P0CAP6 (RIR2_EBVB9) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ribonucleoside-diphosphate reductase small chain
EC=1.17.4.1

Alternative name(s):
Ribonucleotide reductase 38 kDa subunit
Ribonucleotide reductase small subunit

Gene names

ORF Names:

BaRF1

Organism

Epstein-Barr virus (strain B95-8) (HHV-4) (Human herpesvirus 4) [Reference proteome]

Taxonomic identifier

10377 [NCBI]

Taxonomic lineage

Viruses › dsDNA viruses, no RNA stage › Herpesvirales › Herpesviridae › Gammaherpesvirinae › Lymphocryptovirus › Epstein-Barr virus (strain GD1)

Virus host

Homo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length	302 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Ribonucleoside-diphosphate reductase holoenzyme provides the precursors necessary for viral DNA synthesis. Allows virus growth in non-dividing cells, as well as reactivation from latency in infected hosts. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides By similarity.
Catalytic activity	2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin.
Cofactor	Binds 2 iron ions per subunit. Ref.4
Pathway	Genetic information processing; DNA replication.
Subunit structure	Heterotetramer composed of a homodimer of the large subunit BORF2 (R1) and a homodimer of the small subunit (R2). Larger multisubunit protein complex are also active, composed of (R1)n(R2)n By similarity.
Sequence similarities	Belongs to the ribonucleoside diphosphate reductase small chain family.

Ontologies

Keywords
Biological process	DNA replication
Ligand	Iron Metal-binding
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA replication Inferred from electronic annotation. Source: UniProtKB-UniPathway deoxyribonucleoside diphosphate metabolic process Inferred from electronic annotation. Source: InterPro
Cellular_component	ribonucleoside-diphosphate reductase complex Inferred from electronic annotation. Source: InterPro
Molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Inferred from electronic annotation. Source: EC transition metal ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 302

302

Ribonucleoside-diphosphate reductase small chain

PRO_0000190502

Sites

Active site

98

1

Ref.4

Metal binding

61

1

Iron 1

Metal binding

91

1

Iron 1

Metal binding

91

1

Iron 2

Metal binding

94

1

Iron 1

Metal binding

154

1

Iron 2

Metal binding

188

1

Iron 2

Metal binding

191

1

Iron 2

Experimental info

Sequence conflict

122

1

A → T no nucleotide entry Ref.4

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

302

Helix Strand Turn

Details...

Helix

11 – 23

13

Helix

27 – 29

3

Helix

33 – 38

6

Helix

39 – 41

3

Helix

44 – 72

29

Helix

78 – 105

28

Turn

106 – 108

3

Helix

110 – 121

12

Helix

124 – 126

3

Helix

127 – 139

13

Helix

143 – 155

13

Turn

156 – 158

3

Helix

159 – 171

13

Helix

175 – 202

28

Helix

205 – 207

3

Helix

211 – 232

22

Turn

233 – 235

3

Helix

241 – 258

18

Sequences

	Sequence		Length	Mass (Da)
	P0CAP6 [UniParc]. Last modified May 26, 2009. Version 1. Checksum: 473BF0BDFB7F0637	FASTA	302	34,359
	10 20 30 40 50 60 MSKLLYVRDH EGFACLTVET HRNRWFAAHI VLTKDCGCLK LLNERDLEFY KFLFTFLAMA 70 80 90 100 110 120 EKLVNFNIDE LVTSFESHDI DHYYTEQKAM ENVHGETYAN ILNMLFDGDR AAMNAYAEAI 130 140 150 160 170 180 MADEALQAKI SWLRDKVAAA VTLPEKILVF LLIEGIFFIS SFYSIALLRV RGLMPGICLA 190 200 210 220 230 240 NNYISRDELL HTRAASLLYN SMTAKADRPR ATWIQELFRT AVEVETAFIE ARGEGVTLVD 250 260 270 280 290 300 VRAIKQFLEA TADRILGDIG QAPLYGTPPP KDCPLTYMTS IKQTNFFEQE SSDYTMLVVD DL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"DNA sequence and expression of the B95-8 Epstein-Barr virus genome." Baer R., Bankier A.T., Biggin M.D., Deininger P.L., Farrell P.J., Gibson T.J., Hatfull G., Hudson G.S., Satchwell S.C., Seguin C., Tuffnell P.S., Barrell B.G. Nature 310:207-211(1984) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[2]	"Homology between two EBV early genes and HSV ribonucleotide reductase and 38K genes." Gibson T.J., Stockwell P., Ginsburg M., Barrell B.G. Nucleic Acids Res. 12:5087-5099(1984) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION OF PROTEIN.
[3]	"Tinkering with a viral ribonucleotide reductase." Lembo D., Brune W. Trends Biochem. Sci. 34:25-32(2009) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW.
[4]	"Mechanistic basis for Epstein-Barr Virus ribonucleotide-reductase small-subunit function." Schmitzberger F., Gurmu D., Dahlroth S.L., Nordlund P. ACS Chem. Biol. 7:1764-1764(2012) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH IRON IONS, COFACTOR, ACTIVE SITE.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

V01555 Genomic DNA. Translation: CAA24843.1.
AJ507799 Genomic DNA. Translation: CAD53406.1.

PIR

WMBE12. A00530.

RefSeq

YP_401656.1. NC_007605.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4A58	X-ray	1.68	A/B	1-302	[»]
4A5C	X-ray	2.01	A/B	1-302	[»]
4A5D	X-ray	1.79	A/B	1-302	[»]
4A5E	X-ray	2.01	A/B	1-302	[»]
4A5F	X-ray	2.14	A/B	1-302	[»]
4A5H	X-ray	1.85	A/B	1-302	[»]
4A5I	X-ray	2.05	A/B	1-302	[»]
4A5J	X-ray	1.88	A/B	1-302	[»]

ProteinModelPortal

P0CAP6.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

3783683.

Phylogenomic databases

ProtClustDB

CLSP2509600.

Enzyme and pathway databases

UniPathway

UPA00326.

Family and domain databases

Gene3D

1.10.620.20. 1 hit.

InterPro

IPR009078. Ferritin-like_SF.
IPR012348. RNR-rel.
IPR000358. RNR_small.
[Graphical view]

PANTHER

PTHR23409. PTHR23409. 1 hit.

Pfam

PF00268. Ribonuc_red_sm. 1 hit.
[Graphical view]

SUPFAM

SSF47240. Ferritin/RR_like. 1 hit.

PROSITE

PS00368. RIBORED_SMALL. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RIR2_EBVB9

Accession

Primary (citable) accession number: P0CAP6
Secondary accession number(s): P03175, Q777G0

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 26, 2009
Last sequence update:	May 26, 2009
Last modified:	May 1, 2013
This is version 31 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program