P21524 (RIR1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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

Alternative name(s):
Ribonucleotide reductase R1 subunit 1
Ribonucleotide reductase large subunit 1

Gene names

Name:	RNR1
Synonyms:	CRT7, RIR1, SDS12
Ordered Locus Names:	YER070W

Organism

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

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	888 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. Ref.7
Catalytic activity	2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin.
Enzyme regulation	Under complex allosteric control mediated by deoxynucleoside triphosphates and ATP binding to separate specificity and activation sites on the R1 subunit. The type of nucleotide bound at the specificity site determines substrate preference. It seems probable that ATP makes the enzyme reduce CDP and UDP, dGTP favors ADP reduction and dTTP favors GDP reduction. Stimulated by ATP and inhibited by dATP binding to the activity site. Inhibited by SML1. Ref.5
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. RNR1 interacts with the ribonucleotide reductase inhibitor SML1. Ref.5 Ref.6 Ref.14 Ref.15
Subcellular location	Cytoplasm Ref.9.
Induction	Cell cycle-regulated with highest activity in S phase. Moderately induced by DNA-damage. Ref.3 Ref.5
Miscellaneous	Two distinct regulatory sites have been defined: the specificity site, which controls substrate specificity, and the activity site which regulates overall catalytic activity. A substrate-binding catalytic site, located on R1, is formed only in the presence of the second subunit R2 By similarity. Present with 293000 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the ribonucleoside diphosphate reductase large chain family. Contains 1 ATP-cone domain.
Biophysicochemical properties	Kinetic parameters: Vmax=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	Cytoplasm
Ligand	ATP-binding Nucleotide-binding
Molecular function	Oxidoreductase
PTM	Disulfide bond Phosphoprotein
Technical term	3D-structure Allosteric enzyme Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA replication Inferred from electronic annotation. Source: UniProtKB-UniPathway deoxyribonucleotide biosynthetic process Inferred from sequence or structural similarity. Source: UniProtKB
Cellular_component	nucleus Inferred from direct assay PubMed 22842922. Source: SGD ribonucleoside-diphosphate reductase complex Inferred from direct assay Ref.6. Source: SGD
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW nucleotide binding Inferred from direct assay Ref.13. Source: SGD ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Inferred from sequence or structural similarity. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 888

888

Ribonucleoside-diphosphate reductase large chain 1

PRO_0000187203

Regions

Domain

1 – 92

92

ATP-cone

Region

11 – 17

7

Allosteric activator binding By similarity

Region

217 – 218

2

Substrate binding

Region

285 – 288

4

Allosteric effector binding, determines substrate specificity

Region

426 – 430

5

Substrate binding

Region

607 – 611

5

Substrate binding

Sites

Active site

426

1

Proton acceptor

Active site

428

1

Cysteine radical intermediate

Active site

430

1

Proton acceptor

Binding site

5

1

Allosteric activator By similarity

Binding site

53

1

Allosteric activator By similarity

Binding site

88

1

Allosteric activator By similarity

Binding site

202

1

Substrate

Binding site

247

1

Substrate; via amide nitrogen

Site

218

1

Important for hydrogen atom transfer By similarity

Site

226

1

Allosteric effector binding, determines substrate specificity

Site

256

1

Allosteric effector binding, determines substrate specificity

Site

443

1

Important for hydrogen atom transfer By similarity

Site

741

1

Important for electron transfer By similarity

Site

742

1

Important for electron transfer By similarity

Site

883

1

Interacts with thioredoxin/glutaredoxin By similarity

Site

886

1

Interacts with thioredoxin/glutaredoxin By similarity

Amino acid modifications

Modified residue

227

1

Phosphoserine Ref.12

Modified residue

809

1

Phosphoserine Ref.12

Modified residue

812

1

Phosphoserine Ref.12

Modified residue

816

1

Phosphoserine Ref.10 Ref.11 Ref.12

Modified residue

837

1

Phosphoserine Ref.12

Modified residue

887

1

Phosphoserine Ref.12

Disulfide bond

218 ↔ 443

Redox-active Ref.13

Experimental info

Mutagenesis

428

1

C → A: Completely abolishes reductase activity. Ref.7

Sequence conflict

329

1

F → L in CAA49151. Ref.4

Sequence conflict

587 – 589

3

TLR → NLK in CAA49150. Ref.4

Sequence conflict

666

1

Q → E no nucleotide entry Ref.3

Sequence conflict

679

1

E → Q no nucleotide entry Ref.3

Secondary structure

1

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888

Helix Strand Turn

Details...

Helix

19 – 23

5

Turn

31 – 33

3

Helix

36 – 41

6

Helix

53 – 66

14

Turn

67 – 70

4

Helix

79 – 89

11

Helix

94 – 102

9

Turn

107 – 110

4

Helix

118 – 126

9

Helix

128 – 132

5

Helix

137 – 142

6

Helix

145 – 154

10

Beta strand

158 – 163

6

Helix

167 – 179

13

Helix

183 – 194

12

Beta strand

197 – 200

4

Helix

202 – 207

6

Beta strand

210 – 212

3

Beta strand

218 – 222

5

Helix

228 – 242

15

Turn

243 – 245

3

Beta strand

247 – 251

5

Turn

263 – 266

4

Helix

272 – 285

14

Turn

288 – 291

4

Beta strand

297 – 301

5

Helix

308 – 311

4

Turn

312 – 315

4

Beta strand

317 – 319

3

Helix

321 – 323

3

Beta strand

328 – 334

7

Helix

336 – 343

8

Beta strand

347 – 351

5

Turn

353 – 355

3

Helix

359 – 361

3

Helix

364 – 376

13

Beta strand

380 – 384

5

Helix

385 – 399

15

Beta strand

403 – 406

4

Helix

407 – 412

6

Turn

415 – 419

5

Beta strand

427 – 429

3

Beta strand

441 – 443

3

Beta strand

445 – 449

5

Helix

450 – 453

4

Beta strand

454 – 456

3

Beta strand

458 – 462

5

Beta strand

463 – 465

3

Helix

467 – 487

21

Helix

493 – 502

10

Beta strand

506 – 510

5

Helix

512 – 519

8

Helix

526 – 554

29

Helix

564 – 567

4

Helix

571 – 574

4

Beta strand

581 – 583

3

Helix

585 – 595

11

Helix

611 – 615

5

Beta strand

619 – 622

4

Beta strand

627 – 629

3

Beta strand

634 – 636

3

Beta strand

638 – 641

4

Helix

643 – 651

9

Helix

657 – 664

8

Turn

665 – 668

4

Helix

678 – 683

6

Helix

687 – 689

3

Helix

692 – 703

12

Beta strand

714 – 718

5

Helix

721 – 734

14

Beta strand

737 – 741

5

Beta strand

743 – 745

3

Turn

748 – 751

4

Helix

760 – 763

4

Helix

764 – 766

3

Turn

789 – 791

3

Sequences

	Sequence		Length	Mass (Da)
	P21524 [UniParc]. Last modified February 1, 1995. Version 2. Checksum: 56BE1B077916E419	FASTA	888	99,561
	10 20 30 40 50 60 MYVYKRDGRK EPVQFDKITA RISRLCYGLD PKHIDAVKVT QRIISGVYEG VTTIELDNLA 70 80 90 100 110 120 AETCAYMTTV HPDYATLAAR IAISNLHKQT TKQFSKVVED LYRYVNAATG KPAPMISDDV 130 140 150 160 170 180 YNIVMENKDK LNSAIVYDRD FQYSYFGFKT LERSYLLRIN GQVAERPQHL IMRVALGIHG 190 200 210 220 230 240 RDIEAALETY NLMSLKYFTH ASPTLFNAGT PKPQMSSCFL VAMKEDSIEG IYDTLKECAL 250 260 270 280 290 300 ISKTAGGIGL HIHNIRSTGS YIAGTNGTSN GLIPMIRVFN NTARYVDQGG NKRPGAFALY 310 320 330 340 350 360 LEPWHADIFD FIDIRKNHGK EEIRARDLFP ALWIPDLFMK RVEENGTWTL FSPTSAPGLS 370 380 390 400 410 420 DCYGDEFEAL YTRYEKEGRG KTIKAQKLWY SILEAQTETG TPFVVYKDAC NRKSNQKNLG 430 440 450 460 470 480 VIKSSNLCCE IVEYSAPDET AVCNLASVAL PAFIETSEDG KTSTYNFKKL HEIAKVVTRN 490 500 510 520 530 540 LNRVIDRNYY PVEEARKSNM RHRPIALGVQ GLADTFMLLR LPFDSEEARL LNIQIFETIY 550 560 570 580 590 600 HASMEASCEL AQKDGPYETF QGSPASQGIL QFDMWDQKPY GMWDWDTLRK DIMKHGVRNS 610 620 630 640 650 660 LTMAPMPTAS TSQILGYNEC FEPVTSNMYS RRVLSGEFQV VNPYLLRDLV DLGIWDEGMK 670 680 690 700 710 720 QYLITQNGSI QGLPNVPQEL KDLYKTVWEI SQKTIINMAA DRSVYIDQSH SLNLFLRAPT 730 740 750 760 770 780 MGKLTSMHFY GWKKGLKTGM YYLRTQAASA AIQFTIDQKI ADQATENVAD ISNLKRPSYM 790 800 810 820 830 840 PSSASYAASD FVPAAVTANA TIPSLDSSSE ASREASPAPT GSHSLTKGMA ELNVQESKVE 850 860 870 880 VPEVPAPTKN EEKAAPIVDD EETEFDIYNS KVIACAIDNP EACEMCSG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome V." Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E., Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S., Hyman R.W. , Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X., Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y., Botstein D., Davis R.W. Nature 387:78-81(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[3]	"Two genes differentially regulated in the cell cycle and by DNA-damaging agents encode alternative regulatory subunits of ribonucleotide reductase." Elledge S.J., Davis R.W. Genes Dev. 4:740-751(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-100 AND 653-682, INDUCTION.
[4]	"Use of synthetic lethal mutants to clone and characterize a novel CTP synthetase gene in Saccharomyces cerevisiae." Ozier-Kalogeropoulos O., Adeline M.-T., Yang W.-L., Carman G.M., Lacroute F. Mol. Gen. Genet. 242:431-439(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 313-384 AND 546-590.
[5]	"Yeast Sml1, a protein inhibitor of ribonucleotide reductase." Chabes A., Domkin V., Thelander L. J. Biol. Chem. 274:36679-36683(1999) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH SML1, ENZYME REGULATION.
[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]	"Yeast DNA damage-inducible Rnr3 has a very low catalytic activity strongly stimulated after the formation of a cross-talking Rnr1/Rnr3 complex." Domkin V., Thelander L., Chabes A. J. Biol. Chem. 277:18574-18578(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF CYS-428.
[8]	"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].
[9]	"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.
[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-816, MASS SPECTROMETRY. Strain: YAL6B.
[11]	"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-816, MASS SPECTROMETRY.
[12]	"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-227; SER-809; SER-812; SER-816; SER-837 AND SER-887, MASS SPECTROMETRY.
[13]	"Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation." Xu H., Faber C., Uchiki T., Fairman J.W., Racca J., Dealwis C. Proc. Natl. Acad. Sci. U.S.A. 103:4022-4027(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEXES WITH CDP; UDP; TTP; GDP; GTP; ADP AND AMPPNP, DISULFIDE BOND.
[14]	"Structures of eukaryotic ribonucleotide reductase I define gemcitabine diphosphate binding and subunit assembly." Xu H., Faber C., Uchiki T., Racca J., Dealwis C. Proc. Natl. Acad. Sci. U.S.A. 103:4028-4033(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) IN COMPLEXES WITH GEMCITABINE DIPHOSPHATE AND R2 PEPTIDES, SUBUNIT.
[15]	"The structural basis for peptidomimetic inhibition of eukaryotic ribonucleotide reductase: a conformationally flexible pharmacophore." Xu H., Fairman J.W., Wijerathna S.R., Kreischer N.R., LaMacchia J., Helmbrecht E., Cooperman B.S., Dealwis C. J. Med. Chem. 51:4653-4659(2008) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.52 ANGSTROMS) IN COMPLEX WITH PEPTIDE INHIBITORS, SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U18813 Genomic DNA. Translation: AAB64606.1.
X69216 Genomic DNA. Translation: CAA49150.1.
X69217 Genomic DNA. Translation: CAA49151.1.
BK006939 Genomic DNA. Translation: DAA07729.1.

PIR

S50573.

RefSeq

NP_010993.1. NM_001178961.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1ZYZ	X-ray	2.90	A/B	1-888	[»]
1ZZD	X-ray	2.60	A	1-888	[»]
2CVS	X-ray	2.60	A	1-888	[»]
2CVT	X-ray	3.20	A	1-888	[»]
2CVU	X-ray	2.90	A	1-888	[»]
2CVV	X-ray	2.90	A	1-888	[»]
2CVW	X-ray	2.40	A	1-888	[»]
2CVX	X-ray	2.20	A	1-888	[»]
2CVY	X-ray	2.40	A	1-888	[»]
2EUD	X-ray	2.30	A	1-888	[»]
2ZLF	X-ray	2.59	A	1-888	[»]
2ZLG	X-ray	2.52	A	1-888	[»]
3K8T	X-ray	2.10	A	1-888	[»]
3PAW	X-ray	6.61	A/B/C/D	1-888	[»]
3RSR	X-ray	2.30	A	1-888	[»]
3S87	X-ray	2.25	A	1-888	[»]
3S8A	X-ray	2.90	A	1-888	[»]
3S8B	X-ray	2.80	A	1-888	[»]
3S8C	X-ray	2.77	A	1-888	[»]
3TB9	X-ray	2.53	A	1-888	[»]
3TBA	X-ray	2.80	A	1-888	[»]

ProteinModelPortal

P21524.

SMR

P21524. Positions 15-796.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6299N.

IntAct

P21524. 11 interactions.

MINT

MINT-680321.

STRING

4932.YER070W.

Proteomic databases

PaxDb

P21524.

PeptideAtlas

P21524.

PRIDE

P21524.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YER070W; YER070W; YER070W.

GeneID

856801.

KEGG

sce:YER070W.

Organism-specific databases

CYGD

YER070w.

SGD

S000000872. RNR1.

Phylogenomic databases

eggNOG

COG0209.

GeneTree

ENSGT00390000001372.

HOGENOM

HOG000057035.

KO

K10807.

OMA

ETIYHAS.

OrthoDB

EOG480N4T.

Enzyme and pathway databases

BioCyc

YEAST:YER070W-MONOMER.

UniPathway

UPA00326.

Gene expression databases

Genevestigator

P21524.

GermOnline

YER070W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR005144. ATP-cone.
IPR013346. NrdE_NrdA.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR008926. RNR_R1-su_N.
[Graphical view]

Pfam

PF03477. ATP-cone. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
[Graphical view]

PRINTS

PR01183. RIBORDTASEM1.

SUPFAM

SSF48168. Ribonucleo_red_N. 1 hit.

TIGRFAMs

TIGR02506. NrdE_NrdA. 1 hit.

PROSITE

PS51161. ATP_CONE. 1 hit.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P21524.

NextBio

983047.

Entry information

Entry name

RIR1_YEAST

Accession

Primary (citable) accession number: P21524
Secondary accession number(s): D3DLX5

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1991
Last sequence update:	February 1, 1995
Last modified:	May 29, 2013
This is version 136 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program