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P39452

- RIR3_ECOLI

UniProt

P39452 - RIR3_ECOLI

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Protein

Ribonucleoside-diphosphate reductase 2 subunit alpha

Gene
nrdE, b2675, JW2650
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Protein inferred from homologyi

Functioni

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 activityi

2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin.

Enzyme regulationi

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.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei161 – 1611Substrate By similarity
Sitei178 – 1781Important for hydrogen atom transfer By similarity
Sitei185 – 1851Allosteric effector binding By similarity
Binding sitei206 – 2061Substrate; via amide nitrogen By similarity
Sitei215 – 2151Allosteric effector binding By similarity
Active sitei386 – 3861Proton acceptor By similarity
Active sitei388 – 3881Cysteine radical intermediate By similarity
Active sitei390 – 3901Proton acceptor By similarity
Sitei415 – 4151Important for hydrogen atom transfer By similarity
Sitei692 – 6921Important for electron transfer By similarity
Sitei693 – 6931Important for electron transfer By similarity
Sitei709 – 7091Interacts with thioredoxin/glutaredoxin By similarity
Sitei712 – 7121Interacts with thioredoxin/glutaredoxin By similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: UniProtKB-EC

GO - Biological processi

  1. deoxyribonucleotide biosynthetic process Source: EcoliWiki
  2. DNA replication Source: UniProtKB-UniPathway
  3. nucleobase-containing small molecule interconversion Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:NRDE-MONOMER.
ECOL316407:JW2650-MONOMER.
MetaCyc:NRDE-MONOMER.
UniPathwayiUPA00326.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonucleoside-diphosphate reductase 2 subunit alpha (EC:1.17.4.1)
Alternative name(s):
R1E protein
Ribonucleotide reductase 2
Gene namesi
Name:nrdE
Ordered Locus Names:b2675, JW2650
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG20257. nrdE.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: EcoliWiki
  2. ribonucleoside-diphosphate reductase complex Source: EcoliWiki
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed By similarity
Chaini2 – 714713Ribonucleoside-diphosphate reductase 2 subunit alphaPRO_0000187224Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi178 ↔ 415Redox-active By similarity

Keywords - PTMi

Disulfide bond

Proteomic databases

PaxDbiP39452.
PRIDEiP39452.

Expressioni

Gene expression databases

GenevestigatoriP39452.

Interactioni

Subunit structurei

Tetramer of two alpha and two beta subunits By similarity.

Protein-protein interaction databases

DIPiDIP-359N.
IntActiP39452. 9 interactions.
STRINGi511145.b2675.

Structurei

3D structure databases

ProteinModelPortaliP39452.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni177 – 1782Substrate binding By similarity
Regioni386 – 3905Substrate binding By similarity
Regioni588 – 5925Substrate binding By similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0209.
HOGENOMiHOG000246165.
KOiK00525.
OMAiIYYIRIR.
OrthoDBiEOG6J48HC.
PhylomeDBiP39452.

Family and domain databases

InterProiIPR013346. NrdE_NrdA.
IPR026459. RNR_1b_NrdE.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR013554. RNR_N.
IPR008926. RNR_R1-su_N.
[Graphical view]
PfamiPF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
PF08343. RNR_N. 1 hit.
[Graphical view]
PRINTSiPR01183. RIBORDTASEM1.
SUPFAMiSSF48168. SSF48168. 1 hit.
TIGRFAMsiTIGR02506. NrdE_NrdA. 1 hit.
TIGR04170. RNR_1b_NrdE. 1 hit.
PROSITEiPS00089. RIBORED_LARGE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P39452-1 [UniParc]FASTAAdd to Basket

« Hide

MATTTAECLT QETMDYHALN AMLNLYDSAG RIQFDKDRQA VDAFIATHVR    50
PNSVTFSSQQ QRLNWLVNEG YYDESVLNRY SRDFVITLFT HAHTSGFRFQ 100
TFLGAWKFYT SYTLKTFDGK RYLEDFADRV TMVALTLAQG DETLALQLTD 150
EMLSGRFQPA TPTFLNCGKQ QRGELVSCFL LRIEDNMESI GRAVNSALQL 200
SKRGGGVAFL LSNLREAGAP IKRIENQSSG VIPVMKMLED AFSYANQLGA 250
RQGAGAVYLH AHHPDILRFL DTKRENADEK IRIKTLSLGV VIPDITFHLA 300
KENAQMALFS PYDVERVYGK PFADVAISQH YDELVADERI RKKYLNARDF 350
FQRLAEIQFE SGYPYIMYED TVNRANPIAG RINMSNLCSE ILQVNSASEY 400
DENLDYTRTG HDISCNLGSL NIAHTMDSPD FARTVETAVR GLTAVSDMSH 450
IRSVPSIEAG NAASHAIGLG QMNLHGYLAR EGIAYGSPEA LDFTNLYFYA 500
ITWHALRTSM LLARERGETF AGFKQSRYAS GEYFSQYLQG NWQPKTAKVG 550
ELFTRSGITL PTREMWAQLR DDVMRYGIYN QNLQAVPPTG SISYINHATS 600
SIHPIVAKVE IRKEGKTGRV YYPAPFMTNE NLALYQDAYE IGAEKIIDTY 650
AEATRHVDQG LSLTLFFPDT ATTRDINKAQ IYAWRKGIKT LYYIRLRQMA 700
LEGTEIEGCV SCAL 714
Length:714
Mass (Da):80,479
Last modified:January 23, 2007 - v3
Checksum:i6DAD735BF78C1B77
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti545 – 5451K → P1 Publication
Sequence conflicti548 – 5481K → H1 Publication
Sequence conflicti551 – 5522EL → AP1 Publication
Sequence conflicti556 – 5561S → R1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U00096 Genomic DNA. Translation: AAC75722.1.
AP009048 Genomic DNA. Translation: BAA16539.2.
X79787 Genomic DNA. Translation: CAA56186.1.
M31530 Genomic DNA. No translation available.
PIRiD65047.
RefSeqiNP_417161.1. NC_000913.3.
YP_490890.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC75722; AAC75722; b2675.
BAA16539; BAA16539; BAA16539.
GeneIDi12930227.
947155.
KEGGiecj:Y75_p2618.
eco:b2675.
PATRICi32120740. VBIEscCol129921_2767.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U00096 Genomic DNA. Translation: AAC75722.1 .
AP009048 Genomic DNA. Translation: BAA16539.2 .
X79787 Genomic DNA. Translation: CAA56186.1 .
M31530 Genomic DNA. No translation available.
PIRi D65047.
RefSeqi NP_417161.1. NC_000913.3.
YP_490890.1. NC_007779.1.

3D structure databases

ProteinModelPortali P39452.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-359N.
IntActi P39452. 9 interactions.
STRINGi 511145.b2675.

Proteomic databases

PaxDbi P39452.
PRIDEi P39452.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC75722 ; AAC75722 ; b2675 .
BAA16539 ; BAA16539 ; BAA16539 .
GeneIDi 12930227.
947155.
KEGGi ecj:Y75_p2618.
eco:b2675.
PATRICi 32120740. VBIEscCol129921_2767.

Organism-specific databases

EchoBASEi EB4158.
EcoGenei EG20257. nrdE.

Phylogenomic databases

eggNOGi COG0209.
HOGENOMi HOG000246165.
KOi K00525.
OMAi IYYIRIR.
OrthoDBi EOG6J48HC.
PhylomeDBi P39452.

Enzyme and pathway databases

UniPathwayi UPA00326 .
BioCyci EcoCyc:NRDE-MONOMER.
ECOL316407:JW2650-MONOMER.
MetaCyc:NRDE-MONOMER.

Miscellaneous databases

PROi P39452.

Gene expression databases

Genevestigatori P39452.

Family and domain databases

InterProi 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 ]
Pfami PF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
PF08343. RNR_N. 1 hit.
[Graphical view ]
PRINTSi PR01183. RIBORDTASEM1.
SUPFAMi SSF48168. SSF48168. 1 hit.
TIGRFAMsi TIGR02506. NrdE_NrdA. 1 hit.
TIGR04170. RNR_1b_NrdE. 1 hit.
PROSITEi PS00089. RIBORED_LARGE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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.
  2. 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.

Entry informationi

Entry nameiRIR3_ECOLI
AccessioniPrimary (citable) accession number: P39452
Secondary accession number(s): P78101
, P78210, P78211, Q59417
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: January 23, 2007
Last modified: June 11, 2014
This is version 124 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Allosteric enzyme, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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