P0A7Y4 (RNH_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ribonuclease HI
Short name=RNase HI
EC=3.1.26.4

Alternative name(s):
Ribonuclease H
Short name=RNase H

Gene names

Name:	rnhA
Synonyms:	dasF, herA, rnh, sdrA
Ordered Locus Names:	b0214, JW0204

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	155 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. HAMAP MF_00042
Catalytic activity	Endonucleolytic cleavage to 5'-phosphomonoester. HAMAP MF_00042
Cofactor	Binds 1 magnesium ion per subunit in the absence of substrate. Requires millimolar levels of magnesium for maximal activity. Has low activity at micromolar concentrations of manganese and is inhibited at higher manganese levels. Can bind a second metal ion at a regulatory site, or after substrate binding. Ref.11
Subunit structure	Monomer. Ref.13
Subcellular location	Cytoplasm Potential HAMAP MF_00042.
Sequence similarities	Belongs to the RNase H family. Contains 1 RNase H domain.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	Magnesium Metal-binding
Molecular function	Endonuclease Hydrolase Nuclease
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW nucleic acid binding Inferred from electronic annotation. Source: InterPro ribonuclease H activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 155

155

Ribonuclease HI HAMAP MF_00042

PRO_0000195372

Regions

Domain

1 – 142

142

RNase H

Sites

Metal binding

10

1

Magnesium 1

Metal binding

10

1

Magnesium 2

Metal binding

48

1

Magnesium 1

Metal binding

70

1

Magnesium 1

Metal binding

134

1

Magnesium 2

Experimental info

Mutagenesis

10

1

D → N: Loss of activity. Ref.9 Ref.10

Mutagenesis

48

1

E → Q: Loss of activity. Ref.9 Ref.10

Mutagenesis

70

1

D → N: Loss of activity. Ref.9 Ref.10

Mutagenesis

124

1

H → A: Reduces activity. Ref.9 Ref.10 Ref.11 Ref.19

Mutagenesis

130

1

N → A: Reduces activity. Ref.9 Ref.10

Mutagenesis

134

1

D → A: Loss of activity. Ref.9 Ref.10 Ref.11 Ref.19

Mutagenesis

134

1

D → H or N: Slight decrease of activity. Ref.9 Ref.10 Ref.11 Ref.19

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

155

Helix Strand Turn

Details...

Beta strand

5 – 15

11

Beta strand

18 – 28

11

Beta strand

31 – 42

12

Helix

44 – 57

14

Beta strand

64 – 69

6

Helix

72 – 79

8

Helix

82 – 87

6

Turn

88 – 90

3

Helix

101 – 111

11

Beta strand

114 – 120

7

Helix

128 – 142

15

Sequences

	Sequence		Length	Mass (Da)
	P0A7Y4 [UniParc]. Last modified July 21, 1986. Version 1. Checksum: B8EF81EEB2F94CBE	FASTA	155	17,597
	10 20 30 40 50 60 MLKQVEIFTD GSCLGNPGPG GYGAILRYRG REKTFSAGYT RTTNNRMELM AAIVALEALK 70 80 90 100 110 120 EHCEVILSTD SQYVRQGITQ WIHNWKKRGW KTADKKPVKN VDLWQRLDAA LGQHQIKWEW 130 140 150 VKGHAGHPEN ERCDELARAA AMNPTLEDTG YQVEV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"DNA sequence of the gene coding for Escherichia coli ribonuclease H." Kanaya S., Crouch R.J. J. Biol. Chem. 258:1276-1281(1983) [PubMed: 6296074] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Structure and expression of the dnaQ mutator and the RNase H genes of Escherichia coli: overlap of the promoter regions." Maki H., Horiuchi T., Sekiguchi M. Proc. Natl. Acad. Sci. U.S.A. 80:7137-7141(1983) [PubMed: 6316347] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: FB2.
[3]	"Low levels of RNase H activity in Escherichia coli FB2 rnh result from a single-base change in the structural gene of RNase H." Kanaya S., Crouch R.J. J. Bacteriol. 154:1021-1026(1983) [PubMed: 6302075] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"DNA sequence and coding properties of mutD(dnaQ) a dominant Escherichia coli mutator gene." Cox E.C., Horner D.L. J. Mol. Biol. 190:113-117(1986) [PubMed: 3023634] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[5]	"Systematic sequencing of the Escherichia coli genome: analysis of the 4.0 - 6.0 min (189,987 - 281,416bp) region." Takemoto K., Mori H., Murayama N., Kataoka K., Yano M., Itoh T., Yamamoto Y., Inokuchi H., Miki T., Hatada E., Fukuda R., Ichihara S., Mizuno T., Makino K., Nakata A., Yura T., Sampei G., Mizobuchi K. Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"Sequence of minutes 4-25 of Escherichia coli." Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W. Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[7]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[8]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[9]	"Role of cysteine residues in ribonuclease H from Escherichia coli. Site-directed mutagenesis and chemical modification." Kanaya S., Kimura S., Katsuda C., Ikehara M. Biochem. J. 271:59-66(1990) [PubMed: 2171503] [Abstract] Cited for: PARTIAL PROTEIN SEQUENCE, MUTAGENESIS OF CYSTEINE RESIDUES.
[10]	"Identification of the amino acid residues involved in an active site of Escherichia coli ribonuclease H by site-directed mutagenesis." Kanaya S., Kohara A., Miura Y., Sekiguchi A., Iwai S., Inoue H., Ohtsuka E., Ikehara M. J. Biol. Chem. 265:4615-4621(1990) [PubMed: 1689729] [Abstract] Cited for: MUTAGENESIS OF ASP-10; GLU-48; ASP-70; HIS-124; ASN-130 AND ASP-134.
[11]	"Activation/attenuation model for RNase H. A one-metal mechanism with second-metal inhibition." Keck J.L., Goedken E.R., Marqusee S. J. Biol. Chem. 273:34128-34133(1998) [PubMed: 9852071] [Abstract] Cited for: COFACTOR, MUTAGENESIS OF HIS-124 AND ASP-134.
[12]	"Three-dimensional structure of ribonuclease H from E. coli." Katayanagi K., Miyagawa M., Matsushima M., Ishikawa M., Kanaya S., Ikehara M., Matsuzaki T., Morikawa K. Nature 347:306-309(1990) [PubMed: 1698262] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
[13]	"Structure of ribonuclease H phased at 2-A resolution by MAD analysis of the selenomethionyl protein." Yang W., Hendrickson W.A., Crouch R.J., Satow Y. Science 249:1398-1405(1990) [PubMed: 2169648] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), SUBUNIT.
[14]	"Assignments of backbone 1H, 13C, and 15N resonances and secondary structure of ribonuclease H from Escherichia coli by heteronuclear three-dimensional NMR spectroscopy." Yamazaki T., Yoshida M., Kanaya S., Nakamura H., Nagayama K. Biochemistry 30:6036-6047(1991) [PubMed: 1646006] [Abstract] Cited for: STRUCTURE BY NMR.
[15]	"Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution." Katayanagi K., Miyagawa M., Matsushima M., Ishikawa M., Kanaya S., Nakamura H., Ikehara M., Matsuzaki T., Morikawa K. J. Mol. Biol. 223:1029-1052(1992) [PubMed: 1311386] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.48 ANGSTROMS) IN COMPLEX WITH MAGNESIUM.
[16]	"Structural study of mutants of Escherichia coli ribonuclease HI with enhanced thermostability." Ishikawa K., Kimura S., Kanaya S., Morikawa K., Nakamura H. Protein Eng. 6:85-91(1993) [PubMed: 8381958] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF MUTANTS.
[17]	"Crystal structures of ribonuclease HI active site mutants from Escherichia coli." Katayanagi K., Ishikawa K., Okumura M., Ariyoshi M., Kanaya S., Kawano Y., Suzuki M., Tanaka I., Morikawa K. J. Biol. Chem. 268:22092-22099(1993) [PubMed: 8408067] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF MUTANTS ASN-10; GLN-48 AND ASN-70.
[18]	"Folding pathway of Escherichia coli ribonuclease HI: a circular dichroism, fluorescence, and NMR study." Yamazaki T., Ogasahara K., Yutani K., Oobatake M., Kanaya S. Biochemistry 34:16552-16562(1995) [PubMed: 8527428] [Abstract] Cited for: STRUCTURE BY NMR.
[19]	"Proposal for new catalytic roles for two invariant residues in Escherichia coli ribonuclease HI." Kashiwagi T., Jeanteur D., Haruki M., Katayanagi K., Kanaya S., Morikawa K. Protein Eng. 9:857-867(1996) [PubMed: 8931125] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), MUTAGENESIS OF HIS-124 AND ASP-134.
[20]	"Divalent metal cofactor binding in the kinetic folding trajectory of Escherichia coli ribonuclease HI." Goedken E.R., Keck J.L., Berger J.M., Marqusee S. Protein Sci. 9:1914-1921(2000) [PubMed: 11106164] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS).
[21]	"Co-crystal of Escherichia coli RNase HI with Mn2+ ions reveals two divalent metals bound in the active site." Goedken E.R., Marqusee S. J. Biol. Chem. 276:7266-7271(2001) [PubMed: 11083878] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH MANGANESE IONS.
[22]	"Identification of single Mn(2+) binding sites required for activation of the mutant proteins of E.coli RNase HI at Glu48 and/or Asp134 by X-ray crystallography." Tsunaka Y., Takano K., Matsumura H., Yamagata Y., Kanaya S. J. Mol. Biol. 345:1171-1183(2005) [PubMed: 15644213] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF MUTANTS ALA-48 AND ASN-134 IN COMPLEX WITH MANGANESE IONS.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

PIR

NRECH. A92401.

RefSeq

NP_414750.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1F21	X-ray	1.40	A	1-155	[»]
1G15	X-ray	1.90	A	1-155	[»]
1GOA	X-ray	1.90	A	1-155	[»]
1GOB	X-ray	2.00	A	1-155	[»]
1GOC	X-ray	2.00	A	1-155	[»]
1JL1	X-ray	1.30	A	1-155	[»]
1JL2	X-ray	1.76	A/B/C/D	1-155	[»]
1JXB	X-ray	1.60	A	1-155	[»]
1KVA	X-ray	1.80	A	1-155	[»]
1KVB	X-ray	1.90	A	1-155	[»]
1KVC	X-ray	1.90	A	1-155	[»]
1LAV	X-ray	1.80	A	1-155	[»]
1LAW	X-ray	1.80	A	1-155	[»]
1RBR	X-ray	1.80	A	1-155	[»]
1RBS	X-ray	1.80	A	1-155	[»]
1RBT	X-ray	1.80	A	1-155	[»]
1RBU	X-ray	1.80	A	1-155	[»]
1RBV	X-ray	1.80	A	1-155	[»]
1RCH	NMR	-	A	1-155	[»]
1RDA	X-ray	2.15	A	1-155	[»]
1RDB	X-ray	1.90	A	1-155	[»]
1RDC	X-ray	2.30	A	1-155	[»]
1RDD	X-ray	2.80	A	1-155	[»]
1RNH	X-ray	2.00	A	1-155	[»]
1WSE	X-ray	2.30	A/B	1-155	[»]
1WSF	X-ray	2.30	A/B/C/D	1-155	[»]
1WSG	X-ray	2.20	A/B/C/D	1-155	[»]
1WSH	X-ray	1.90	A/B/C/D	1-155	[»]
1WSI	X-ray	2.00	A/B/C/D	1-155	[»]
1WSJ	X-ray	2.00	A/B/C/D/E/F/G/H	1-155	[»]
2RN2	X-ray	1.48	A	1-155	[»]
2YV0	X-ray	1.40	X	1-155	[»]
2Z1G	X-ray	2.10	A	1-155	[»]
2Z1H	X-ray	2.60	A	1-155	[»]
2Z1I	X-ray	2.00	A/B	1-155	[»]
2Z1J	X-ray	2.38	A	1-155	[»]
3AA2	X-ray	1.90	A	1-155	[»]
3AA3	X-ray	2.20	A	1-155	[»]
3AA4	X-ray	1.79	A	1-155	[»]
3AA5	X-ray	2.10	X	1-155	[»]
3QIN	X-ray	1.70	A	79-102	[»]
3QIO	X-ray	1.40	A	79-102	[»]

ProteinModelPortal

P0A7Y4.

SMR

P0A7Y4. Positions 1-155.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-47864N.

IntAct

P0A7Y4. 21 interactions.

MINT

MINT-1224022.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000004699; EBESCP00000004699; EBESCG00000003837.
EBESCT00000018225; EBESCP00000017516; EBESCG00000017280.

GeneID

946955.

GenomeReviews

Gene locus JW0204 in contig AP009048_GR.
Gene locus b0214 in contig U00096_GR.

KEGG

ecj:JW0204.
eco:b0214.

PATRIC

32115541. VBIEscCol129921_0216.

Organism-specific databases

EchoBASE

EB0853.

EcoGene

EG10860. rnhA.

Phylogenomic databases

eggNOG

COG0328.

GeneTree

EBGT00050000011291.

HOGENOM

HBG742437.

OMA

NGWRTAD.

PhylomeDB

P0A7Y4.

ProtClustDB

PRK00203.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10860-MONOMER.
MetaCyc:EG10860-MONOMER.

Gene expression databases

Genevestigator

P0A7Y4.

Family and domain databases

HAMAP

MF_00042. RNase_H.
[Tree]

InterPro

IPR022892. RNaseH.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
[Graphical view]

KO

K03469.

Pfam

PF00075. RNase_H. 1 hit.
[Graphical view]

SUPFAM

SSF53098. RNaseH_fold. 1 hit.

PROSITE

PS50879. RNASE_H. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RNH_ECOLI

Accession

Primary (citable) accession number: P0A7Y4
Secondary accession number(s): P00647, Q8FKY5

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 21, 1986
Last modified:	January 25, 2012
This is version 67 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program