O74035 (RNH2_PYRKO) 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:	TK0805

Organism

Pyrococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Thermococcus kodakaraensis (strain KOD1))

Taxonomic identifier

69014 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Thermococcus

Protein attributes

Sequence length	228 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.
Subunit structure	Monomer.
Subcellular location	Cytoplasm Potential HAMAP MF_00052_A.
Sequence similarities	Belongs to the RNase HII family.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	Cobalt Magnesium Metal-binding
Molecular function	Endonuclease Hydrolase Nuclease
Technical term	3D-structure Complete proteome Reference 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 – 228

228

Ribonuclease HII HAMAP MF_00052_A

PRO_0000111671

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

Experimental info

Mutagenesis

7

1

D → A: Loss of activity. Ref.3

Mutagenesis

8

1

E → A: Reduces activity by 99%. Ref.3

Mutagenesis

105

1

D → A: Loss of activity. Ref.3

Mutagenesis

132

1

H → A: Reduces activity by 75%. Ref.3

Mutagenesis

135

1

D → A: Reduces activity by 98%. Ref.3

Secondary structure

1

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228

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 – 35

6

Helix

38 – 40

3

Helix

46 – 57

12

Beta strand

61 – 68

8

Helix

70 – 74

5

Helix

80 – 94

15

Beta strand

100 – 105

6

Helix

111 – 120

10

Beta strand

127 – 131

5

Helix

134 – 137

4

Helix

139 – 163

25

Helix

174 – 187

14

Helix

199 – 211

13

Sequences

	Sequence		Length	Mass (Da)
	O74035 [UniParc]. Last modified November 1, 1998. Version 1. Checksum: 6578C937BBB60F2C	FASTA	228	25,801
	10 20 30 40 50 60 MKIAGIDEAG RGPVIGPMVI AAVVVDENSL PKLEELKVRD SKKLTPKRRE KLFNEILGVL 70 80 90 100 110 120 DDYVILELPP DVIGSREGTL NEFEVENFAK ALNSLKVKPD VIYADAADVD EERFARELGE 130 140 150 160 170 180 RLNFEAEVVA KHKADDIFPV VSAASILAKV TRDRAVEKLK EEYGEIGSGY PSDPRTRAFL 190 200 210 220 ENYYREHGEF PPIVRKGWKT LKKIAEKVES EKKAEERQAT LDRYFRKV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Gene cloning and characterization of recombinant RNase HII from a hyperthermophilic archaeon." Haruki M., Hayashi K., Kochi T., Muroya A., Koga Y., Morikawa M., Imanaka T., Kanaya S. J. Bacteriol. 180:6207-6214(1998) [PubMed: 9829929] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION. Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[2]	"Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes." Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T. Genome Res. 15:352-363(2005) [PubMed: 15710748] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[3]	"Catalytic center of an archaeal type 2 ribonuclease H as revealed by X-ray crystallographic and mutational analyses." Muroya A., Tsuchiya D., Ishikawa M., Haruki M., Morikawa M., Kanaya S., Morikawa K. Protein Sci. 10:707-714(2001) [PubMed: 11274461] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 1-213, MUTAGENESIS OF ASP-7; GLU-8; ASP-105; HIS-132 AND ASP-135. Strain: ATCC BAA-918 / JCM 12380 / KOD1.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AB012613 Genomic DNA. Translation: BAA32803.1.
AP006878 Genomic DNA. Translation: BAD84994.1.

PIR

T43891.

RefSeq

YP_183218.1. NC_006624.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1IO2	X-ray	2.00	A	1-213	[»]
1X1P	X-ray	2.80	A	1-197	[»]
2DFE	X-ray	2.40	A	1-200	[»]
2DFF	X-ray	2.70	A	1-204	[»]
2DFH	X-ray	2.27	A	1-212	[»]

ProteinModelPortal

O74035.

SMR

O74035. Positions 1-213.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBPYRT00000007742; EBPYRP00000007523; EBPYRG00000007741.

GeneID

3233981.

GenomeReviews

Gene locus TK0805 in contig AP006878_GR.

KEGG

tko:TK0805.

NMPDR

fig|69014.3.peg.1165.

Phylogenomic databases

eggNOG

arNOG07713.

GeneTree

EBGT00050000022530.

HOGENOM

HBG584843.

OMA

AYVDACD.

PhylomeDB

O74035.

ProtClustDB

PRK00015.

Enzyme and pathway databases

BioCyc

TKOD69014:TK0805-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_PYRKO

Accession

Primary (citable) accession number: O74035

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	November 1, 1998
Last modified:	December 14, 2011
This is version 92 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program