P28903 (NRDD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Anaerobic ribonucleoside-triphosphate reductase
EC=1.17.4.2

Gene names

Name:	nrdD
Ordered Locus Names:	b4238, JW4197

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	712 AA.
Sequence status	Complete.
Protein existence	Evidence 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.

Ontologies

Keywords
Ligand	ATP-binding Metal-binding Nucleotide-binding Zinc
Molecular function	Oxidoreductase
PTM	Organic radical
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	DNA replication Inferred from electronic annotation. Source: InterPro nucleobase-containing small molecule interconversion Inferred from mutant phenotype PubMed 8954104. Source: EcoliWiki
Cellular_component	anaerobic ribonucleoside-triphosphate reductase complex Inferred from mutant phenotype PubMed 8954104. Source: EcoliWiki
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW CTP reductase activity Inferred from direct assay PubMed 1460049. Source: EcoCyc zinc ion binding Inferred from direct assay PubMed 19381696. Source: EcoCyc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
nadE	P18843	1	EBI-370011,EBI-548960

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 712	712	Anaerobic ribonucleoside-triphosphate reductase		PRO_0000166683
Regions
	Domain	3 – 92	90	ATP-cone
	Domain	583 – 708	126	Glycine radical
Sites
	Metal binding	644	1	Zinc
	Metal binding	647	1	Zinc
	Metal binding	662	1	Zinc
	Metal binding	665	1	Zinc
Amino acid modifications
	Modified residue	681	1	Glycine radical By similarity
Experimental info
	Sequence conflict	257	1	G → R in AAA24226. Ref.1
	Sequence conflict	420	1	A → P in AAA24226. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P28903 [UniParc]. Last modified August 29, 2003. Version 2. Checksum: 943589D653EB0C38	FASTA	712	80,023
	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

References

	« Hide 'large scale' referencesShow '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 277:1453-1474(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.
PIR	A47331.
RefSeq	NP_418659.1. NC_000913.2. YP_492378.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P28903.
SMR	P28903. Positions 121-687.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-10358N.
IntAct	P28903. 3 interactions.
STRING	511145.b4238.
Proteomic databases
PaxDb	P28903.
PRIDE	P28903.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC77195; AAC77195; b4238. BAE78237; BAE78237; BAE78237.
GeneID	12930324. 948755.
KEGG	ecj:Y75_p4123. eco:b4238.
PATRIC	32124049. VBIEscCol129921_4369.
Organism-specific databases
EchoBASE	EB1388.
EcoGene	EG11417. nrdD.
Phylogenomic databases
eggNOG	COG1328.
HOGENOM	HOG000222474.
KO	K00527.
OMA	HKTAVFP.
ProtClustDB	PRK09263.
Enzyme and pathway databases
BioCyc	EcoCyc:RIBONUCLEOSIDE-TRIP-REDUCT-MONOMER. ECOL316407:JW4197-MONOMER. MetaCyc:RIBONUCLEOSIDE-TRIP-REDUCT-MONOMER.
Gene expression databases
Genevestigator	P28903.
Family and domain databases
InterPro	IPR005144. ATP-cone. IPR019777. Form_AcTrfase_GR_CS. IPR001150. Gly_radical. IPR012833. NrdD. [Graphical view]
Pfam	PF03477. ATP-cone. 1 hit. [Graphical view]
TIGRFAMs	TIGR02487. NrdD. 1 hit.
PROSITE	PS51161. ATP_CONE. 1 hit. PS00850. GLY_RADICAL_1. 1 hit. PS51149. GLY_RADICAL_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

NRDD_ECOLI

Accession

Primary (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:	May 1, 2013
This is version 114 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program