NRDJ_RHOBA
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 03-AUG-2022, entry version 101.
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; Planctomycetes; 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 PRIDE; Q7UI46; -.
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 OMA; WACADPG; -.
DR OrthoDB; 357568at2; -.
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 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..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
