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Protein

Ribonucleoside-diphosphate reductase 2 subunit alpha

Gene

nrdE

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: 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).By similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei161 – 1611SubstrateBy similarity
Sitei178 – 1781Important for hydrogen atom transferBy similarity
Sitei185 – 1851Allosteric effector bindingBy similarity
Binding sitei206 – 2061Substrate; via amide nitrogenBy similarity
Sitei215 – 2151Allosteric effector bindingBy similarity
Active sitei386 – 3861Proton acceptorBy similarity
Active sitei388 – 3881Cysteine radical intermediateBy similarity
Active sitei390 – 3901Proton acceptorBy similarity
Sitei415 – 4151Important for hydrogen atom transferBy similarity
Sitei692 – 6921Important for electron transferBy similarity
Sitei693 – 6931Important for electron transferBy similarity
Sitei709 – 7091Interacts with thioredoxin/glutaredoxinBy similarity
Sitei712 – 7121Interacts with thioredoxin/glutaredoxinBy 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.
BRENDAi1.17.4.1. 2026.
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 Componenti: Chromosome UP000000625 Componenti: 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 – 11RemovedBy similarity
Chaini2 – 714713Ribonucleoside-diphosphate reductase 2 subunit alphaPRO_0000187224Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi178 ↔ 415Redox-activeBy 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

IntActiP39452. 9 interactions.
STRINGi511145.b2675.

Structurei

3D structure databases

ProteinModelPortaliP39452.
SMRiP39452. Positions 13-699.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

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

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0209.
HOGENOMiHOG000246165.
InParanoidiP39452.
KOiK00525.
OMAiIYFYTVT.
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

        10         20         30         40         50
MATTTAECLT QETMDYHALN AMLNLYDSAG RIQFDKDRQA VDAFIATHVR
60 70 80 90 100
PNSVTFSSQQ QRLNWLVNEG YYDESVLNRY SRDFVITLFT HAHTSGFRFQ
110 120 130 140 150
TFLGAWKFYT SYTLKTFDGK RYLEDFADRV TMVALTLAQG DETLALQLTD
160 170 180 190 200
EMLSGRFQPA TPTFLNCGKQ QRGELVSCFL LRIEDNMESI GRAVNSALQL
210 220 230 240 250
SKRGGGVAFL LSNLREAGAP IKRIENQSSG VIPVMKMLED AFSYANQLGA
260 270 280 290 300
RQGAGAVYLH AHHPDILRFL DTKRENADEK IRIKTLSLGV VIPDITFHLA
310 320 330 340 350
KENAQMALFS PYDVERVYGK PFADVAISQH YDELVADERI RKKYLNARDF
360 370 380 390 400
FQRLAEIQFE SGYPYIMYED TVNRANPIAG RINMSNLCSE ILQVNSASEY
410 420 430 440 450
DENLDYTRTG HDISCNLGSL NIAHTMDSPD FARTVETAVR GLTAVSDMSH
460 470 480 490 500
IRSVPSIEAG NAASHAIGLG QMNLHGYLAR EGIAYGSPEA LDFTNLYFYA
510 520 530 540 550
ITWHALRTSM LLARERGETF AGFKQSRYAS GEYFSQYLQG NWQPKTAKVG
560 570 580 590 600
ELFTRSGITL PTREMWAQLR DDVMRYGIYN QNLQAVPPTG SISYINHATS
610 620 630 640 650
SIHPIVAKVE IRKEGKTGRV YYPAPFMTNE NLALYQDAYE IGAEKIIDTY
660 670 680 690 700
AEATRHVDQG LSLTLFFPDT ATTRDINKAQ IYAWRKGIKT LYYIRLRQMA
710
LEGTEIEGCV SCAL
Length:714
Mass (Da):80,479
Last modified:January 23, 2007 - v3
Checksum:i6DAD735BF78C1B77
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti545 – 5451K → P (PubMed:2158980).Curated
Sequence conflicti548 – 5481K → H (PubMed:2158980).Curated
Sequence conflicti551 – 5522EL → AP (PubMed:2158980).Curated
Sequence conflicti556 – 5561S → R (PubMed:2158980).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

ProteinModelPortaliP39452.
SMRiP39452. Positions 13-699.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP39452. 9 interactions.
STRINGi511145.b2675.

Proteomic databases

PaxDbiP39452.
PRIDEiP39452.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EchoBASEiEB4158.
EcoGeneiEG20257. nrdE.

Phylogenomic databases

eggNOGiCOG0209.
HOGENOMiHOG000246165.
InParanoidiP39452.
KOiK00525.
OMAiIYFYTVT.
OrthoDBiEOG6J48HC.
PhylomeDBiP39452.

Enzyme and pathway databases

UniPathwayiUPA00326.
BioCyciEcoCyc:NRDE-MONOMER.
ECOL316407:JW2650-MONOMER.
MetaCyc:NRDE-MONOMER.
BRENDAi1.17.4.1. 2026.

Miscellaneous databases

PROiP39452.

Gene expression databases

GenevestigatoriP39452.

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]
ProtoNetiSearch...

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(1996) [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(2005) [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(1995) [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(1989) [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: April 1, 2015
This is version 128 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.