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P39452 (RIR3_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 122. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length714 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceInferred 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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed By similarity
Chain2 – 714713Ribonucleoside-diphosphate reductase 2 subunit alpha
PRO_0000187224

Regions

Region177 – 1782Substrate binding By similarity
Region386 – 3905Substrate binding By similarity
Region588 – 5925Substrate binding By similarity

Sites

Active site3861Proton acceptor By similarity
Active site3881Cysteine radical intermediate By similarity
Active site3901Proton acceptor By similarity
Binding site1611Substrate By similarity
Binding site2061Substrate; via amide nitrogen By similarity
Site1781Important for hydrogen atom transfer By similarity
Site1851Allosteric effector binding By similarity
Site2151Allosteric effector binding By similarity
Site4151Important for hydrogen atom transfer By similarity
Site6921Important for electron transfer By similarity
Site6931Important for electron transfer By similarity
Site7091Interacts with thioredoxin/glutaredoxin By similarity
Site7121Interacts with thioredoxin/glutaredoxin By similarity

Amino acid modifications

Disulfide bond178 ↔ 415Redox-active By similarity

Experimental info

Sequence conflict5451K → P Ref.5
Sequence conflict5481K → H Ref.5
Sequence conflict551 – 5522EL → AP Ref.5
Sequence conflict5561S → R Ref.5

Sequences

Sequence LengthMass (Da)Tools
P39452 [UniParc].

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

FASTA71480,479
        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' 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. expand/collapse author list , 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]"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 277:1453-1462(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.
PIRD65047.
RefSeqNP_417161.1. NC_000913.3.
YP_490890.1. NC_007779.1.

3D structure databases

ProteinModelPortalP39452.
SMRP39452. Positions 13-699.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-359N.
IntActP39452. 9 interactions.
STRING511145.b2675.

Proteomic databases

PaxDbP39452.
PRIDEP39452.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75722; AAC75722; b2675.
BAA16539; BAA16539; BAA16539.
GeneID12930227.
947155.
KEGGecj:Y75_p2618.
eco:b2675.
PATRIC32120740. VBIEscCol129921_2767.

Organism-specific databases

EchoBASEEB4158.
EcoGeneEG20257. nrdE.

Phylogenomic databases

eggNOGCOG0209.
HOGENOMHOG000246165.
KOK00525.
OMAIHPIVSR.
OrthoDBEOG6J48HC.
PhylomeDBP39452.
ProtClustDBPRK08188.

Enzyme and pathway databases

BioCycEcoCyc:NRDE-MONOMER.
ECOL316407:JW2650-MONOMER.
MetaCyc:NRDE-MONOMER.
UniPathwayUPA00326.

Gene expression databases

GenevestigatorP39452.

Family and domain databases

InterProIPR013346. NrdE_NrdA.
IPR026459. RNR_1b_NrdE.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR013554. RNR_N.
IPR008926. RNR_R1-su_N.
[Graphical view]
PfamPF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
PF08343. RNR_N. 1 hit.
[Graphical view]
PRINTSPR01183. RIBORDTASEM1.
SUPFAMSSF48168. SSF48168. 1 hit.
TIGRFAMsTIGR02506. NrdE_NrdA. 1 hit.
TIGR04170. RNR_1b_NrdE. 1 hit.
PROSITEPS00089. RIBORED_LARGE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

PROP39452.

Entry information

Entry nameRIR3_ECOLI
AccessionPrimary (citable) accession number: P39452
Secondary accession number(s): P78101 expand/collapse secondary AC list , P78210, P78211, Q59417
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: January 23, 2007
Last modified: April 16, 2014
This is version 122 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

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