ID   NRDJ_BDEBA              Reviewed;         764 AA.
AC   Q6MNP6;
DT   04-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT   05-JUL-2004, sequence version 1.
DT   03-AUG-2022, entry version 98.
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=Bd1196;
OS   Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 /
OS   HD100).
OC   Bacteria; Proteobacteria; Oligoflexia; Bdellovibrionales;
OC   Bdellovibrionaceae; Bdellovibrio.
OX   NCBI_TaxID=264462;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100;
RX   PubMed=14752164; DOI=10.1126/science.1093027;
RA   Rendulic S., Jagtap P., Rosinus A., Eppinger M., Baar C., Lanz C.,
RA   Keller H., Lambert C., Evans K.J., Goesmann A., Meyer F., Sockett R.E.,
RA   Schuster S.C.;
RT   "A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a
RT   genomic perspective.";
RL   Science 303:689-692(2004).
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; BX842649; CAE79105.1; -; Genomic_DNA.
DR   RefSeq; WP_011163707.1; NC_005363.1.
DR   AlphaFoldDB; Q6MNP6; -.
DR   SMR; Q6MNP6; -.
DR   STRING; 264462.Bd1196; -.
DR   PRIDE; Q6MNP6; -.
DR   EnsemblBacteria; CAE79105; CAE79105; Bd1196.
DR   KEGG; bba:Bd1196; -.
DR   eggNOG; COG0209; Bacteria.
DR   HOGENOM; CLU_000404_0_1_7; -.
DR   OMA; FIDRIND; -.
DR   OrthoDB; 357568at2; -.
DR   Proteomes; UP000008080; 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; 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   Pfam; PF08471; Ribonuc_red_2_N; 1.
DR   Pfam; PF02867; Ribonuc_red_lgC; 1.
DR   PRINTS; PR01183; RIBORDTASEM1.
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..764
FT                   /note="Vitamin B12-dependent ribonucleotide reductase"
FT                   /id="PRO_0000231656"
FT   ACT_SITE        376
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250"
FT   ACT_SITE        378
FT                   /note="Cysteine radical intermediate"
FT                   /evidence="ECO:0000250"
FT   ACT_SITE        380
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250"
FT   BINDING         127
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         171..172
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         200
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         376..380
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         561..565
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   DISULFID        172..389
FT                   /note="Redox-active"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   764 AA;  84408 MW;  B9B5369BEE85DB1E CRC64;
     MKKQTLHSPS YFVSGGKNPE SLFAWKNVNC EIRNRKGEVF FEMKNVEAPE GWSQLAIDIA
     ASKYFRKVGV PKTGHETSVR QMVDRVVKAI VASAIRQGGY FATRKEADIF AKELKFILLS
     QRGAFNSPVW FNAGLWEAYK AQSPSEHFAW DEKKKSIQAT KNAYERPQCS ACFIQSVDDS
     IESIFDLAKT EAKLFKYGSG TGSNFSKIRS KYEATGSGGK SSGLISFLEV LDKGAGAIKS
     GGTTRRAAKM VVVDIDHPEV LDFIDWKMRE EQKAHLLIAA GLSADFEGEA YRTVSGQNAN
     NSVRVSDAFM KAVEQERPWK LKARLTGKVL REIPAGEVWN RITRAAWMCA DPGIQFHDTI
     NKWHTCPETD IIHSSNPCSE YMFLDDSACN LASINLVKFL NDTGDFDFES FIHTARTLFV
     AQEILVDYSS YPTQRVAQNS HDYRPLGLGF ANLGSLLMRK GVAYDSDEGR AWAGALTSLM
     SGVAYLTSSE MARAKGPFAG YRKNSKSMLK VMKMHERALN QVAWKMLPAG IDKAVRNLWK
     GVLYNGEKYG YRNAQATVIA PTGTIGLLMD CDTTGIEPDF SLIKFKKLVG GGEIQIVNQS
     VDAALASLQY FEDERQAILK YVEENNSVVG APQMHPEDLP VFDTATAMPG QRVLSPESHV
     KMMAAVQPFI SGAISKTVNM PSTATEEDIS RIYFLAWKLG VKAVAVYRDG SKQSQPLNLK
     EKPKVVEEVG VPNFTMKCPE CGSDTVLTSG CYRCPNCGTT VGCS