Q89MB9 (NRDJ_BRAJA) 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:	bll4274

Organism

Bradyrhizobium japonicum

Taxonomic identifier

375 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Bradyrhizobiaceae › Bradyrhizobium

Protein attributes

Sequence length	1254 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 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 – 1254	1254	Vitamin B12-dependent ribonucleotide reductase		PRO_0000231658
Sites
	Active site	199	1	By similarity
	Active site	476	1	By similarity
	Active site	487	1	By similarity
	Active site	1247	1	By similarity
	Active site	1253	1	By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q89MB9 [UniParc]. Last modified June 1, 2003. Version 1. Checksum: FF888DB9EE21A33B	FASTA	1,254	137,465
	10 20 30 40 50 60 MRIERRHTTT GQSPYAGIDF RLTTSEIRNP DGSVVFKLDN VEVPTEWSQV ASDVLAQKYF 70 80 90 100 110 120 RKAGVAARLK KVEEESVPSF LWRSVPDTEA LSQLPEKERY VSELSAKQVF DRLAGCWTYW 130 140 150 160 170 180 GWKGGYFTND EDAQAFYDEL RYMLAMQMVA PNSPQWFNTG LHWAYGIDGP GQGHYYVDPF 190 200 210 220 230 240 TGKLTKSKSA YEHPQPHACF IQGVGDDLVN EGGIMDLWVR EARLFKYGSG TGSNFSRLRG 250 260 270 280 290 300 EGEKLSGGGR SSGLMSFLKI GDRAAGAIKS GGTTRRAAKM VVVDVDHPDI ETYIDWKVKE 310 320 330 340 350 360 EQKVAALVTG SKINQKHLKA VLKACVNCEG SGDDCFDPEK NPALRREIKL ARRSLVPDNY 370 380 390 400 410 420 IKRVIQFAKQ GYKDIQFDVY DTDWDSEAYL TVSGQNSNNS VSLKDDFLRA VETDGDWNLN 430 440 450 460 470 480 ARTSKKVTKT LKARDLWEKI GYAAWASADP GLHFNTTMND WHTCKASGDI RASNPCSEYM 490 500 510 520 530 540 FLDDTACNLA SANLLTFYNV ATKHFDVEGY EHLCRLWTVV LEISVMMAQF PSKAIAELSY 550 560 570 580 590 600 EFRTLGLGYA NIGGLLMTMG LPYDSKEGRA LCGALTAVMT GITYKTSAEI AAELGTFPGY 610 620 630 640 650 660 KKNAAHMLRV IRNHRRAAHG QSNGYEALSV NPVPLDLVSC PQADLVSHAQ AAWDAALELG 670 680 690 700 710 720 EKHGYRNAQT TVIAPTGTIG LVMDCDTTGI EPDFALVKFK KLAGGGYFKI INRAVPAALR 730 740 750 760 770 780 ALGYRESEIA EIEAYAVGHG SLSNAPGINA STLKAKGFTD EAIAKVEKAL PTAFDIKFAF 790 800 810 820 830 840 NKWTFGEDFI RDQLGIGAEA IAAPGFDLLQ AVGFTKREIE AANVHICGAM TVEGAPHLKA 850 860 870 880 890 900 EHYPVFDCAN PCGKIGKRYL SVESHIRMMA AAQPFISGAI SKTINMPNDA TVEDCKSAYM 910 920 930 940 950 960 LSWKLALKAN ALYRDGSKLS QPLNSQLIAD DEDEDDAVES LYEKPMAART AQVSEKIVEK 970 980 990 1000 1010 1020 LVERIIVMRE REKMPDRRKG YTQKAVVGGH KVYLRTGEYD DGRLGEIFID MHKEGAALRS 1030 1040 1050 1060 1070 1080 FINNFAIAVS LGLQYGVPLD EYVDAFTFTR FEPAGPVQGN DSIKYATSIL DYVFRELAVS 1090 1100 1110 1120 1130 1140 YMSRFDLAHV DPTESNFDAL GKGVEEGKEP DEGHHASKLV SRGLTRSRTD NLVVMRGGST 1150 1160 1170 1180 1190 1200 AVAQGNDSAP SGGSKVTALA SHGASARVGD VLEGAVALKQ EVSHDLSPTE KLEALQWSKS 1210 1220 1230 1240 1250 GTAQTLVPSK AERRAEAKAK GYEGEMCSEC GNFTLVRNGT CMKCDTCGST TGCS

References

[1]

"Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110." Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S., Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M., Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S. DNA Res. 9:189-197(2002) [PubMed: 12597275] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: USDA 110.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BA000040 Genomic DNA. Translation: BAC49539.1.
RefSeq	NP_770914.1. NC_004463.1.
3D structure databases
ProteinModelPortal	Q89MB9.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	1053203.
GenomeReviews	Gene locus bll4274 in contig BA000040_GR.
KEGG	bja:bll4274.
NMPDR	fig|224911.1.peg.4274.
PATRIC	21192088. VBIBraJap65052_4300.
Phylogenomic databases
HOGENOM	HBG414188.
OMA	FLWRSVP.
PhylomeDB	Q89MB9.
ProtClustDB	PRK07562.
Enzyme and pathway databases
BioCyc	BJAP224911:BLL4274-MONOMER.
Family and domain databases
InterPro	IPR002876. DUF28. IPR017856. Integrase_Zn-bd_dom-like_N. IPR013344. RDP_Rdtase_AdoCbl-dep. IPR000788. Ribncl_red_lg_C. IPR013678. Ribonuc_red_2_N. IPR024434. TSCPD_dom. [Graphical view]
Gene3D	G3DSA:1.10.10.200. Intgrase_N_Zn_bd. 1 hit.
KO	K00525.
Pfam	PF08471. Ribonuc_red_2_N. 1 hit. PF02867. Ribonuc_red_lgC. 2 hits. PF12637. TSCPD. 1 hit. [Graphical view]
PRINTS	PR01183. RIBORDTASEM1.
SUPFAM	SSF75625. DUF28. 1 hit.
TIGRFAMs	TIGR02504. NrdJ_Z. 1 hit.
ProtoNet	Search...

Entry information

Entry name

NRDJ_BRAJA

Accession

Primary (citable) accession number: Q89MB9

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 4, 2006
Last sequence update:	June 1, 2003
Last modified:	January 25, 2012
This is version 59 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program