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P28903 (NRDD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 123. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | 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:
Anaerobic ribonucleoside-triphosphate reductase

EC=1.17.4.2
Gene names
Name:nrdD
Ordered Locus Names:b4238, JW4197
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length712 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Catalytic activity

2'-deoxyribonucleoside triphosphate + thioredoxin disulfide + H2O = ribonucleoside triphosphate + thioredoxin. Ref.7

Subunit structure

Tetramer consisting of 2 alpha (NrdD) and 2 beta (NrdG) subunits.

Induction

Probably by NrdD-activating enzyme under anaerobic conditions by generation of an organic free radical. Exposure of activated NrdD to oxygen may result in cleavage at the glycine residue harboring its organic radical with loss of the 31 C-terminal AA.

Sequence similarities

Belongs to the anaerobic ribonucleoside-triphosphate reductase family.

Contains 1 ATP-cone domain.

Contains 1 glycine radical domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 712712Anaerobic ribonucleoside-triphosphate reductase
PRO_0000166683

Regions

Domain3 – 9290ATP-cone
Domain583 – 708126Glycine radical

Sites

Metal binding6441Zinc
Metal binding6471Zinc
Metal binding6621Zinc
Metal binding6651Zinc

Amino acid modifications

Modified residue6811Glycine radical By similarity

Experimental info

Sequence conflict2571G → R in AAA24226. Ref.1
Sequence conflict4201A → P in AAA24226. Ref.1

Sequences

Sequence LengthMass (Da)Tools
P28903 [UniParc].

Last modified August 29, 2003. Version 2.
Checksum: 943589D653EB0C38

FASTA71280,023
        10         20         30         40         50         60 
MTPHVMKRDG CKVPFKSERI KEAILRAAKA AEVDDADYCA TVAAVVSEQM QGRNQVDINE 

        70         80         90        100        110        120 
IQTAVENQLM SGPYKQLARA YIEYRHDRDI EREKRGRLNQ EIRGLVEQTN ASLLNENANK 

       130        140        150        160        170        180 
DSKVIPTQRD LLAGIVAKHY ARQHLLPRDV VQAHERGDIH YHDLDYSPFF PMFNCMLIDL 

       190        200        210        220        230        240 
KGMLTQGFKM GNAEIEPPKS ISTATAVTAQ IIAQVASHIY GGTTINRIDE VLAPFVTASY 

       250        260        270        280        290        300 
NKHRKTAEEW NIPDAEGYAN SRTIKECYDA FQSLEYEVNT LHTANGQTPF VTFGFGLGTS 

       310        320        330        340        350        360 
WESRLIQESI LRNRIAGLGK NRKTAVFPKL VFAIRDGLNH KKGDPNYDIK QLALECASKR 

       370        380        390        400        410        420 
MYPDILNYDQ VVKVTGSFKT PMGCRSFLGV WENENGEQIH DGRNNLGVIS LNLPRIALEA 

       430        440        450        460        470        480 
KGDEATFWKL LDERLVLARK ALMTRIARLE GVKARVAPIL YMEGACGVRL NADDDVSEIF 

       490        500        510        520        530        540 
KNGRASISLG YIGIHETINA LFGGEHVYDN EQLRAKGIAI VERLRQAVDQ WKEETGYGFS 

       550        560        570        580        590        600 
LYSTPSENLC DRFCRLDTAE FGVVPGVTDK GYYTNSFHLD VEKKVNPYDK IDFEAPYPPL 

       610        620        630        640        650        660 
ANGGFICYGE YPNIQHNLKA LEDVWDYSYQ HVPYYGTNTP IDECYECGFT GEFECTSKGF 

       670        680        690        700        710 
TCPKCGNHDA SRVSVTRRVC GYLGSPDARP FNAGKQEEVK RRVKHLGNGQ IG 

« Hide

References

« Hide 'large scale' references
[1]"A possible glycine radical in anaerobic ribonucleotide reductase from Escherichia coli: nucleotide sequence of the cloned nrdD gene."
Sun X., Harder J., Krook M., Joernvall H., Sjoeberg B.-M., Reichard P.
Proc. Natl. Acad. Sci. U.S.A. 90:577-581(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[2]"Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[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 277:1453-1462(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]"Trehalose-6-phosphate hydrolase of Escherichia coli."
Rimmele M., Boos W.
J. Bacteriol. 176:5654-5664(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-229.
Strain: K12.
[6]"Generation of the glycyl radical of the anaerobic Escherichia coli ribonucleotide reductase requires a specific activating enzyme."
Sun X., Eliasson R., Pontis E., Andersson J., Buist G., Sjoeberg B.-M., Reichard P.
J. Biol. Chem. 270:2443-2446(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 703-712.
Strain: K12.
[7]"A metal-binding site in the catalytic subunit of anaerobic ribonucleotide reductase."
Logan D.T., Mulliez E., Larsson K.-M., Bodevin S., Atta M., Garnaud P.E., Sjoeberg B.-M., Fontecave M.
Proc. Natl. Acad. Sci. U.S.A. 100:3826-3831(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF CYSTEINE RESIDUES, ENZYME ACTIVITY.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
L06097 Genomic DNA. Translation: AAA24226.1.
U14003 Genomic DNA. Translation: AAA97135.1.
U00096 Genomic DNA. Translation: AAC77195.1.
AP009048 Genomic DNA. Translation: BAE78237.1.
U06195 Genomic DNA. Translation: AAC43383.1.
Z46865 Genomic DNA. Translation: CAA86938.1.
PIRA47331.
RefSeqNP_418659.1. NC_000913.3.
YP_492378.1. NC_007779.1.

3D structure databases

ProteinModelPortalP28903.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-10358N.
IntActP28903. 6 interactions.
STRING511145.b4238.

Proteomic databases

PaxDbP28903.
PRIDEP28903.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC77195; AAC77195; b4238.
BAE78237; BAE78237; BAE78237.
GeneID12930324.
948755.
KEGGecj:Y75_p4123.
eco:b4238.
PATRIC32124049. VBIEscCol129921_4369.

Organism-specific databases

EchoBASEEB1388.
EcoGeneEG11417. nrdD.

Phylogenomic databases

eggNOGCOG1328.
HOGENOMHOG000222474.
KOK00527.
OMAKRRVKHM.
OrthoDBEOG622PMK.
PhylomeDBP28903.

Enzyme and pathway databases

BioCycEcoCyc:RIBONUCLEOSIDE-TRIP-REDUCT-MONOMER.
ECOL316407:JW4197-MONOMER.
MetaCyc:RIBONUCLEOSIDE-TRIP-REDUCT-MONOMER.
SABIO-RKP28903.

Gene expression databases

GenevestigatorP28903.

Family and domain databases

InterProIPR005144. ATP-cone.
IPR019777. Form_AcTrfase_GR_CS.
IPR001150. Gly_radical.
IPR012833. NrdD.
[Graphical view]
PfamPF03477. ATP-cone. 1 hit.
[Graphical view]
TIGRFAMsTIGR02487. NrdD. 1 hit.
PROSITEPS51161. ATP_CONE. 1 hit.
PS00850. GLY_RADICAL_1. 1 hit.
PS51149. GLY_RADICAL_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

PROP28903.

Entry information

Entry nameNRDD_ECOLI
AccessionPrimary (citable) accession number: P28903
Secondary accession number(s): Q2M669
Entry history
Integrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: August 29, 2003
Last modified: July 9, 2014
This is version 123 of the entry and version 2 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

Escherichia coli

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