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Protein

Ribonuclease HI

Gene

rnhA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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

GO - Biological processi

  • DNA replication, removal of RNA primer Source: EcoCyc
  • RNA phosphodiester bond hydrolysis, endonucleolytic Source: GO_Central

Keywordsi

Molecular functionEndonuclease, Hydrolase, Nuclease
LigandMagnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10860-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

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, 263 interactors
DIPiDIP-47864N
IntActiP0A7Y4, 22 interactors
STRINGi316385.ECDH10B_0195

Chemistry databases

BindingDBiP0A7Y4

Structurei

Secondary structure

1155
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

Phylogenomic databases

eggNOGiENOG4108UMW Bacteria
COG0328 LUCA
HOGENOMiHOG000040465
InParanoidiP0A7Y4
KOiK03469
PhylomeDBiP0A7Y4

Family and domain databases

CDDicd09278 RNase_HI_prokaryote_like, 1 hit
Gene3Di3.30.420.10, 1 hit
HAMAPiMF_00042 RNase_H, 1 hit
InterProiView protein in InterPro
IPR012337 RNaseH-like_sf
IPR002156 RNaseH_domain
IPR036397 RNaseH_sf
IPR022892 RNaseHI
PfamiView protein in Pfam
PF00075 RNase_H, 1 hit
SUPFAMiSSF53098 SSF53098, 1 hit
PROSITEiView protein in PROSITE
PS50879 RNASE_H, 1 hit

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
PATRICifig|1411691.4.peg.2070

Similar proteinsi

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/D1-49[»]
A/B/C/D121-155[»]
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, 263 interactors
DIPiDIP-47864N
IntActiP0A7Y4, 22 interactors
STRINGi316385.ECDH10B_0195

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
PATRICifig|1411691.4.peg.2070

Organism-specific databases

EchoBASEiEB0853
EcoGeneiEG10860 rnhA

Phylogenomic databases

eggNOGiENOG4108UMW Bacteria
COG0328 LUCA
HOGENOMiHOG000040465
InParanoidiP0A7Y4
KOiK03469
PhylomeDBiP0A7Y4

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP0A7Y4
PROiPR:P0A7Y4

Family and domain databases

CDDicd09278 RNase_HI_prokaryote_like, 1 hit
Gene3Di3.30.420.10, 1 hit
HAMAPiMF_00042 RNase_H, 1 hit
InterProiView protein in InterPro
IPR012337 RNaseH-like_sf
IPR002156 RNaseH_domain
IPR036397 RNaseH_sf
IPR022892 RNaseHI
PfamiView protein in Pfam
PF00075 RNase_H, 1 hit
SUPFAMiSSF53098 SSF53098, 1 hit
PROSITEiView protein in PROSITE
PS50879 RNASE_H, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRNH_ECOLI
AccessioniPrimary (citable) accession number: P0A7Y4
Secondary accession number(s): P00647, Q8FKY5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: November 7, 2018
This is version 122 of the entry and version 1 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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