ID   NRDJ_RHOBA              Reviewed;        1040 AA.
AC   Q7UI46;
DT   04-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2003, sequence version 1.
DT   27-MAR-2024, entry version 105.
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=RB12762;
OS   Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1).
OC   Bacteria; Planctomycetota; Planctomycetia; Pirellulales; Pirellulaceae;
OC   Rhodopirellula.
OX   NCBI_TaxID=243090;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 10527 / NCIMB 13988 / SH1;
RX   PubMed=12835416; DOI=10.1073/pnas.1431443100;
RA   Gloeckner F.O., Kube M., Bauer M., Teeling H., Lombardot T., Ludwig W.,
RA   Gade D., Beck A., Borzym K., Heitmann K., Rabus R., Schlesner H., Amann R.,
RA   Reinhardt R.;
RT   "Complete genome sequence of the marine planctomycete Pirellula sp. strain
RT   1.";
RL   Proc. Natl. Acad. Sci. U.S.A. 100:8298-8303(2003).
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; BX294155; CAD77768.1; -; Genomic_DNA.
DR   RefSeq; NP_870691.1; NC_005027.1.
DR   RefSeq; WP_011123898.1; NC_005027.1.
DR   AlphaFoldDB; Q7UI46; -.
DR   SMR; Q7UI46; -.
DR   STRING; 243090.RB12762; -.
DR   EnsemblBacteria; CAD77768; CAD77768; RB12762.
DR   KEGG; rba:RB12762; -.
DR   PATRIC; fig|243090.15.peg.6184; -.
DR   eggNOG; COG0209; Bacteria.
DR   HOGENOM; CLU_000404_0_1_0; -.
DR   InParanoid; Q7UI46; -.
DR   OrthoDB; 9762933at2; -.
DR   Proteomes; UP000001025; 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   CDD; cd02888; RNR_II_dimer; 1.
DR   Gene3D; 3.20.70.20; -; 1.
DR   InterPro; IPR013678; RNR_2_N.
DR   InterPro; IPR000788; RNR_lg_C.
DR   InterPro; IPR013344; RNR_NrdJ/NrdZ.
DR   NCBIfam; TIGR02504; NrdJ_Z; 1.
DR   PANTHER; PTHR43371:SF1; RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE; 1.
DR   PANTHER; PTHR43371; VITAMIN B12-DEPENDENT RIBONUCLEOTIDE REDUCTASE; 1.
DR   Pfam; PF08471; Ribonuc_red_2_N; 1.
DR   Pfam; PF02867; Ribonuc_red_lgC; 1.
DR   PRINTS; PR01183; RIBORDTASEM1.
DR   SUPFAM; SSF51998; PFL-like glycyl radical enzymes; 1.
PE   3: Inferred from homology;
KW   Cobalamin; Cobalt; Disulfide bond; DNA synthesis; Nucleotide-binding;
KW   Oxidoreductase; Reference proteome.
FT   CHAIN           1..1040
FT                   /note="Vitamin B12-dependent ribonucleotide reductase"
FT                   /id="PRO_0000231655"
FT   REGION          909..932
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          969..988
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        969..984
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        420
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250"
FT   ACT_SITE        422
FT                   /note="Cysteine radical intermediate"
FT                   /evidence="ECO:0000250"
FT   ACT_SITE        424
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250"
FT   BINDING         169
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         213..214
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         242
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         420..424
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         604..608
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   DISULFID        214..433
FT                   /note="Redox-active"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   1040 AA;  113464 MW;  D640951F588F5C03 CRC64;
     MSTVLPESNA TSRIPANDPA LEKVDSEHGV EYAREKFGTA LRGDRAGLKF ESKFCPDDGR
     TPFATTAWDL RSAAIKDESG NALFEQTDCE VPASWSQLAT NVVVSKYFYG DPKNTDERER
     SVRQLIHRVT RTISDWGLAD GYFDTPEDGE RFYRDLTWLS LHQHGAFNSP VWFNVGLHAQ
     YDVEGDMCNW HWDRTENTTA QPDNPYEYPQ GSACFIQSVD DNMEDIMRLA CSEAMLFKFG
     SGTGTDLSTI RSQREKLSGG GTPSGPLSFM RVYDSIAGVV KSGGKTRRAA KMQSLKVWHP
     DILEFIECKW AEEKKAHALI REGYDSNFNG EAYASVCFQN ANLSVRLTDD YMEAVRKNEN
     FQTRWITDKP TTEPPSYVAK ELLNKMAECA WHCGDPGVQY DTTINKWHTC PNSGAINASN
     PCSEYMFLDD TACNLASINL MKFVQQDGSF DHERFRAACR TFFIAQEILV DHASYPTEPI
     ARNSHKFRPL GLGYSNLGSV IMTAGLPYDS DAARGMCGSL TALLHGEANR TSAELASVVG
     TFDGYVENEA PMLRVMQMHR DACDQINDDG PAELKEAARE LWDGVLEIGE KYGFRNAQAT
     VLAPTGTISF MMDCDTTGIE PDIALVKYKQ LAGGGMLKIV NQTVKLGLKT LGYDADTIDE
     ILKYVDANDT IEGAPGLQDE HLAVFDCAFK PANGVRSIGW RAHITMMAAA QPFLSGAISK
     TVNMPTDVTP QDIADAYFWG WELGLKAIAI YRDGSKQSQP LNTKSDEQKA TDAAEAAKVE
     TVEKIVYKPR RERLPDTRQS LTHKFSIAGH EGYLCVGLYP DGRPGEMFIT MAKEGSTIGG
     IMDSFGTALS IAMQYGVPLE VIVNKFSHTR FEPMGHTSNK DIRIAKSVVD YIARWLGITF
     MSGNDYSPSA EGAAKTGGNG PDLTTAPAGA TANNNSPVMA ELRADAGAAV ALVERATLLA
     SLQNGVSNGS ATNGHSNGQS AGGSSDGAVA ERAVDGLGGQ ADQFSRFQTD APSCDNCGSI
     TVRNGNCYLC HNCGNSMGCS
//