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Protein

Anaerobic ribonucleoside-triphosphate reductase

Gene

nrdD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

2'-deoxyribonucleoside triphosphate + thioredoxin disulfide + H2O = ribonucleoside triphosphate + thioredoxin.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi644 – 6441Zinc
Metal bindingi647 – 6471Zinc
Metal bindingi662 – 6621Zinc
Metal bindingi665 – 6651Zinc

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. CTP reductase activity Source: EcoCyc
  3. ribonucleoside-triphosphate reductase activity Source: EcoCyc
  4. zinc ion binding Source: EcoCyc

GO - Biological processi

  1. DNA replication Source: InterPro
  2. nucleobase-containing small molecule interconversion Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

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

Names & Taxonomyi

Protein namesi
Recommended name:
Anaerobic ribonucleoside-triphosphate reductase (EC:1.17.4.2)
Gene namesi
Name:nrdD
Ordered Locus Names:b4238, JW4197
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11417. nrdD.

Subcellular locationi

GO - Cellular componenti

  1. anaerobic ribonucleoside-triphosphate reductase complex Source: EcoliWiki
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 712712Anaerobic ribonucleoside-triphosphate reductasePRO_0000166683Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei681 – 6811Glycine radicalPROSITE-ProRule annotation

Keywords - PTMi

Organic radical

Proteomic databases

PaxDbiP28903.
PRIDEiP28903.

Expressioni

Inductioni

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.

Gene expression databases

GenevestigatoriP28903.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

DIPiDIP-10358N.
IntActiP28903. 6 interactions.
STRINGi511145.b4238.

Structurei

3D structure databases

ProteinModelPortaliP28903.
SMRiP28903. Positions 121-687.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 9290ATP-conePROSITE-ProRule annotationAdd
BLAST
Domaini583 – 708126Glycine radicalPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 ATP-cone domain.PROSITE-ProRule annotation
Contains 1 glycine radical domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG1328.
HOGENOMiHOG000222474.
InParanoidiP28903.
KOiK00527.
OMAiHKTAVFP.
OrthoDBiEOG622PMK.
PhylomeDBiP28903.

Family and domain databases

InterProiIPR005144. ATP-cone.
IPR019777. Form_AcTrfase_GR_CS.
IPR001150. Gly_radical.
IPR012833. NrdD.
[Graphical view]
PfamiPF03477. ATP-cone. 1 hit.
[Graphical view]
TIGRFAMsiTIGR02487. NrdD. 1 hit.
PROSITEiPS51161. ATP_CONE. 1 hit.
PS00850. GLY_RADICAL_1. 1 hit.
PS51149. GLY_RADICAL_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P28903-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTPHVMKRDG CKVPFKSERI KEAILRAAKA AEVDDADYCA TVAAVVSEQM
60 70 80 90 100
QGRNQVDINE IQTAVENQLM SGPYKQLARA YIEYRHDRDI EREKRGRLNQ
110 120 130 140 150
EIRGLVEQTN ASLLNENANK DSKVIPTQRD LLAGIVAKHY ARQHLLPRDV
160 170 180 190 200
VQAHERGDIH YHDLDYSPFF PMFNCMLIDL KGMLTQGFKM GNAEIEPPKS
210 220 230 240 250
ISTATAVTAQ IIAQVASHIY GGTTINRIDE VLAPFVTASY NKHRKTAEEW
260 270 280 290 300
NIPDAEGYAN SRTIKECYDA FQSLEYEVNT LHTANGQTPF VTFGFGLGTS
310 320 330 340 350
WESRLIQESI LRNRIAGLGK NRKTAVFPKL VFAIRDGLNH KKGDPNYDIK
360 370 380 390 400
QLALECASKR MYPDILNYDQ VVKVTGSFKT PMGCRSFLGV WENENGEQIH
410 420 430 440 450
DGRNNLGVIS LNLPRIALEA KGDEATFWKL LDERLVLARK ALMTRIARLE
460 470 480 490 500
GVKARVAPIL YMEGACGVRL NADDDVSEIF KNGRASISLG YIGIHETINA
510 520 530 540 550
LFGGEHVYDN EQLRAKGIAI VERLRQAVDQ WKEETGYGFS LYSTPSENLC
560 570 580 590 600
DRFCRLDTAE FGVVPGVTDK GYYTNSFHLD VEKKVNPYDK IDFEAPYPPL
610 620 630 640 650
ANGGFICYGE YPNIQHNLKA LEDVWDYSYQ HVPYYGTNTP IDECYECGFT
660 670 680 690 700
GEFECTSKGF TCPKCGNHDA SRVSVTRRVC GYLGSPDARP FNAGKQEEVK
710
RRVKHLGNGQ IG
Length:712
Mass (Da):80,023
Last modified:August 29, 2003 - v2
Checksum:i943589D653EB0C38
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti257 – 2571G → R in AAA24226 (PubMed:8421692).Curated
Sequence conflicti420 – 4201A → P in AAA24226 (PubMed:8421692).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiA47331.
RefSeqiNP_418659.1. NC_000913.3.
YP_492378.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC77195; AAC77195; b4238.
BAE78237; BAE78237; BAE78237.
GeneIDi12930324.
948755.
KEGGiecj:Y75_p4123.
eco:b4238.
PATRICi32124049. VBIEscCol129921_4369.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiA47331.
RefSeqiNP_418659.1. NC_000913.3.
YP_492378.1. NC_007779.1.

3D structure databases

ProteinModelPortaliP28903.
SMRiP28903. Positions 121-687.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-10358N.
IntActiP28903. 6 interactions.
STRINGi511145.b4238.

Proteomic databases

PaxDbiP28903.
PRIDEiP28903.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC77195; AAC77195; b4238.
BAE78237; BAE78237; BAE78237.
GeneIDi12930324.
948755.
KEGGiecj:Y75_p4123.
eco:b4238.
PATRICi32124049. VBIEscCol129921_4369.

Organism-specific databases

EchoBASEiEB1388.
EcoGeneiEG11417. nrdD.

Phylogenomic databases

eggNOGiCOG1328.
HOGENOMiHOG000222474.
InParanoidiP28903.
KOiK00527.
OMAiHKTAVFP.
OrthoDBiEOG622PMK.
PhylomeDBiP28903.

Enzyme and pathway databases

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

Miscellaneous databases

PROiP28903.

Gene expression databases

GenevestigatoriP28903.

Family and domain databases

InterProiIPR005144. ATP-cone.
IPR019777. Form_AcTrfase_GR_CS.
IPR001150. Gly_radical.
IPR012833. NrdD.
[Graphical view]
PfamiPF03477. ATP-cone. 1 hit.
[Graphical view]
TIGRFAMsiTIGR02487. NrdD. 1 hit.
PROSITEiPS51161. ATP_CONE. 1 hit.
PS00850. GLY_RADICAL_1. 1 hit.
PS51149. GLY_RADICAL_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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. 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.

Entry informationi

Entry nameiNRDD_ECOLI
AccessioniPrimary (citable) accession number: P28903
Secondary accession number(s): Q2M669
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: August 29, 2003
Last modified: January 7, 2015
This is version 126 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. 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.