NRDJ_BRADU
ID NRDJ_BRADU Reviewed; 1254 AA.
AC Q89MB9;
DT 04-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 111.
DE RecName: Full=Vitamin B12-dependent ribonucleotide reductase;
DE EC=1.17.4.1;
DE AltName: Full=Ribonucleoside-diphosphate reductase NrdJ;
GN Name=nrdJ; OrderedLocusNames=bll4274;
OS Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 /
OS NBRC 14792 / USDA 110).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Bradyrhizobiaceae; Bradyrhizobium.
OX NCBI_TaxID=224911;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110;
RX PubMed=12597275; DOI=10.1093/dnares/9.6.189;
RA Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S.,
RA Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M.,
RA Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S.;
RT "Complete genomic sequence of nitrogen-fixing symbiotic bacterium
RT Bradyrhizobium japonicum USDA110.";
RL DNA Res. 9:189-197(2002).
CC -!- FUNCTION: Catalyzes the reduction of ribonucleotides to
CC deoxyribonucleotides. May function to provide a pool of
CC deoxyribonucleotide precursors for DNA repair during oxygen limitation
CC and/or for immediate growth after restoration of oxygen (By
CC similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[thioredoxin]-disulfide + a 2'-deoxyribonucleoside 5'-
CC diphosphate + H2O = [thioredoxin]-dithiol + a ribonucleoside 5'-
CC diphosphate; Xref=Rhea:RHEA:23252, Rhea:RHEA-COMP:10698, Rhea:RHEA-
CC COMP:10700, ChEBI:CHEBI:15377, ChEBI:CHEBI:29950, ChEBI:CHEBI:50058,
CC ChEBI:CHEBI:57930, ChEBI:CHEBI:73316; EC=1.17.4.1;
CC -!- COFACTOR:
CC Name=adenosylcob(III)alamin; Xref=ChEBI:CHEBI:18408;
CC Evidence={ECO:0000250};
CC Note=5'-deoxyadenosylcobalamine (coenzyme B12). {ECO:0000250};
CC -!- SIMILARITY: Belongs to the ribonucleoside diphosphate reductase class-2
CC family. {ECO:0000305}.
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DR EMBL; BA000040; BAC49539.1; -; Genomic_DNA.
DR RefSeq; NP_770914.1; NC_004463.1.
DR RefSeq; WP_011087047.1; NZ_CP011360.1.
DR AlphaFoldDB; Q89MB9; -.
DR SMR; Q89MB9; -.
DR STRING; 224911.27352536; -.
DR EnsemblBacteria; BAC49539; BAC49539; BAC49539.
DR GeneID; 64024005; -.
DR KEGG; bja:bll4274; -.
DR PATRIC; fig|224911.44.peg.4013; -.
DR eggNOG; COG0209; Bacteria.
DR HOGENOM; CLU_000404_0_1_5; -.
DR InParanoid; Q89MB9; -.
DR OMA; WACADPG; -.
DR PhylomeDB; Q89MB9; -.
DR Proteomes; UP000002526; Chromosome.
DR GO; GO:0031419; F:cobalamin binding; IEA:UniProtKB-KW.
DR GO; GO:0050897; F:cobalt ion binding; IEA:InterPro.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0004748; F:ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor; IBA:GO_Central.
DR GO; GO:0071897; P:DNA biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0006260; P:DNA replication; IEA:InterPro.
DR CDD; cd02888; RNR_II_dimer; 1.
DR InterPro; IPR013678; RNR_2_N.
DR InterPro; IPR000788; RNR_lg_C.
DR InterPro; IPR013344; RNR_NrdJ/NrdZ.
DR InterPro; IPR029072; YebC-like.
DR Pfam; PF08471; Ribonuc_red_2_N; 1.
DR Pfam; PF02867; Ribonuc_red_lgC; 2.
DR PRINTS; PR01183; RIBORDTASEM1.
DR SUPFAM; SSF75625; SSF75625; 1.
DR TIGRFAMs; TIGR02504; NrdJ_Z; 1.
PE 3: Inferred from homology;
KW Cobalamin; Cobalt; Disulfide bond; DNA synthesis; Nucleotide-binding;
KW Oxidoreductase; Reference proteome.
FT CHAIN 1..1254
FT /note="Vitamin B12-dependent ribonucleotide reductase"
FT /id="PRO_0000231658"
FT ACT_SITE 474
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 476
FT /note="Cysteine radical intermediate"
FT /evidence="ECO:0000250"
FT ACT_SITE 478
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 153
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 198..199
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 230
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 474..478
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 675..679
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT DISULFID 199..487
FT /note="Redox-active"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1254 AA; 137465 MW; FF888DB9EE21A33B CRC64;
MRIERRHTTT GQSPYAGIDF RLTTSEIRNP DGSVVFKLDN VEVPTEWSQV ASDVLAQKYF
RKAGVAARLK KVEEESVPSF LWRSVPDTEA LSQLPEKERY VSELSAKQVF DRLAGCWTYW
GWKGGYFTND EDAQAFYDEL RYMLAMQMVA PNSPQWFNTG LHWAYGIDGP GQGHYYVDPF
TGKLTKSKSA YEHPQPHACF IQGVGDDLVN EGGIMDLWVR EARLFKYGSG TGSNFSRLRG
EGEKLSGGGR SSGLMSFLKI GDRAAGAIKS GGTTRRAAKM VVVDVDHPDI ETYIDWKVKE
EQKVAALVTG SKINQKHLKA VLKACVNCEG SGDDCFDPEK NPALRREIKL ARRSLVPDNY
IKRVIQFAKQ GYKDIQFDVY DTDWDSEAYL TVSGQNSNNS VSLKDDFLRA VETDGDWNLN
ARTSKKVTKT LKARDLWEKI GYAAWASADP GLHFNTTMND WHTCKASGDI RASNPCSEYM
FLDDTACNLA SANLLTFYNV ATKHFDVEGY EHLCRLWTVV LEISVMMAQF PSKAIAELSY
EFRTLGLGYA NIGGLLMTMG LPYDSKEGRA LCGALTAVMT GITYKTSAEI AAELGTFPGY
KKNAAHMLRV IRNHRRAAHG QSNGYEALSV NPVPLDLVSC PQADLVSHAQ AAWDAALELG
EKHGYRNAQT TVIAPTGTIG LVMDCDTTGI EPDFALVKFK KLAGGGYFKI INRAVPAALR
ALGYRESEIA EIEAYAVGHG SLSNAPGINA STLKAKGFTD EAIAKVEKAL PTAFDIKFAF
NKWTFGEDFI RDQLGIGAEA IAAPGFDLLQ AVGFTKREIE AANVHICGAM TVEGAPHLKA
EHYPVFDCAN PCGKIGKRYL SVESHIRMMA AAQPFISGAI SKTINMPNDA TVEDCKSAYM
LSWKLALKAN ALYRDGSKLS QPLNSQLIAD DEDEDDAVES LYEKPMAART AQVSEKIVEK
LVERIIVMRE REKMPDRRKG YTQKAVVGGH KVYLRTGEYD DGRLGEIFID MHKEGAALRS
FINNFAIAVS LGLQYGVPLD EYVDAFTFTR FEPAGPVQGN DSIKYATSIL DYVFRELAVS
YMSRFDLAHV DPTESNFDAL GKGVEEGKEP DEGHHASKLV SRGLTRSRTD NLVVMRGGST
AVAQGNDSAP SGGSKVTALA SHGASARVGD VLEGAVALKQ EVSHDLSPTE KLEALQWSKS
GTAQTLVPSK AERRAEAKAK GYEGEMCSEC GNFTLVRNGT CMKCDTCGST TGCS
