Q8UEM4 (NRDJ_AGRT5) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Vitamin B12-dependent ribonucleotide reductase
EC=1.17.4.1

Alternative name(s):
Ribonucleoside-diphosphate reductase NrdJ

Gene names

Name:	nrdJ
Ordered Locus Names:	Atu1733
ORF Names:	AGR_C_3183

Organism

Agrobacterium tumefaciens (strain C58 / ATCC 33970) [Reference proteome] [HAMAP]

Taxonomic identifier

176299 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Rhizobiaceae › Rhizobium/Agrobacterium group › Agrobacterium › Agrobacterium tumefaciens complex › Agrobacterium fabrum

Protein attributes

Sequence length	1272 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Catalyzes the reduction of ribonucleotides to deoxyribonucleotides. May function to provide a pool of deoxyribonucleotide precursors for DNA repair during oxygen limitation and/or for immediate growth after restoration of oxygen By similarity.
Catalytic activity	2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin.
Cofactor	5'-deoxyadenosylcobalamine (coenzyme B12) By similarity.
Sequence similarities	Belongs to the ribonucleoside diphosphate reductase class-2 family.

Ontologies

Keywords
Biological process	DNA synthesis
Ligand	Cobalamin Cobalt Nucleotide-binding
Molecular function	Oxidoreductase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA replication Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	ribonucleoside-diphosphate reductase complex Inferred from electronic annotation. Source: InterPro
Molecular_function	cobalamin binding Inferred from electronic annotation. Source: UniProtKB-KW cobalt ion binding Inferred from electronic annotation. Source: InterPro nucleotide binding Inferred from electronic annotation. Source: UniProtKB-KW ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1272	1272	Vitamin B12-dependent ribonucleotide reductase		PRO_0000231657
Sites
	Active site	199	1	By similarity
	Active site	476	1	By similarity
	Active site	487	1	By similarity
	Active site	1265	1	By similarity
	Active site	1271	1	By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q8UEM4 [UniParc]. Last modified June 1, 2002. Version 1. Checksum: 3FA22DCC85AC6E2D	FASTA	1,272	139,623
	10 20 30 40 50 60 MRIERRFTKP GQSSYAEIEF RKAVSEIKNP DGSVVFRLAD IDVPAQFSQV ATDVLAQKYF 70 80 90 100 110 120 RKAGVPKLLK KVEENDVPSF LWRSVADEKA LKELPEAERY GSETDARQVF DRLAGTWAYW 130 140 150 160 170 180 GWKGKYFSTE EDASAFKDEL AYMLATQRVA PNSPQWFNTG LHWAYGIDGP GQGHFYVDPF 190 200 210 220 230 240 TGKLTKSKSA YEHPQPHACF IQSVEDDLVN EGGIMDLWVR EARLFKYGSG TGSNFSYLRG 250 260 270 280 290 300 EGEKLSGGGK SSGLMSFLKI GDRAAGAIKS GGTTRRAAKM VVVDADHPDI EAYIDWKVNE 310 320 330 340 350 360 EQKVAALVTG SKIVAKHLKA IMKACVNCEA DNGDCFDPAK NPALKREIRA AKKDMVPENY 370 380 390 400 410 420 VKRVIQFAEQ GYKDIQFKTY DTDWDSEAYL TVSGQNSNNS VSLKDDFLRA VENDGNWNLT 430 440 450 460 470 480 ARKDGKVMKT LKARDLWEKI SHAAWASADP GLHFNTTMND WHTSPAEGPI RASNPCSEYM 490 500 510 520 530 540 FLDDTACNLA SLNLLQFKDA KTKRIDIADY EHAVRLWTVV LEVSVMMAQF PSRQIAERSY 550 560 570 580 590 600 EYRTLGLGYA NIGGLLMSSG IPYDSDEGRA IAGALTAIMT GVSYATSAEM AGELGPFPSF 610 620 630 640 650 660 APNRDNMLRV IRNHRRAAHG QSEGYEGLSV NPVALIHADC TDQDLVAHAT AAWDKALELG 670 680 690 700 710 720 EKHGYRNAQT TVIAPTGTIG LVMDCDTTGI EPDFALVKFK KLAGGGYFKI INRAVPESLR 730 740 750 760 770 780 SLGYSESQIA EIEAYAVGHG NLNQAPAINP STLKAKGFTD EKIEAVNAAL KSAFDIKFVF 790 800 810 820 830 840 NQWTLGADFL KGTLKVSDEQ LSDMSFNLLD HLGFAKKDIE AANVHVCGAM TLEGAPFLKN 850 860 870 880 890 900 EHLAVFDCAN PCGKIGKRYL SVESHIRMMA AAQPFISGAI SKTINMPNDA TVEDCGAAYM 910 920 930 940 950 960 LSWKLALKAN ALYRDGSKLS QPLNASLVED EDDEDFVEEL IQQPLAQQAV TITEKIVERV 970 980 990 1000 1010 1020 IERVSREREK LPNRRQGYTQ KATVGGHKVY LRTGEFGDGR IGEIFIDMHK EGAAFRAMMN 1030 1040 1050 1060 1070 1080 NFAIAISLGL QYGVPLEEYV EAFTFTKFEP AGMVQGNDAI KNATSILDYV FRELAVSYLG 1090 1100 1110 1120 1130 1140 RHDLAHVDTS DFSNTALGKG IQEGKTNLLS TGWTRGYKPT LVSSNEGDRA ASEPKGSATA 1150 1160 1170 1180 1190 1200 APARGSANVT SFAGSAARKL EPTVAITTSE IVSFKRDYEE RAKELAEEIA EEVIDEVVQE 1210 1220 1230 1240 1250 1260 AQQTATALFS DKAAADAASA KAEAKKKENE RRMRSIAQGY TGNMCSECQN FTMVRNGTCE 1270 KCDTCGATSG CS

References

[1]

"The genome of the natural genetic engineer Agrobacterium tumefaciens C58." Wood D.W., Setubal J.C., Kaul R., Monks D.E., Kitajima J.P., Okura V.K., Zhou Y., Chen L., Wood G.E., Almeida N.F. Jr., Woo L., Chen Y., Paulsen I.T., Eisen J.A., Karp P.D., Bovee D. Sr., Chapman P., Clendenning J. , Deatherage G., Gillet W., Grant C., Kutyavin T., Levy R., Li M.-J., McClelland E., Palmieri A., Raymond C., Rouse G., Saenphimmachak C., Wu Z., Romero P., Gordon D., Zhang S., Yoo H., Tao Y., Biddle P., Jung M., Krespan W., Perry M., Gordon-Kamm B., Liao L., Kim S., Hendrick C., Zhao Z.-Y., Dolan M., Chumley F., Tingey S.V., Tomb J.-F., Gordon M.P., Olson M.V., Nester E.W. Science 294:2317-2323(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: C58 / ATCC 33970.

[2]

"Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58." Goodner B., Hinkle G., Gattung S., Miller N., Blanchard M., Qurollo B., Goldman B.S., Cao Y., Askenazi M., Halling C., Mullin L., Houmiel K., Gordon J., Vaudin M., Iartchouk O., Epp A., Liu F., Wollam C. , Allinger M., Doughty D., Scott C., Lappas C., Markelz B., Flanagan C., Crowell C., Gurson J., Lomo C., Sear C., Strub G., Cielo C., Slater S. Science 294:2323-2328(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: C58 / ATCC 33970.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE007869 Genomic DNA. Translation: AAK87503.1.
PIR	AF2789. F97568.
RefSeq	NP_354718.1. NC_003062.2.
3D structure databases
ProteinModelPortal	Q8UEM4.
ModBase	Search...
Protein-protein interaction databases
STRING	176299.Atu1733.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	1139199.
KEGG	atu:Atu1733.
PATRIC	20813235. VBIAgrTum91616_1745.
Phylogenomic databases
eggNOG	COG0209.
HOGENOM	HOG000021770.
KO	K00525.
OMA	FLWRSVP.
ProtClustDB	PRK07562.
Family and domain databases
Gene3D	1.10.10.200. 1 hit.
InterPro	IPR017856. Integrase_Zn-bd_dom-like_N. IPR013678. RNR_2_N. IPR000788. RNR_lg_C. IPR013344. RNR_NrdJ/NrdZ. IPR024434. TSCPD_dom. [Graphical view]
Pfam	PF08471. Ribonuc_red_2_N. 1 hit. PF02867. Ribonuc_red_lgC. 2 hits. PF12637. TSCPD. 1 hit. [Graphical view]
PRINTS	PR01183. RIBORDTASEM1.
TIGRFAMs	TIGR02504. NrdJ_Z. 1 hit.
ProtoNet	Search...

Entry information

Entry name

NRDJ_AGRT5

Accession

Primary (citable) accession number: Q8UEM4
Secondary accession number(s): Q7CYN2

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 4, 2006
Last sequence update:	June 1, 2002
Last modified:	May 1, 2013
This is version 75 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program