P69924 (RIR2_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ribonucleoside-diphosphate reductase 1 subunit beta
EC=1.17.4.1

Alternative name(s):
Protein B2
Protein R2
Ribonucleotide reductase 1

Gene names

Name:	nrdB
Synonyms:	ftsB
Ordered Locus Names:	b2235, JW2229

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	376 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
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. R2 contains the tyrosyl radical required for catalysis.
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	Tetramer of two alpha (R1) and two beta (R2) subunits. The B1 protein is a dimer of alpha subunits. A radical transfer pathway occurs between Tyr-123 of R2 and R1.
Miscellaneous	E.coli produces two separate class I enzymes. This one is the functional enzyme during growth. A substrate-binding catalytic site, located on R1, is formed only in the presence of the second subunit R2.
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 Direct protein sequencing 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 PubMed 13973714. Source: EcoliWiki nucleobase-containing small molecule interconversion Inferred from direct assay PubMed 4902211. Source: EcoliWiki
Cellular_component	cytosol Inferred from direct assay PubMed 16858726. Source: UniProtKB ribonucleoside-diphosphate reductase complex Inferred from direct assay PubMed 13973714. Source: EcoliWiki
Molecular_function	iron ion binding Inferred from direct assay PubMed 18314964. Source: EcoCyc ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Inferred from electronic annotation. Source: EC
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		2	EBI-555196,EBI-555196

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.5

Chain

2 – 376

375

Ribonucleoside-diphosphate reductase 1 subunit beta

PRO_0000190476

Sites

Active site

123

1

Metal binding

85

1

Iron 1

Metal binding

116

1

Iron 1

Metal binding

116

1

Iron 2

Metal binding

119

1

Iron 1

Metal binding

205

1

Iron 2

Metal binding

239

1

Iron 2

Metal binding

242

1

Iron 2

Secondary structure

1

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376

Helix Strand Turn

Details...

Helix

13 – 15

3

Beta strand

18 – 22

5

Helix

35 – 46

12

Helix

51 – 53

3

Helix

59 – 64

6

Helix

68 – 95

28

Helix

97 – 99

3

Helix

103 – 128

26

Helix

134 – 143

10

Helix

145 – 151

7

Helix

154 – 171

18

Beta strand

173 – 178

6

Beta strand

181 – 185

5

Helix

187 – 206

20

Helix

208 – 221

14

Helix

226 – 255

30

Beta strand

256 – 258

3

Helix

260 – 268

9

Helix

270 – 291

22

Turn

292 – 294

3

Helix

302 – 319

18

Helix

334 – 338

5

Helix

368 – 371

4

Sequences

	Sequence		Length	Mass (Da)
	P69924 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: BF2D9A49B643E84A	FASTA	376	43,517
	10 20 30 40 50 60 MAYTTFSQTK NDQLKEPMFF GQPVNVARYD QQKYDIFEKL IEKQLSFFWR PEEVDVSRDR 70 80 90 100 110 120 IDYQALPEHE KHIFISNLKY QTLLDSIQGR SPNVALLPLI SIPELETWVE TWAFSETIHS 130 140 150 160 170 180 RSYTHIIRNI VNDPSVVFDD IVTNEQIQKR AEGISSYYDE LIEMTSYWHL LGEGTHTVNG 190 200 210 220 230 240 KTVTVSLREL KKKLYLCLMS VNALEAIRFY VSFACSFAFA ERELMEGNAK IIRLIARDEA 250 260 270 280 290 300 LHLTGTQHML NLLRSGADDP EMAEIAEECK QECYDLFVQA AQQEKDWADY LFRDGSMIGL 310 320 330 340 350 360 NKDILCQYVE YITNIRMQAV GLDLPFQTRS NPIPWINTWL VSDNVQVAPQ EVEVSSYLVG 370 QIDSEVDTDD LSNFQL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Primary structure of the Escherichia coli ribonucleoside diphosphate reductase operon." Carlson J., Fuchs J.A., Messing J. Proc. Natl. Acad. Sci. U.S.A. 81:4294-4297(1984) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features." Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T. , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T. DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Cloning, overproduction, and purification of the B2 subunit of ribonucleoside-diphosphate reductase." Salowe S.P., Stubbe J. J. Bacteriol. 165:363-366(1986) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-21.
[6]	"Three-dimensional structure of the free radical protein of ribonucleotide reductase." Nordlund P., Sjoeberg B.-M., Eklund H. Nature 345:593-598(1990) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
[7]	"Structure and function of the Escherichia coli ribonucleotide reductase protein R2." Nordlund P., Eklund H. J. Mol. Biol. 232:123-164(1993) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
[8]	"Crystal structure of reduced protein R2 of ribonucleotide reductase: the structural basis for oxygen activation at a dinuclear iron site." Logan D.T., Su X.-D., Aaberg A., Regnstroem K., Hajdu J., Eklund H., Nordlund P. Structure 4:1053-1064(1996) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS).
[9]	"Binding of allosteric effectors to ribonucleotide reductase protein R1: reduction of active-site cysteines promotes substrate binding." Eriksson M., Uhlin U., Ramaswamy S., Ekberg M., Regnstroem K., Sjoeberg B.-M., Eklund H. Structure 5:1077-1092(1997) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS).
[10]	"Characterization of Y122F R2 of Escherichia coli ribonucleotide reductase by time-resolved physical biochemical methods and X-ray crystallography." Tong W., Burdi D., Riggs-Gelasco P., Chen S., Edmondson D., Huynh B.H., Stubbe J., Han S., Arvai A., Tainer J. Biochemistry 37:5840-5848(1998) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.46 ANGSTROMS) OF MUTANT PHE-103.
[11]	"Crystal structures of two self-hydroxylating ribonucleotide reductase protein R2 mutants: structural basis for the oxygen-insertion step of hydroxylation reactions catalyzed by diiron proteins." Logan D.T., DeMare F., Persson B.O., Slaby A., Sjoeberg B.-M., Nordlund P. Biochemistry 37:10798-10807(1998) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS).
[12]	"Crystal structures of oxidized dinuclear manganese centres in Mn-substituted class I ribonucleotide reductase from Escherichia coli: carboxylate shifts with implications for O2 activation and radical generation." Hogbom M., Andersson M.E., Nordlund P. J. Biol. Inorg. Chem. 6:315-323(2001) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.61 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

K02672 Genomic DNA. Translation: AAA24224.1.
U00096 Genomic DNA. Translation: AAC75295.1.
AP009048 Genomic DNA. Translation: BAA16054.1.

PIR

RDEC2R. A00527.

RefSeq

NP_416738.1. NC_000913.2.
YP_490474.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AV8	X-ray	2.80	A/B	2-341	[»]
1BIQ	X-ray	2.05	A/B	2-376	[»]
1JPR	X-ray	1.88	A/B	2-376	[»]
1JQC	X-ray	1.61	A/B	2-376	[»]
1MRR	X-ray	2.50	A/B	2-375	[»]
1MXR	X-ray	1.42	A/B	2-375	[»]
1PFR	X-ray	2.20	A/B	2-341	[»]
1PIM	X-ray	2.00	A/B	2-375	[»]
1PIU	X-ray	2.20	A/B	2-375	[»]
1PIY	X-ray	1.68	A/B	2-375	[»]
1PIZ	X-ray	1.90	A/B	2-375	[»]
1PJ0	X-ray	1.90	A/B	2-375	[»]
1PJ1	X-ray	1.95	A/B	2-375	[»]
1PM2	X-ray	1.80	A/B	2-339	[»]
1R1R	X-ray	2.90	D/E/F/P	357-376	[»]
1R65	X-ray	1.95	A/B	2-375	[»]
1RIB	X-ray	2.20	A/B	2-376	[»]
1RNR	X-ray	2.50	A/B	2-375	[»]
1RSR	X-ray	2.00	A/B	2-375	[»]
1RSV	X-ray	2.20	A/B	2-375	[»]
1XIK	X-ray	1.70	A/B	2-376	[»]
1YFD	X-ray	1.90	A/B	2-375	[»]
2ALX	X-ray	2.60	A	1-340	[»]
2AV8	X-ray	2.46	A/B	2-341	[»]
2R1R	X-ray	3.00	D/E/F/P	357-376	[»]
2X0X	X-ray	2.30	D/E/F/P	357-376	[»]
2XAK	X-ray	2.80	D/E/F/P	357-376	[»]
2XAP	X-ray	2.10	D/E/F/P	357-376	[»]
2XAV	X-ray	2.80	D/E/F/P	357-376	[»]
2XAW	X-ray	3.10	D/E/F/P	357-376	[»]
2XAX	X-ray	2.75	D/E/F/P	357-376	[»]
2XAY	X-ray	2.65	D/E/F/P	357-376	[»]
2XAZ	X-ray	2.60	D/E/F/P	357-376	[»]
2XO4	X-ray	2.50	D/E/F/P	357-376	[»]
2XO5	X-ray	2.70	D/E/F/P	357-376	[»]
2XOF	X-ray	2.20	A/B	2-376	[»]
3R1R	X-ray	3.00	D/E/F/P	357-376	[»]
3UUS	X-ray	5.65	E/F/G/H	2-376	[»]
4ERM	X-ray	3.95	E/F/G/H	2-376	[»]
4ERP	X-ray	4.45	E/F/G/H	2-376	[»]
4R1R	X-ray	3.20	D/E/F/P	357-376	[»]
5R1R	X-ray	3.10	D/E/F/P	357-376	[»]
6R1R	X-ray	3.10	D/E/F/P	357-376	[»]
7R1R	X-ray	3.10	D/E/F/P	357-376	[»]

ProteinModelPortal

P69924.

SMR

P69924. Positions 2-376.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-36213N.

IntAct

P69924. 12 interactions.

MINT

MINT-1269534.

STRING

511145.b2235.

Proteomic databases

PaxDb

P69924.

PRIDE

P69924.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75295; AAC75295; b2235.
BAA16054; BAA16054; BAA16054.

GeneID

12931498.
946732.

KEGG

ecj:Y75_p2197.
eco:b2235.

PATRIC

32119829. VBIEscCol129921_2324.

Organism-specific databases

EchoBASE

EB0655.

EcoGene

EG10661. nrdB.

Phylogenomic databases

eggNOG

COG0208.

HOGENOM

HOG000278087.

KO

K00526.

OMA

LEPMFLG.

ProtClustDB

PRK09101.

Enzyme and pathway databases

BioCyc

EcoCyc:NRDB-MONOMER.
ECOL316407:JW2229-MONOMER.
MetaCyc:NRDB-MONOMER.

SABIO-RK

P69924.

UniPathway

UPA00326.

Gene expression databases

Genevestigator

P69924.

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. 2 hits.
[Graphical view]

SUPFAM

SSF47240. Ferritin/RR_like. 1 hit.

PROSITE

PS00368. RIBORED_SMALL. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P69924.

Entry information

Entry name

RIR2_ECOLI

Accession

Primary (citable) accession number: P69924
Secondary accession number(s): P00453

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 91 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program