ID   NRDJ_AGRFC              Reviewed;        1272 AA.
AC   Q8UEM4; Q7CYN2;
DT   04-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-2002, sequence version 1.
DT   03-AUG-2022, entry version 106.
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=Atu1733; ORFNames=AGR_C_3183;
OS   Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens
OS   (strain C58)).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC   Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium;
OC   Agrobacterium tumefaciens complex.
OX   NCBI_TaxID=176299;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=C58 / ATCC 33970;
RX   PubMed=11743193; DOI=10.1126/science.1066804;
RA   Wood D.W., Setubal J.C., Kaul R., Monks D.E., Kitajima J.P., Okura V.K.,
RA   Zhou Y., Chen L., Wood G.E., Almeida N.F. Jr., Woo L., Chen Y.,
RA   Paulsen I.T., Eisen J.A., Karp P.D., Bovee D. Sr., Chapman P.,
RA   Clendenning J., Deatherage G., Gillet W., Grant C., Kutyavin T., Levy R.,
RA   Li M.-J., McClelland E., Palmieri A., Raymond C., Rouse G.,
RA   Saenphimmachak C., Wu Z., Romero P., Gordon D., Zhang S., Yoo H., Tao Y.,
RA   Biddle P., Jung M., Krespan W., Perry M., Gordon-Kamm B., Liao L., Kim S.,
RA   Hendrick C., Zhao Z.-Y., Dolan M., Chumley F., Tingey S.V., Tomb J.-F.,
RA   Gordon M.P., Olson M.V., Nester E.W.;
RT   "The genome of the natural genetic engineer Agrobacterium tumefaciens
RT   C58.";
RL   Science 294:2317-2323(2001).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=C58 / ATCC 33970;
RX   PubMed=11743194; DOI=10.1126/science.1066803;
RA   Goodner B., Hinkle G., Gattung S., Miller N., Blanchard M., Qurollo B.,
RA   Goldman B.S., Cao Y., Askenazi M., Halling C., Mullin L., Houmiel K.,
RA   Gordon J., Vaudin M., Iartchouk O., Epp A., Liu F., Wollam C., Allinger M.,
RA   Doughty D., Scott C., Lappas C., Markelz B., Flanagan C., Crowell C.,
RA   Gurson J., Lomo C., Sear C., Strub G., Cielo C., Slater S.;
RT   "Genome sequence of the plant pathogen and biotechnology agent
RT   Agrobacterium tumefaciens C58.";
RL   Science 294:2323-2328(2001).
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; AE007869; AAK87503.1; -; Genomic_DNA.
DR   PIR; AF2789; AF2789.
DR   PIR; F97568; F97568.
DR   RefSeq; NP_354718.1; NC_003062.2.
DR   RefSeq; WP_010971830.1; NC_003062.2.
DR   AlphaFoldDB; Q8UEM4; -.
DR   SMR; Q8UEM4; -.
DR   STRING; 176299.Atu1733; -.
DR   EnsemblBacteria; AAK87503; AAK87503; Atu1733.
DR   KEGG; atu:Atu1733; -.
DR   PATRIC; fig|176299.10.peg.1745; -.
DR   eggNOG; COG0209; Bacteria.
DR   HOGENOM; CLU_000404_0_1_5; -.
DR   OMA; WACADPG; -.
DR   PhylomeDB; Q8UEM4; -.
DR   BioCyc; AGRO:ATU1733-MON; -.
DR   Proteomes; UP000000813; Chromosome circular.
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; IEA:UniProtKB-EC.
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..1272
FT                   /note="Vitamin B12-dependent ribonucleotide reductase"
FT                   /id="PRO_0000231657"
FT   REGION          1120..1147
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
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   1272 AA;  139623 MW;  3FA22DCC85AC6E2D CRC64;
     MRIERRFTKP GQSSYAEIEF RKAVSEIKNP DGSVVFRLAD IDVPAQFSQV ATDVLAQKYF
     RKAGVPKLLK KVEENDVPSF LWRSVADEKA LKELPEAERY GSETDARQVF DRLAGTWAYW
     GWKGKYFSTE EDASAFKDEL AYMLATQRVA PNSPQWFNTG LHWAYGIDGP GQGHFYVDPF
     TGKLTKSKSA YEHPQPHACF IQSVEDDLVN EGGIMDLWVR EARLFKYGSG TGSNFSYLRG
     EGEKLSGGGK SSGLMSFLKI GDRAAGAIKS GGTTRRAAKM VVVDADHPDI EAYIDWKVNE
     EQKVAALVTG SKIVAKHLKA IMKACVNCEA DNGDCFDPAK NPALKREIRA AKKDMVPENY
     VKRVIQFAEQ GYKDIQFKTY DTDWDSEAYL TVSGQNSNNS VSLKDDFLRA VENDGNWNLT
     ARKDGKVMKT LKARDLWEKI SHAAWASADP GLHFNTTMND WHTSPAEGPI RASNPCSEYM
     FLDDTACNLA SLNLLQFKDA KTKRIDIADY EHAVRLWTVV LEVSVMMAQF PSRQIAERSY
     EYRTLGLGYA NIGGLLMSSG IPYDSDEGRA IAGALTAIMT GVSYATSAEM AGELGPFPSF
     APNRDNMLRV IRNHRRAAHG QSEGYEGLSV NPVALIHADC TDQDLVAHAT AAWDKALELG
     EKHGYRNAQT TVIAPTGTIG LVMDCDTTGI EPDFALVKFK KLAGGGYFKI INRAVPESLR
     SLGYSESQIA EIEAYAVGHG NLNQAPAINP STLKAKGFTD EKIEAVNAAL KSAFDIKFVF
     NQWTLGADFL KGTLKVSDEQ LSDMSFNLLD HLGFAKKDIE AANVHVCGAM TLEGAPFLKN
     EHLAVFDCAN PCGKIGKRYL SVESHIRMMA AAQPFISGAI SKTINMPNDA TVEDCGAAYM
     LSWKLALKAN ALYRDGSKLS QPLNASLVED EDDEDFVEEL IQQPLAQQAV TITEKIVERV
     IERVSREREK LPNRRQGYTQ KATVGGHKVY LRTGEFGDGR IGEIFIDMHK EGAAFRAMMN
     NFAIAISLGL QYGVPLEEYV EAFTFTKFEP AGMVQGNDAI KNATSILDYV FRELAVSYLG
     RHDLAHVDTS DFSNTALGKG IQEGKTNLLS TGWTRGYKPT LVSSNEGDRA ASEPKGSATA
     APARGSANVT SFAGSAARKL EPTVAITTSE IVSFKRDYEE RAKELAEEIA EEVIDEVVQE
     AQQTATALFS DKAAADAASA KAEAKKKENE RRMRSIAQGY TGNMCSECQN FTMVRNGTCE
     KCDTCGATSG CS