ID D6V648_9BRAD Unreviewed; 1250 AA.
AC D6V648;
DT 10-AUG-2010, integrated into UniProtKB/TrEMBL.
DT 10-AUG-2010, sequence version 1.
DT 24-JAN-2024, entry version 48.
DE RecName: Full=Vitamin B12-dependent ribonucleotide reductase {ECO:0000256|ARBA:ARBA00014409, ECO:0000256|RuleBase:RU364064};
DE EC=1.17.4.1 {ECO:0000256|ARBA:ARBA00012274, ECO:0000256|RuleBase:RU364064};
GN ORFNames=AfiDRAFT_2081 {ECO:0000313|EMBL:EFI51795.1};
OS Afipia sp. 1NLS2.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC Nitrobacteraceae; Afipia.
OX NCBI_TaxID=666684 {ECO:0000313|EMBL:EFI51795.1, ECO:0000313|Proteomes:UP000004041};
RN [1] {ECO:0000313|EMBL:EFI51795.1, ECO:0000313|Proteomes:UP000004041}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1NLS2 {ECO:0000313|EMBL:EFI51795.1,
RC ECO:0000313|Proteomes:UP000004041};
RG US DOE Joint Genome Institute (JGI-PGF);
RA Lucas S., Copeland A., Lapidus A., Cheng J.-F., Bruce D., Goodwin L.,
RA Pitluck S., Land M.L., Hauser L., Chang Y.-J., Jeffries C., Prakah O.,
RA Elkins J.G., Brown S.D., Palumbo A.V., Hemme C., Zhou J., Watson D.B.,
RA Jardine P.M., Kostka J.E., Green S.J., Woyke T.J.;
RT "The draft genome of Afipia sp. 1NLS2.";
RL Submitted (MAY-2010) to the EMBL/GenBank/DDBJ databases.
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.
CC {ECO:0000256|ARBA:ARBA00025437, ECO:0000256|RuleBase:RU364064}.
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 Evidence={ECO:0000256|ARBA:ARBA00000206,
CC ECO:0000256|RuleBase:RU364064};
CC -!- COFACTOR:
CC Name=adenosylcob(III)alamin; Xref=ChEBI:CHEBI:18408;
CC Evidence={ECO:0000256|ARBA:ARBA00001922,
CC ECO:0000256|RuleBase:RU364064};
CC -!- SIMILARITY: Belongs to the ribonucleoside diphosphate reductase class-2
CC family. {ECO:0000256|ARBA:ARBA00007405, ECO:0000256|RuleBase:RU364064}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:EFI51795.1}.
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DR EMBL; ADVZ01000002; EFI51795.1; -; Genomic_DNA.
DR RefSeq; WP_009339332.1; NZ_ADVZ01000002.1.
DR AlphaFoldDB; D6V648; -.
DR eggNOG; COG0209; Bacteria.
DR Proteomes; UP000004041; Unassembled WGS sequence.
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 CDD; cd02888; RNR_II_dimer; 1.
DR Gene3D; 3.20.70.20; -; 3.
DR InterPro; IPR013678; RNR_2_N.
DR InterPro; IPR000788; RNR_lg_C.
DR InterPro; IPR013344; RNR_NrdJ/NrdZ.
DR InterPro; IPR029072; YebC-like.
DR InterPro; IPR013087; Znf_C2H2_type.
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; 2.
DR PRINTS; PR01183; RIBORDTASEM1.
DR SUPFAM; SSF51998; PFL-like glycyl radical enzymes; 1.
DR SUPFAM; SSF75625; YebC-like; 1.
DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 1.
PE 3: Inferred from homology;
KW Cobalamin {ECO:0000256|ARBA:ARBA00022628, ECO:0000256|RuleBase:RU364064};
KW Cobalt {ECO:0000256|ARBA:ARBA00023285, ECO:0000256|RuleBase:RU364064};
KW Disulfide bond {ECO:0000256|ARBA:ARBA00023157};
KW DNA synthesis {ECO:0000256|ARBA:ARBA00022634,
KW ECO:0000256|RuleBase:RU364064};
KW Metal-binding {ECO:0000256|PROSITE-ProRule:PRU00042};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741,
KW ECO:0000256|RuleBase:RU364064};
KW Oxidoreductase {ECO:0000256|ARBA:ARBA00023002,
KW ECO:0000256|RuleBase:RU364064};
KW Zinc {ECO:0000256|PROSITE-ProRule:PRU00042};
KW Zinc-finger {ECO:0000256|PROSITE-ProRule:PRU00042}.
FT DOMAIN 846..874
FT /note="C2H2-type"
FT /evidence="ECO:0000259|PROSITE:PS50157"
FT REGION 1140..1213
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1180..1194
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 1250 AA; 136816 MW; 56329D1E8C53DB2C CRC64;
MRIQRRYTKA DQSPYADISF RLTTSEIRNP DGSVVFKLDN VEVPEFWSQV ASDVLAQKYF
RKAGVAARLK KVEEETVPSW LWRSVPDAEA LAALPESERF VGELTAKQVF DRLAGCWTYW
GWKGGYFTSE DDAHAFHDEL RFMLARQMVA PNSPQWFNTG LHWAYGIDGP GQGHYYVDWK
TGKLTKSKSS YEHPQPHACF IQGIEDDLVN EGGIMDLWVR EARLFKYGSG TGSNFSRLRG
EGEKLSGGGR SSGLMSFLKI GDRAAGAIKS GGTTRRAAKM VVVDADHPDI ETYIDWKVRE
EQKVAALVTG SKINQKHLKA IMKACVNCEG PGDDCYLPEK NPALKREIKL ARRALVTDNM
IKRVIQFARQ GYTDIAFDTY DTDWDSEAYL TVSGQNSNNS VSLKDDFLRA VETDGPWNLI
GRTNGKVTKT LKARDLWEKI GYAAWASADP GLHFNTTMND WHTCKASGDI RASNPCSEYM
FLDDTACNLA SANLLTFYDT HTRRFDADAY EHLCRLWTIV LEISVMMAQF PSKAIAELSY
EFRTLGLGYA NIGGLLMTMG LPYDSKEGRA LCGALSAIMT GTAYATSAEM AAELGTFPGY
KKNASHMLRV IRNHRRAAHG EAAGYEALAV NPVPLDHASC PQADIVDHAK AVWDRALELG
KANGFRNAQT TVVAPTGTIG LVMDCDTTGI EPDFALVKFK KLAGGGYWKI INRAVPEALR
ALGYRESEIA EIEAYAVGHG SLSNAPGINA SSLKTKGFTD EALAKVEKAL PTAFDIKFVF
NKWTLGEDFI RDSLHIAPEV MNVPGFDLLA ALGFSKRDIE AANVHICGAM TVEGAPHLKD
EHYAVFDCAN PCGKVGKRYL SVESHIRMMA ASQPFISGAI SKTINMPNDA TVDDCKSAYL
LSWKLALKAN ALYRDGSKLS QPLNSQLIAD DDDEDDAIEA FHDKPMAARA TQVVEKIVER
VVEHVSRERE RMPDRRKGYT QKAIVGGHKV YLRTGEYDDG RLGEIFVDMH KEGAALRSFI
NNFAIAVSLG LQYGVPLDEY VDAFTFTRFE PAGPVQGNDS IKYATSILDY VFRELAVSYL
SRYDLAHVDP SETQFDALGK GVNEGKAQSG PSKYLSKGLT RSRSDNLVVM QGGASAAVTA
HNDSAPVGGS RVTAMASGGG EGAAALKTAE PERALSPTEK LEAQQWSKAG SAQAATTAAA
PAAPTKAERR AEAKARGYEG DMCSECSNFT LVRNGTCMKC DTCGSTTGCS
//
