O29634 (RNH2_ARCFU) 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:	AF_0621

Organism

Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)

Taxonomic identifier

224325 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Archaeoglobi › Archaeoglobales › Archaeoglobaceae › Archaeoglobus

Protein attributes

Sequence length	205 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. Ref.2
Subcellular location	Cytoplasm Potential HAMAP MF_00052_A.
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 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 – 205

205

Ribonuclease HII HAMAP MF_00052_A

PRO_0000111661

Sites

Metal binding

6

1

Divalent metal cation

Metal binding

7

1

Divalent metal cation

Metal binding

101

1

Divalent metal cation

Binding site

46

1

Substrate Probable

Binding site

143

1

Substrate Probable

Binding site

146

1

Substrate Probable

Binding site

164

1

Substrate Probable

Experimental info

Mutagenesis

6

1

D → N: Loss of activity. Ref.3

Mutagenesis

7

1

E → N: Slight decrease of activity. Ref.3

Mutagenesis

7

1

E → Q: Loss of activity. Ref.3

Mutagenesis

46

1

R → A: Increases Km for RNA 60-fold. Ref.3

Mutagenesis

101

1

D → N: Loss of activity. Ref.3

Mutagenesis

129

1

D → N: Lowers activity by 50%. Ref.3

Mutagenesis

143

1

K → A: Decrease of activity. Increases Km for RNA 30-fold. Ref.3

Mutagenesis

146

1

R → A: Decrease of activity. Increases Km for RNA 26-fold. Ref.3

Mutagenesis

164

1

Y → A: Loss of activity. Increases Km for RNA 44-fold. Ref.3

Secondary structure

1

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205

Helix Strand Turn

Details...

Beta strand

2 – 8

7

Beta strand

13 – 15

3

Beta strand

17 – 25

9

Helix

27 – 32

6

Helix

43 – 56

14

Beta strand

57 – 64

8

Helix

66 – 72

7

Turn

73 – 75

3

Helix

78 – 93

16

Beta strand

96 – 105

10

Helix

108 – 118

11

Beta strand

120 – 127

8

Helix

128 – 130

3

Helix

133 – 157

25

Beta strand

162 – 164

3

Helix

168 – 180

13

Helix

192 – 198

7

Sequences

	Sequence		Length	Mass (Da)
	O29634 [UniParc]. Last modified January 1, 1998. Version 1. Checksum: E7B07EC5BD34F7A3	FASTA	205	23,182
	10 20 30 40 50 60 MKAGIDEAGK GCVIGPLVVA GVACSDEDRL RKLGVKDSKK LSQGRREELA EEIRKICRTE 70 80 90 100 110 120 VLKVSPENLD ERMAAKTINE ILKECYAEII LRLKPEIAYV DSPDVIPERL SRELEEITGL 130 140 150 160 170 180 RVVAEHKADE KYPLVAAASI IAKVEREREI ERLKEKFGDF GSGYASDPRT REVLKEWIAS 190 200 GRIPSCVRMR WKTVSNLRQK TLDDF

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus." Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A., Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L., Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D., Quackenbush J., Lee N.H., Sutton G.G. , Gill S.R., Kirkness E.F., Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N., Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R., Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D., Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P., Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M., Smith H.O., Woese C.R., Venter J.C. Nature 390:364-370(1997) [PubMed: 9389475] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126.
[2]	"Archaeoglobus fulgidus RNase HII in DNA replication: enzymological functions and activity regulation via metal cofactors." Chai Q., Qiu J., Chapados B.R., Shen B. Biochem. Biophys. Res. Commun. 286:1073-1081(2001) [PubMed: 11527410] [Abstract] Cited for: COFACTOR, MUTAGENESIS.
[3]	"Structural biochemistry of a type 2 RNase H: RNA primer recognition and removal during DNA replication." Chapados B.R., Chai Q., Hosfield D.J., Qiu J., Shen B., Tainer J.A. J. Mol. Biol. 307:541-556(2001) [PubMed: 11254381] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH DIVALENT METAL IONS, MUTAGENESIS OF ASP-6; GLU-7; ARG-46; ASP-101; ASP-129; LYS-143; ARG-146 AND TYR-164.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE000782 Genomic DNA. Translation: AAB90620.1.

PIR

E69327.

RefSeq

NP_069455.1. NC_000917.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1I39	X-ray	1.95	A	1-205	[»]
1I3A	X-ray	2.15	A	1-205	[»]
3P83	X-ray	3.05	D/E/F	1-205	[»]

ProteinModelPortal

O29634.

SMR

O29634. Positions 1-200.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1483839.

GenomeReviews

Gene locus AF_0621 in contig AE000782_GR.

KEGG

afu:AF0621.

NMPDR

fig|224325.1.peg.614.

TIGR

AF_0621.

Phylogenomic databases

HOGENOM

HBG584843.

OMA

AYVDACD.

PhylomeDB

O29634.

ProtClustDB

CLSK2746507.

Enzyme and pathway databases

BioCyc

AFUL224325:AF_0621-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_ARCFU

Accession

Primary (citable) accession number: O29634

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	January 1, 1998
Last modified:	December 14, 2011
This is version 88 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program