O59351 (RNH2_PYRHO) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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

Gene names

Name:	rnhB
Ordered Locus Names:	PH1650

Organism

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) [Complete proteome] [HAMAP]

Taxonomic identifier

70601 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus

Protein attributes

Sequence length	220 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Endonuclease that specifically degrades the RNA of RNA-DNA hybrids By similarity. HAMAP MF_00052_A
Catalytic activity	Endonucleolytic cleavage to 5'-phosphomonoester. HAMAP MF_00052_A
Cofactor	Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding By similarity.
Subcellular location	Cytoplasm Potential HAMAP MF_00052_A.
Sequence similarities	Belongs to the RNase HII family.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	Manganese Metal-binding
Molecular function	Endonuclease Hydrolase Nuclease
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	RNA catabolic process Inferred from electronic annotation. Source: InterPro
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	RNA binding Inferred from electronic annotation. Source: InterPro manganese ion 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 – 220

220

Ribonuclease HII HAMAP MF_00052_A

PRO_0000111670

Sites

Metal binding

7

1

Divalent metal cation By similarity

Metal binding

8

1

Divalent metal cation By similarity

Metal binding

105

1

Divalent metal cation By similarity

Secondary structure

1

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220

Helix Strand Turn

Details...

Beta strand

2 – 9

8

Beta strand

14 – 16

3

Beta strand

18 – 26

9

Helix

27 – 29

3

Helix

30 – 36

7

Helix

38 – 40

3

Helix

46 – 59

14

Beta strand

60 – 68

9

Helix

70 – 74

5

Helix

80 – 93

14

Beta strand

100 – 105

6

Helix

111 – 121

11

Beta strand

127 – 131

5

Helix

134 – 137

4

Helix

139 – 163

25

Helix

174 – 187

14

Helix

199 – 208

10

Sequences

	Sequence		Length	Mass (Da)
	O59351 [UniParc]. Last modified August 1, 1998. Version 1. Checksum: 77DB1BDEDB8881D0	FASTA	220	25,283
	10 20 30 40 50 60 MKVAGVDEAG RGPVIGPLVI GVAVIDEKNI ERLRDIGVKD SKQLTPGQRE KLFSKLIDIL 70 80 90 100 110 120 DDYYVLLVTP KEIDERHHSM NELEAEKFVV ALNSLRIKPQ KIYVDSADVD PKRFASLIKA 130 140 150 160 170 180 GLKYEATVIA EHKADAKYEI VSAASIIAKV TRDREIEKLK QKYGEFGSGY PSDPRTKEWL 190 200 210 220 EEYYKQYGDF PPIVRRTWET ARKIEERFRK NQLTLDKFLK

References

[1]

"Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3." Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S., Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K., Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T. , Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T., Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H. DNA Res. 5:55-76(1998) [PubMed: 9679194] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

BA000001 Genomic DNA. Translation: BAA30762.1.

PIR

B71045.

RefSeq

NP_143500.1. NC_000961.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1UAX	X-ray	2.00	A/B	1-220	[»]

ProteinModelPortal

O59351.

SMR

O59351. Positions 1-211.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBPYRT00000000702; EBPYRP00000000702; EBPYRG00000000702.

GeneID

1442499.

GenomeReviews

Gene locus PH1650 in contig BA000001_GR.

KEGG

pho:PH1650.

NMPDR

fig|70601.1.peg.1613.

Organism-specific databases

CMR

Search...

Phylogenomic databases

GeneTree

EBGT00050000022530.

HOGENOM

HBG584843.

OMA

AYVDACD.

PhylomeDB

O59351.

ProtClustDB

PRK00015.

Enzyme and pathway databases

BioCyc

PHOR70601:PH1650-MONOMER.

Family and domain databases

HAMAP

MF_00052_A. RNase_HII_A.
[Tree]

InterPro

IPR004649. RNase_H2_suA.
IPR001352. RNase_HII/HIII.
IPR024567. RNase_HII/HIII_dom.
IPR020787. RNase_HII_arc.
IPR023160. RNase_HII_hlx-loop-hlx_cap_dom.
IPR012337. RNaseH-like_dom.
[Graphical view]

Gene3D

G3DSA:1.10.10.460. RNase_HII_hlx-loop-hlx_cap_dom. 1 hit.

KO

K03470.

PANTHER

PTHR10954. RNase_HII/HIII. 1 hit.

Pfam

PF01351. RNase_HII. 1 hit.
[Graphical view]

SUPFAM

SSF53098. RNaseH_fold. 1 hit.

TIGRFAMs

TIGR00729. TIGR00729. 1 hit.

ProtoNet

Search...

Entry information

Entry name

RNH2_PYRHO

Accession

Primary (citable) accession number: O59351

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	August 1, 1998
Last modified:	December 14, 2011
This is version 80 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program