Reviewed, UniProtKB/Swiss-Prot Q57599 (RNH2_METJA)

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:	MJ0135

Organism

Methanocaldococcus jannaschii (Methanococcus jannaschii) [Complete proteome] [HAMAP]

Taxonomic identifier

2190 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Methanococci › Methanococcales › Methanocaldococcaceae › Methanocaldococcus

Protein attributes

Sequence length	230 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. HAMAP MF_00052
Catalytic activity	Endonucleolytic cleavage to 5'-phosphomonoester. HAMAP MF_00052
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.
Sequence similarities	Belongs to the RNase HII family.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	Magnesium 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: HAMAP
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	RNA binding Inferred from electronic annotation. Source: InterPro magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese ion binding Inferred from electronic annotation. Source: HAMAP ribonuclease H activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 230

230

Ribonuclease HII HAMAP MF_00052

PRO_0000111663

Sites

Metal binding

7

1

Divalent metal cation By similarity

Metal binding

8

1

Divalent metal cation By similarity

Metal binding

112

1

Divalent metal cation By similarity

Experimental info

Mutagenesis

7

1

D → N: Reduces activity 800-fold. Ref.2

Mutagenesis

8

1

E → Q: Reduces activity 700-fold. Ref.2

Mutagenesis

112

1

D → N: Reduces activity 600-fold. Ref.2

Mutagenesis

149

1

D → N: Reduces activity 800-fold. Ref.2

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

230

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 – 34

5

Turn

35 – 37

3

Helix

46 – 59

14

Beta strand

60 – 67

8

Helix

69 – 75

7

Turn

76 – 78

3

Helix

81 – 99

19

Beta strand

104 – 112

9

Helix

118 – 133

16

Turn

134 – 137

4

Beta strand

139 – 145

7

Helix

148 – 150

3

Helix

153 – 176

24

Helix

188 – 201

14

Helix

213 – 221

9

Sequences

	Sequence		Length	Mass (Da)
	Q57599-1 [UniParc]. Last modified November 1, 1997. Version 1. Checksum: C454324C0C801299	FASTA	230	26,506
	10 20 30 40 50 60 MIIIGIDEAG RGPVLGPMVV CAFAIEKERE EELKKLGVKD SKELTKNKRA YLKKLLENLG 70 80 90 100 110 120 YVEKRILEAE EINQLMNSIN LNDIEINAFS KVAKNLIEKL NIRDDEIEIY IDACSTNTKK 130 140 150 160 170 180 FEDSFKDKIE DIIKERNLNI KIIAEHKADA KYPVVSAASI IAKAERDEII DYYKKIYGDI 190 200 210 220 230 GSGYPSDPKT IKFLEDYFKK HKKLPDIART HWKTCKRILD KSKQTKLIIE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii." Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G., Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R., Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R., Kirkness E.F., Weinstock K.G. , Merrick J.M., Glodek A., Scott J.L., Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R., Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D., Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P., Fraser C.M., Smith H.O., Woese C.R., Venter J.C. Science 273:1058-1073(1996) [PubMed: 8688087] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
[2]	"Metal ion binding and enzymatic mechanism of Methanococcus jannaschii RNase HII." Lai B., Li Y., Cao A., Lai L. Biochemistry 42:785-791(2003) [PubMed: 12534291] [Abstract] Cited for: COFACTOR, MUTAGENESIS OF ASP-7; GLU-8; ASP-112 AND ASP-149.
[3]	"Crystal structure of archaeal RNase HII: a homologue of human major RNase H." Lai L., Yokota H., Hung L.-W., Kim R., Kim S.-H. Structure 8:897-904(2000) [PubMed: 10997908] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).

Cross-references

Sequence databases

EMBLGenBankDDBJ

L77117 Genomic DNA. Translation: AAB98116.1.

PIR

G64316.

RefSeq

NP_247101.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1EKE	X-ray	2.00	A/B	1-230	[»]

ModBase

Search...

Genome annotation databases

GeneID

1450976.

GenomeReviews

Gene locus MJ0135 in contig L77117_GR.

KEGG

mja:MJ0135.

NMPDR

fig|243232.1.peg.138.

TIGR

MJ0135.

Phylogenomic databases

HOGENOM

Q57599.

OMA

PSDPKTK.

Enzyme and pathway databases

BioCyc

MJAN243232:MJ_0135-MON.

BRENDA

3.1.26.4. 256362.

Family and domain databases

HAMAP

MF_00052.
[Tree]

InterPro

IPR004649. RNase_H2_suA.
IPR001352. RNase_HII/HIII.
[Graphical view]

PANTHER

PTHR10954. RNase_HII/HIII. 1 hit.

Pfam

PF01351. RNase_HII. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00729. RnhII. 1 hit.

ProtoNet

Search...

Entry information

Entry name

RNH2_METJA

Accession

Primary (citable) accession number: Q57599

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1997
Last modified:	November 3, 2009
This is version 71 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)