Ribonucleoside-diphosphate reductase small chain 1 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P09938 (RIR2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 147. History...

Clusters with 100%, 90%, 50% identity |

Documents (5) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Ribonucleoside-diphosphate reductase small chain 1
EC=1.17.4.1

Alternative name(s):
Ribonucleotide reductase R2 subunit 1
Ribonucleotide reductase small subunit 1

Gene names

Name:	RNR2
Synonyms:	CRT6
Ordered Locus Names:	YJL026W
ORF Names:	J1271

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length	399 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. RNR2 provides the diiron-tyrosyl radical center. Ref.5
Catalytic activity	2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H₂O = ribonucleoside diphosphate + thioredoxin.
Cofactor	Binds 2 iron ions per subunit.
Pathway	Genetic information processing; DNA replication.
Subunit structure	Heterotetramer of two large (R1) and two small (R2) subunits. S.cerevisiae has two different R1 subunits (RNR1 and RNR3) and two different R2 subunits (RNR2 and RNR4). The functional form of the small subunits is a RNR2-RNR4 heterodimer, where RNR2 provides the iron-radical center and RNR4 is required for proper folding of RNR2 and assembly with the large subunits. Under normal growth conditions, the active form of the large subunits is a homodimer of the constitutively expressed RNR1. In damaged cells or cells arrested for DNA synthesis, the reductase consists of multiple species because of the association of the small subunits (RNR2-RNR4) with either the RNR1 homodimer or a heterodimer of RNR1 and the damage-inducible RNR3. Interacts with DIF1. Ref.5 Ref.6 Ref.14
Subcellular location	Nucleus. Note: Found predominantly in the nucleus under normal growth conditions and is redistributed to the cytoplasm in damaged cells in a DNA replication and damage checkpoint-dependent manner. Nuclear localization is mediated by DIF1. Ref.8 Ref.14
Induction	Induced by DNA-damage. Ref.1 Ref.2
Miscellaneous	Present with 538 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the ribonucleoside diphosphate reductase small chain family.
Biophysicochemical properties	Kinetic parameters: V_max=2250 nmol/min/mg enzyme for cytidine 5'-diphosphate Ref.6 Temperature dependence: Optimum temperature is 30 degrees Celsius.

Ontologies

Keywords
Biological process	DNA replication
Cellular component	Nucleus
Ligand	Iron Metal-binding
Molecular function	Oxidoreductase
PTM	Phosphoprotein
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 deoxyribonucleotide biosynthetic process Inferred from direct assay Ref.5 PubMed 5459124. Source: SGD
Cellular_component	nucleus Inferred from direct assay Ref.8. Source: SGD ribonucleoside-diphosphate reductase complex Inferred from direct assay Ref.6. Source: SGD
Molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Inferred from direct assay Ref.5. Source: SGD transition metal ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
RNR4	P49723	6	EBI-15240,EBI-15251
WTM2	Q12206	3	EBI-15240,EBI-20571

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 399

399

Ribonucleoside-diphosphate reductase small chain 1

PRO_0000190464

Sites

Active site

183

Metal binding

145

Iron 1

Metal binding

176

Iron 1

Metal binding

176

Iron 2

Metal binding

179

Iron 1

Metal binding

239

Iron 2

Metal binding

273

Iron 2

Metal binding

276

Iron 2

Amino acid modifications

Modified residue

Phosphoserine Ref.15

Modified residue

Phosphoserine Ref.9 Ref.10 Ref.11 Ref.13 Ref.15

Modified residue

Phosphoserine Ref.13 Ref.15

Modified residue

Phosphoserine Ref.15

Modified residue

Phosphoserine Ref.12

Modified residue

374

Phosphoserine Ref.13 Ref.15

Experimental info

Sequence conflict

101 – 103

Missing in AAA34987. Ref.1

Sequence conflict

111

E → ETAE Ref.1

Secondary structure

399

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P09938 [UniParc].

Last modified November 1, 1995. Version 2.
Checksum: DB98028408292042
Show »

FASTA

399

46,147

        10         20         30         40         50         60 
MPKETPSKAA ADALSDLEIK DSKSNLNKEL ETLREENRVK SDMLKEKLSK DAENHKAYLK 

        70         80         90        100        110        120 
SHQVHRHKLK EMEKEEPLLN EDKERTVLFP IKYHEIWQAY KRAEASFWTA EEIDLSKDIH 

       130        140        150        160        170        180 
DWNNRMNENE RFFISRVLAF FAASDGIVNE NLVENFSTEV QIPEAKSFYG FQIMIENIHS 

       190        200        210        220        230        240 
ETYSLLIDTY IKDPKESEFL FNAIHTIPEI GEKAEWALRW IQDADALFGE RLVAFASIEG 

       250        260        270        280        290        300 
VFFSGSFASI FWLKKRGMMP GLTFSNELIC RDEGLHTDFA CLLFAHLKNK PDPAIVEKIV 

       310        320        330        340        350        360 
TEAVEIEQRY FLDALPVALL GMNADLMNQY VEFVADRLLV AFGNKKYYKV ENPFDFMENI 

       370        380        390 
SLAGKTNFFE KRVSDYQKAG VMSKSTKQEA GAFTFNEDF

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification and isolation of the gene encoding the small subunit of ribonucleotide reductase from Saccharomyces cerevisiae: DNA damage-inducible gene required for mitotic viability." Elledge S.J., Davis R.W. Mol. Cell. Biol. 7:2783-2793(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], INDUCTION.
[2]	"Identification of the gene for the yeast ribonucleotide reductase small subunit and its inducibility by methyl methanesulfonate." Hurd H.K., Roberts C.W., Roberts J.W. Mol. Cell. Biol. 7:3673-3677(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], INDUCTION.
[3]	"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X." Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K. Karpfinger-Hartl L. EMBO J. 15:2031-2049(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"Purification of ribonucleotide reductase subunits Y1, Y2, Y3, and Y4 from yeast: Y4 plays a key role in diiron cluster assembly." Nguyen H.-H.T., Ge J., Perlstein D.L., Stubbe J. Proc. Natl. Acad. Sci. U.S.A. 96:12339-12344(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBUNIT.
[6]	"Yeast ribonucleotide reductase has a heterodimeric iron-radical-containing subunit." Chabes A., Domkin V., Larsson G., Liu A., Graeslund A., Wijmenga S., Thelander L. Proc. Natl. Acad. Sci. U.S.A. 97:2474-2479(2000) [PubMed] [Europe PMC] [Abstract] Cited for: SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES.
[7]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[8]	"Subcellular localization of yeast ribonucleotide reductase regulated by the DNA replication and damage checkpoint pathways." Yao R., Zhang Z., An X., Bucci B., Perlstein D.L., Stubbe J., Huang M. Proc. Natl. Acad. Sci. U.S.A. 100:6628-6633(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
[9]	"A proteomics approach to understanding protein ubiquitination." Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G., Roelofs J., Finley D., Gygi S.P. Nat. Biotechnol. 21:921-926(2003) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-15, MASS SPECTROMETRY. Strain: SUB592.
[10]	"Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway." Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N. Mol. Cell. Proteomics 4:310-327(2005) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-15, MASS SPECTROMETRY. Strain: YAL6B.
[11]	"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae." Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P. J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-15, MASS SPECTROMETRY. Strain: ADR376.
[12]	"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry." Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F. Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-41, MASS SPECTROMETRY.
[13]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-15; SER-22 AND SER-374, MASS SPECTROMETRY.
[14]	"Dif1 is a DNA-damage-regulated facilitator of nuclear import for ribonucleotide reductase." Lee Y.D., Wang J., Stubbe J., Elledge S.J. Mol. Cell 32:70-80(2008) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION, INTERACTION WITH DIF1 AND RNR4.
[15]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-7; SER-15; SER-22; SER-24 AND SER-374, MASS SPECTROMETRY.
[16]	"Structure of the yeast ribonucleotide reductase Y2Y4 heterodimer." Voegtli W.C., Ge J., Perlstein D.L., Stubbe J., Rosenzweig A.C. Proc. Natl. Acad. Sci. U.S.A. 98:10073-10078(2001) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
[17]	"Structures of the yeast ribonucleotide reductase Rnr2 and Rnr4 homodimers." Sommerhalter M., Voegtli W.C., Perlstein D.L., Ge J., Stubbe J., Rosenzweig A.C. Biochemistry 43:7736-7742(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M17221 Genomic DNA. Translation: AAA34987.1.
M17789 Genomic DNA. Translation: AAA34988.1.
Z49301 Genomic DNA. Translation: CAA89317.1.
BK006943 Genomic DNA. Translation: DAA08772.1.

PIR

A26916.

RefSeq

NP_012508.1. NM_001181460.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1JK0	X-ray	2.80	A	1-399	[»]
1SMQ	X-ray	3.10	A/B/C/D	1-399	[»]
2CVY	X-ray	2.40	B	391-399	[»]

DisProt

DP00487.

ProteinModelPortal

P09938.

SMR

P09938. Positions 26-359.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-5671N.

IntAct

P09938. 27 interactions.

MINT

MINT-547064.

STRING

4932.YJL026W.

Proteomic databases

PaxDb

P09938.

PeptideAtlas

P09938.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YJL026W; YJL026W; YJL026W.

GeneID

853427.

KEGG

sce:YJL026W.

Organism-specific databases

CYGD

YJL026w.

SGD

S000003563. RNR2.

Phylogenomic databases

eggNOG

COG0208.

GeneTree

ENSGT00390000013305.

HOGENOM

HOG000255975.

K10808.

OMA

ICNRRCQ.

OrthoDB

EOG4QZBVT.

Enzyme and pathway databases

UniPathway

UPA00326.

Gene expression databases

Genevestigator

P09938.

GermOnline

YJL026W. Saccharomyces cerevisiae.

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...

Other

EvolutionaryTrace

P09938.

NextBio

973962.

Entry information

Entry name

RIR2_YEAST

Accession

Primary (citable) accession number: P09938
Secondary accession number(s): D6VWF6

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1989
Last sequence update:	November 1, 1995
Last modified:	May 1, 2013
This is version 147 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome X

Yeast (Saccharomyces cerevisiae) chromosome X: entries and gene names

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Sites

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents