Ribonucleoside-diphosphate reductase 2 subunit alpha

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P39452 (RIR3_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 117. History...

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

Documents (3) |

Third-party data

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

Names and origin

Protein names

Recommended name:
Ribonucleoside-diphosphate reductase 2 subunit alpha
EC=1.17.4.1

Alternative name(s):
R1E protein
Ribonucleotide reductase 2

Gene names

Name:	nrdE
Ordered Locus Names:	b2675, JW2650

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	714 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1E contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide.
Catalytic activity	2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H₂O = ribonucleoside diphosphate + thioredoxin.
Enzyme regulation	Under complex allosteric control mediated by deoxynucleoside triphosphates and ATP binding. 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 By similarity.
Pathway	Genetic information processing; DNA replication.
Subunit structure	Tetramer of two alpha and two beta subunits By similarity.
Sequence similarities	Belongs to the ribonucleoside diphosphate reductase large chain family.

Ontologies

Keywords
Biological process	DNA replication
Ligand	ATP-binding Nucleotide-binding
Molecular function	Oxidoreductase
PTM	Disulfide bond
Technical term	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 genetic interaction PubMed 7809142. Source: EcoliWiki nucleobase-containing small molecule interconversion Inferred from genetic interaction PubMed 7809142. Source: EcoliWiki
Cellular_component	ribonucleoside-diphosphate reductase complex Inferred from genetic interaction PubMed 7809142. Source: EcoliWiki
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed By similarity

Chain

2 – 714

713

Ribonucleoside-diphosphate reductase 2 subunit alpha

PRO_0000187224

Regions

Region

177 – 178

Substrate binding By similarity

Region

386 – 390

Substrate binding By similarity

Region

588 – 592

Substrate binding By similarity

Sites

Active site

386

Proton acceptor By similarity

Active site

388

Cysteine radical intermediate By similarity

Active site

390

Proton acceptor By similarity

Binding site

161

Substrate By similarity

Binding site

206

Substrate; via amide nitrogen By similarity

Site

178

Important for hydrogen atom transfer By similarity

Site

185

Allosteric effector binding By similarity

Site

215

Allosteric effector binding By similarity

Site

415

Important for hydrogen atom transfer By similarity

Site

692

Important for electron transfer By similarity

Site

693

Important for electron transfer By similarity

Site

709

Interacts with thioredoxin/glutaredoxin By similarity

Site

712

Interacts with thioredoxin/glutaredoxin By similarity

Amino acid modifications

Disulfide bond

178 ↔ 415

Redox-active By similarity

Experimental info

Sequence conflict

545

K → P Ref.5

Sequence conflict

548

K → H Ref.5

Sequence conflict

551 – 552

EL → AP Ref.5

Sequence conflict

556

S → R Ref.5

Sequences

Sequence

Length

Mass (Da)

Tools

P39452 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 6DAD735BF78C1B77
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FASTA

714

80,479

        10         20         30         40         50         60 
MATTTAECLT QETMDYHALN AMLNLYDSAG RIQFDKDRQA VDAFIATHVR PNSVTFSSQQ 

        70         80         90        100        110        120 
QRLNWLVNEG YYDESVLNRY SRDFVITLFT HAHTSGFRFQ TFLGAWKFYT SYTLKTFDGK 

       130        140        150        160        170        180 
RYLEDFADRV TMVALTLAQG DETLALQLTD EMLSGRFQPA TPTFLNCGKQ QRGELVSCFL 

       190        200        210        220        230        240 
LRIEDNMESI GRAVNSALQL SKRGGGVAFL LSNLREAGAP IKRIENQSSG VIPVMKMLED 

       250        260        270        280        290        300 
AFSYANQLGA RQGAGAVYLH AHHPDILRFL DTKRENADEK IRIKTLSLGV VIPDITFHLA 

       310        320        330        340        350        360 
KENAQMALFS PYDVERVYGK PFADVAISQH YDELVADERI RKKYLNARDF FQRLAEIQFE 

       370        380        390        400        410        420 
SGYPYIMYED TVNRANPIAG RINMSNLCSE ILQVNSASEY DENLDYTRTG HDISCNLGSL 

       430        440        450        460        470        480 
NIAHTMDSPD FARTVETAVR GLTAVSDMSH IRSVPSIEAG NAASHAIGLG QMNLHGYLAR 

       490        500        510        520        530        540 
EGIAYGSPEA LDFTNLYFYA ITWHALRTSM LLARERGETF AGFKQSRYAS GEYFSQYLQG 

       550        560        570        580        590        600 
NWQPKTAKVG ELFTRSGITL PTREMWAQLR DDVMRYGIYN QNLQAVPPTG SISYINHATS 

       610        620        630        640        650        660 
SIHPIVAKVE IRKEGKTGRV YYPAPFMTNE NLALYQDAYE IGAEKIIDTY AEATRHVDQG 

       670        680        690        700        710 
LSLTLFFPDT ATTRDINKAQ IYAWRKGIKT LYYIRLRQMA LEGTEIEGCV SCAL

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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. 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.
[2]	"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.
[3]	"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], SEQUENCE REVISION. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"Promoter identification and expression analysis of Salmonella typhimurium and Escherichia coli nrdEF operons encoding one of two class I ribonucleotide reductases present in both bacteria." Jordan A., Aragall E., Gibert I., Barbe J. Mol. Microbiol. 19:777-790(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-103. Strain: K12.
[5]	"Bacterial transposon Tn7 utilizes two different classes of target sites." Kubo K.M., Craig N.L. J. Bacteriol. 172:2774-2778(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 544-566.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U00096 Genomic DNA. Translation: AAC75722.1. AP009048 Genomic DNA. Translation: BAA16539.2. X79787 Genomic DNA. Translation: CAA56186.1. M31530 Genomic DNA. No translation available.
PIR	D65047.
RefSeq	NP_417161.1. NC_000913.2. YP_490890.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P39452.
SMR	P39452. Positions 13-699.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-359N.
IntAct	P39452. 8 interactions.
STRING	511145.b2675.
Proteomic databases
PaxDb	P39452.
PRIDE	P39452.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC75722; AAC75722; b2675. BAA16539; BAA16539; BAA16539.
GeneID	12930227. 947155.
KEGG	ecj:Y75_p2618. eco:b2675.
PATRIC	32120740. VBIEscCol129921_2767.
Organism-specific databases
EchoBASE	EB4158.
EcoGene	EG20257. nrdE.
Phylogenomic databases
eggNOG	COG0209.
HOGENOM	HOG000246165.
KO	K00525.
OMA	VSRIEIR.
ProtClustDB	PRK08188.
Enzyme and pathway databases
BioCyc	EcoCyc:NRDE-MONOMER. ECOL316407:JW2650-MONOMER. MetaCyc:NRDE-MONOMER.
UniPathway	UPA00326.
Gene expression databases
Genevestigator	P39452.
Family and domain databases
InterPro	IPR013346. NrdE_NrdA. IPR026459. RNR_1b_NrdE. IPR000788. RNR_lg_C. IPR013509. RNR_lsu_N. IPR013554. RNR_N. IPR008926. RNR_R1-su_N. [Graphical view]
Pfam	PF02867. Ribonuc_red_lgC. 1 hit. PF00317. Ribonuc_red_lgN. 1 hit. PF08343. RNR_N. 1 hit. [Graphical view]
PRINTS	PR01183. RIBORDTASEM1.
SUPFAM	SSF48168. Ribonucleo_red_N. 1 hit.
TIGRFAMs	TIGR02506. NrdE_NrdA. 1 hit. TIGR04170. RNR_1b_NrdE. 1 hit.
PROSITE	PS00089. RIBORED_LARGE. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RIR3_ECOLI

Accession

Primary (citable) accession number: P39452
Secondary accession number(s): P78101

Q59417

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 117 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

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

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Experimental info

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

Entry information

Relevant documents