublicationNote: Binds 1 Mg2+ ion per subunit in the absence of substrate. Requires millimolar levels of Mg2+ for maximal activity. Has low activity at micromolar concentrations of Mn2+ and is inhibited at higher Mn2+ levels. Can bind a second metal ion at a regulatory site, or after substrate binding.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi10Magnesium 11 Publication1
Metal bindingi10Magnesium 21 Publication1
Metal bindingi48Magnesium 11 Publication1
Metal bindingi70Magnesium 11 Publication1
Metal bindingi134Magnesium 21 Publication1

GO - Molecular functioni

  • endonuclease activity Source: EcoliWiki
  • magnesium ion binding Source: UniProtKB-HAMAP
  • nucleic acid binding Source: EcoliWiki
  • RNA-DNA hybrid ribonuclease activity Source: EcoCyc

GO - Biological processi

  • DNA replication, removal of RNA primer Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10860-MONOMER.
ECOL316407:JW0204-MONOMER.
MetaCyc:EG10860-MONOMER.
BRENDAi3.1.26.4. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonuclease HI (EC:3.1.26.4)
Short name:
RNase HI
Alternative name(s):
Ribonuclease H
Short name:
RNase H
Gene namesi
Name:rnhA
Synonyms:dasF, herA, rnh, sdrA
Ordered Locus Names:b0214, JW0204
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10860. rnhA.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi10D → N: Loss of activity. 1 Publication1
Mutagenesisi48E → Q: Loss of activity. 1 Publication1
Mutagenesisi70D → N: Loss of activity. 1 Publication1
Mutagenesisi124H → A: Reduces activity. 3 Publications1
Mutagenesisi130N → A: Reduces activity. 1 Publication1
Mutagenesisi134D → A: Loss of activity. 3 Publications1
Mutagenesisi134D → H or N: Slight decrease of activity. 3 Publications1

Chemistry databases

ChEMBLiCHEMBL1770039.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001953721 – 155Ribonuclease HIAdd BLAST155

Proteomic databases

PaxDbiP0A7Y4.
PRIDEiP0A7Y4.

Interactioni

Subunit structurei

Monomer.4 Publications

Protein-protein interaction databases

BioGridi4263455. 204 interactors.
DIPiDIP-47864N.
IntActiP0A7Y4. 21 interactors.
MINTiMINT-1224022.
STRINGi511145.b0214.

Chemistry databases

BindingDBiP0A7Y4.

Structurei

Secondary structure

1155
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 4Combined sources3
Beta strandi5 – 15Combined sources11
Beta strandi18 – 28Combined sources11
Beta strandi31 – 42Combined sources12
Helixi44 – 57Combined sources14
Beta strandi64 – 69Combined sources6
Helixi72 – 79Combined sources8
Helixi82 – 87Combined sources6
Turni88 – 90Combined sources3
Beta strandi95 – 97Combined sources3
Helixi101 – 110Combined sources10
Turni111 – 113Combined sources3
Beta strandi115 – 120Combined sources6
Helixi123 – 125Combined sources3
Helixi128 – 142Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1F21X-ray1.40A1-155[»]
1G15X-ray1.90A1-155[»]
1GOAX-ray1.90A1-155[»]
1GOBX-ray2.00A1-155[»]
1GOCX-ray2.00A1-155[»]
1JL1X-ray1.30A1-155[»]
1JL2X-ray1.76A/B/C/D1-155[»]
1JXBX-ray1.60A1-155[»]
1KVAX-ray1.80A1-155[»]
1KVBX-ray1.90A1-155[»]
1KVCX-ray1.90A1-155[»]
1LAVX-ray1.80A1-155[»]
1LAWX-ray1.80A1-155[»]
1RBRX-ray1.80A1-155[»]
1RBSX-ray1.80A1-155[»]
1RBTX-ray1.80A1-155[»]
1RBUX-ray1.80A1-155[»]
1RBVX-ray1.80A1-155[»]
1RCHNMR-A1-155[»]
1RDAX-ray2.15A1-155[»]
1RDBX-ray1.90A1-155[»]
1RDCX-ray2.30A1-155[»]
1RDDX-ray2.80A1-155[»]
1RNHX-ray2.00A1-155[»]
1WSEX-ray2.30A/B1-155[»]
1WSFX-ray2.30A/B/C/D1-155[»]
1WSGX-ray2.20A/B/C/D1-155[»]
1WSHX-ray1.90A/B/C/D1-155[»]
1WSIX-ray2.00A/B/C/D1-155[»]
1WSJX-ray2.00A/B/C/D/E/F/G/H1-155[»]
2RN2X-ray1.48A1-155[»]
2YV0X-ray1.40X1-155[»]
2Z1GX-ray2.10A1-155[»]
2Z1HX-ray2.60A1-155[»]
2Z1IX-ray2.00A/B1-155[»]
2Z1JX-ray2.38A1-155[»]
3AA2X-ray1.90A1-155[»]
3AA3X-ray2.20A1-155[»]
3AA4X-ray1.79A1-155[»]
3AA5X-ray2.10X1-155[»]
3HYFX-ray1.70A79-102[»]
3QINX-ray1.70A79-102[»]
3QIOX-ray1.40A79-102[»]
4Z0UX-ray2.00A/B1-155[»]
ProteinModelPortaliP0A7Y4.
SMRiP0A7Y4.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A7Y4.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 142RNase HAdd BLAST142

Sequence similaritiesi

Belongs to the RNase H family.Curated
Contains 1 RNase H domain.Curated

Phylogenomic databases

eggNOGiENOG4108UMW. Bacteria.
COG0328. LUCA.
HOGENOMiHOG000040465.
InParanoidiP0A7Y4.
KOiK03469.
OMAiLVTDSQY.
PhylomeDBiP0A7Y4.

Family and domain databases

CDDicd09278. RNase_HI_prokaryote_like. 1 hit.
Gene3Di3.30.420.10. 1 hit.
HAMAPiMF_00042. RNase_H. 1 hit.
InterProiIPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR022892. RNaseHI.
[Graphical view]
PfamiPF00075. RNase_H. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS50879. RNASE_H. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0A7Y4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLKQVEIFTD GSCLGNPGPG GYGAILRYRG REKTFSAGYT RTTNNRMELM
60 70 80 90 100
AAIVALEALK EHCEVILSTD SQYVRQGITQ WIHNWKKRGW KTADKKPVKN
110 120 130 140 150
VDLWQRLDAA LGQHQIKWEW VKGHAGHPEN ERCDELARAA AMNPTLEDTG

YQVEV
Length:155
Mass (Da):17,597
Last modified:July 21, 1986 - v1
Checksum:iB8EF81EEB2F94CBE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
K00985 Genomic DNA. Translation: AAA24565.1.
V00337 Genomic DNA. Translation: CAA23620.1.
X04027 Genomic DNA. Translation: CAA27660.1.
U70214 Genomic DNA. Translation: AAB08636.1.
U00096 Genomic DNA. Translation: AAC73319.1.
AP009048 Genomic DNA. Translation: BAA77885.1.
PIRiA92401. NRECH.
RefSeqiNP_414750.1. NC_000913.3.
WP_000917883.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73319; AAC73319; b0214.
BAA77885; BAA77885; BAA77885.
GeneIDi946955.
KEGGiecj:JW0204.
eco:b0214.
PATRICi32115541. VBIEscCol129921_0216.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
K00985 Genomic DNA. Translation: AAA24565.1.
V00337 Genomic DNA. Translation: CAA23620.1.
X04027 Genomic DNA. Translation: CAA27660.1.
U70214 Genomic DNA. Translation: AAB08636.1.
U00096 Genomic DNA. Translation: AAC73319.1.
AP009048 Genomic DNA. Translation: BAA77885.1.
PIRiA92401. NRECH.
RefSeqiNP_414750.1. NC_000913.3.
WP_000917883.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1F21X-ray1.40A1-155[»]
1G15X-ray1.90A1-155[»]
1GOAX-ray1.90A1-155[»]
1GOBX-ray2.00A1-155[»]
1GOCX-ray2.00A1-155[»]
1JL1X-ray1.30A1-155[»]
1JL2X-ray1.76A/B/C/D1-155[»]
1JXBX-ray1.60A1-155[»]
1KVAX-ray1.80A1-155[»]
1KVBX-ray1.90A1-155[»]
1KVCX-ray1.90A1-155[»]
1LAVX-ray1.80A1-155[»]
1LAWX-ray1.80A1-155[»]
1RBRX-ray1.80A1-155[»]
1RBSX-ray1.80A1-155[»]
1RBTX-ray1.80A1-155[»]
1RBUX-ray1.80A1-155[»]
1RBVX-ray1.80A1-155[»]
1RCHNMR-A1-155[»]
1RDAX-ray2.15A1-155[»]
1RDBX-ray1.90A1-155[»]
1RDCX-ray2.30A1-155[»]
1RDDX-ray2.80A1-155[»]
1RNHX-ray2.00A1-155[»]
1WSEX-ray2.30A/B1-155[»]
1WSFX-ray2.30A/B/C/D1-155[»]
1WSGX-ray2.20A/B/C/D1-155[»]
1WSHX-ray1.90A/B/C/D1-155[»]
1WSIX-ray2.00A/B/C/D1-155[»]
1WSJX-ray2.00A/B/C/D/E/F/G/H1-155[»]
2RN2X-ray1.48A1-155[»]
2YV0X-ray1.40X1-155[»]
2Z1GX-ray2.10A1-155[»]
2Z1HX-ray2.60A1-155[»]
2Z1IX-ray2.00A/B1-155[»]
2Z1JX-ray2.38A1-155[»]
3AA2X-ray1.90A1-155[»]
3AA3X-ray2.20A1-155[»]
3AA4X-ray1.79A1-155[»]
3AA5X-ray2.10X1-155[»]
3HYFX-ray1.70A79-102[»]
3QINX-ray1.70A79-102[»]
3QIOX-ray1.40A79-102[»]
4Z0UX-ray2.00A/B1-155[»]
ProteinModelPortaliP0A7Y4.
SMRiP0A7Y4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263455. 204 interactors.
DIPiDIP-47864N.
IntActiP0A7Y4. 21 interactors.
MINTiMINT-1224022.
STRINGi511145.b0214.

Chemistry databases

BindingDBiP0A7Y4.
ChEMBLiCHEMBL1770039.

Proteomic databases

PaxDbiP0A7Y4.
PRIDEiP0A7Y4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73319; AAC73319; b0214.
BAA77885; BAA77885; BAA77885.
GeneIDi946955.
KEGGiecj:JW0204.
eco:b0214.
PATRICi32115541. VBIEscCol129921_0216.

Organism-specific databases

EchoBASEiEB0853.
EcoGeneiEG10860. rnhA.

Phylogenomic databases

eggNOGiENOG4108UMW. Bacteria.
COG0328. LUCA.
HOGENOMiHOG000040465.
InParanoidiP0A7Y4.
KOiK03469.
OMAiLVTDSQY.
PhylomeDBiP0A7Y4.

Enzyme and pathway databases

BioCyciEcoCyc:EG10860-MONOMER.
ECOL316407:JW0204-MONOMER.
MetaCyc:EG10860-MONOMER.
BRENDAi3.1.26.4. 2026.

Miscellaneous databases

EvolutionaryTraceiP0A7Y4.
PROiP0A7Y4.

Family and domain databases

CDDicd09278. RNase_HI_prokaryote_like. 1 hit.
Gene3Di3.30.420.10. 1 hit.
HAMAPiMF_00042. RNase_H. 1 hit.
InterProiIPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR022892. RNaseHI.
[Graphical view]
PfamiPF00075. RNase_H. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS50879. RNASE_H. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRNH_ECOLI
AccessioniPrimary (citable) accession number: P0A7Y4
Secondary accession number(s): P00647, Q8FKY5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: November 2, 2016
This is version 110 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.