ID B1I483_DESAP Unreviewed; 1121 AA.
AC B1I483;
DT 29-APR-2008, integrated into UniProtKB/TrEMBL.
DT 29-APR-2008, sequence version 1.
DT 27-MAR-2024, entry version 93.
DE RecName: Full=Ribonucleoside-diphosphate reductase {ECO:0000256|ARBA:ARBA00012274, ECO:0000256|RuleBase:RU003410};
DE EC=1.17.4.1 {ECO:0000256|ARBA:ARBA00012274, ECO:0000256|RuleBase:RU003410};
GN OrderedLocusNames=Daud_1269 {ECO:0000313|EMBL:ACA59780.1};
OS Desulforudis audaxviator (strain MP104C).
OC Bacteria; Bacillota; Clostridia; Eubacteriales; Peptococcaceae;
OC Desulforudis.
OX NCBI_TaxID=477974 {ECO:0000313|EMBL:ACA59780.1, ECO:0000313|Proteomes:UP000008544};
RN [1] {ECO:0000313|Proteomes:UP000008544}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MP104C {ECO:0000313|Proteomes:UP000008544};
RA Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E.,
RA Tice H., Bruce D., Pitluck S., Lowry S.R., Larimer F., Land M.L.,
RA Hauser L., Kyrpides N., Ivanova N.N., Richardson P.;
RT "Complete sequence of chromosome of Desulforudis audaxviator MP104C.";
RL Submitted (OCT-2007) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:ACA59780.1, ECO:0000313|Proteomes:UP000008544}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MP104C {ECO:0000313|EMBL:ACA59780.1,
RC ECO:0000313|Proteomes:UP000008544};
RX PubMed=18845759; DOI=10.1126/science.1155495;
RA Chivian D., Brodie E.L., Alm E.J., Culley D.E., Dehal P.S., Desantis T.Z.,
RA Gihring T.M., Lapidus A., Lin L.H., Lowry S.R., Moser D.P.,
RA Richardson P.M., Southam G., Wanger G., Pratt L.M., Andersen G.L.,
RA Hazen T.C., Brockman F.J., Arkin A.P., Onstott T.C.;
RT "Environmental genomics reveals a single-species ecosystem deep within
RT Earth.";
RL Science 322:275-278(2008).
CC -!- FUNCTION: Provides the precursors necessary for DNA synthesis.
CC Catalyzes the biosynthesis of deoxyribonucleotides from the
CC corresponding ribonucleotides. {ECO:0000256|RuleBase:RU003410}.
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:RU003410};
CC -!- COFACTOR:
CC Name=adenosylcob(III)alamin; Xref=ChEBI:CHEBI:18408;
CC Evidence={ECO:0000256|ARBA:ARBA00001922};
CC -!- SIMILARITY: Belongs to the ribonucleoside diphosphate reductase large
CC chain family. {ECO:0000256|RuleBase:RU003410}.
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DR EMBL; CP000860; ACA59780.1; -; Genomic_DNA.
DR RefSeq; WP_012302365.1; NC_010424.1.
DR AlphaFoldDB; B1I483; -.
DR STRING; 477974.Daud_1269; -.
DR KEGG; dau:Daud_1269; -.
DR eggNOG; COG0209; Bacteria.
DR eggNOG; COG1372; Bacteria.
DR HOGENOM; CLU_000404_2_1_9; -.
DR OrthoDB; 9762933at2; -.
DR UniPathway; UPA00326; -.
DR Proteomes; UP000008544; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:InterPro.
DR GO; GO:0031419; F:cobalamin binding; IEA:UniProtKB-KW.
DR GO; GO:0004519; F:endonuclease activity; IEA:InterPro.
DR GO; GO:0004748; F:ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor; IEA:UniProtKB-EC.
DR GO; GO:0009263; P:deoxyribonucleotide biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0006260; P:DNA replication; IEA:InterPro.
DR GO; GO:0016539; P:intein-mediated protein splicing; IEA:InterPro.
DR CDD; cd00081; Hint; 1.
DR Gene3D; 3.20.70.20; -; 2.
DR Gene3D; 2.170.16.10; Hedgehog/Intein (Hint) domain; 1.
DR Gene3D; 3.10.28.10; Homing endonucleases; 1.
DR InterPro; IPR003586; Hint_dom_C.
DR InterPro; IPR003587; Hint_dom_N.
DR InterPro; IPR036844; Hint_dom_sf.
DR InterPro; IPR027434; Homing_endonucl.
DR InterPro; IPR006142; INTEIN.
DR InterPro; IPR030934; Intein_C.
DR InterPro; IPR004042; Intein_endonuc.
DR InterPro; IPR006141; Intein_N.
DR InterPro; IPR004860; LAGLIDADG_2.
DR InterPro; IPR000788; RNR_lg_C.
DR InterPro; IPR013509; RNR_lsu_N.
DR InterPro; IPR008926; RNR_R1-su_N.
DR NCBIfam; TIGR01443; intein_Cterm; 1.
DR PANTHER; PTHR43371:SF1; RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE; 1.
DR PANTHER; PTHR43371; VITAMIN B12-DEPENDENT RIBONUCLEOTIDE REDUCTASE; 1.
DR Pfam; PF14890; Intein_splicing; 1.
DR Pfam; PF14528; LAGLIDADG_3; 1.
DR Pfam; PF02867; Ribonuc_red_lgC; 2.
DR Pfam; PF00317; Ribonuc_red_lgN; 1.
DR PRINTS; PR00379; INTEIN.
DR SMART; SM00305; HintC; 1.
DR SMART; SM00306; HintN; 1.
DR SUPFAM; SSF51294; Hedgehog/intein (Hint) domain; 1.
DR SUPFAM; SSF55608; Homing endonucleases; 1.
DR SUPFAM; SSF51998; PFL-like glycyl radical enzymes; 1.
DR SUPFAM; SSF48168; R1 subunit of ribonucleotide reductase, N-terminal domain; 1.
DR PROSITE; PS50818; INTEIN_C_TER; 1.
DR PROSITE; PS50819; INTEIN_ENDONUCLEASE; 1.
DR PROSITE; PS50817; INTEIN_N_TER; 1.
PE 3: Inferred from homology;
KW Autocatalytic cleavage {ECO:0000256|ARBA:ARBA00022813};
KW Cobalamin {ECO:0000256|ARBA:ARBA00022628};
KW Cobalt {ECO:0000256|ARBA:ARBA00023285};
KW Deoxyribonucleotide synthesis {ECO:0000256|ARBA:ARBA00023116,
KW ECO:0000256|RuleBase:RU003410};
KW Oxidoreductase {ECO:0000256|ARBA:ARBA00023002,
KW ECO:0000256|RuleBase:RU003410};
KW Protein splicing {ECO:0000256|ARBA:ARBA00023000};
KW Reference proteome {ECO:0000313|Proteomes:UP000008544}.
FT DOMAIN 385..533
FT /note="DOD-type homing endonuclease"
FT /evidence="ECO:0000259|PROSITE:PS50819"
FT DOMAIN 622..644
FT /note="Intein C-terminal splicing"
FT /evidence="ECO:0000259|PROSITE:PS50818"
SQ SEQUENCE 1121 AA; 122394 MW; DA86A60A4E8AB0DF CRC64;
MVEIAQLSDS GQKVFEARYA AKDEQGRVTE TFEQAVHRLA RTTALAEKAQ DRAAWEEKFA
ASIGGLLFVP STPIWANIGK TDRPWQPGAC FVLAVEDSLE SMYQTLKDTA MVFKSGGGVG
YNFSAIRPRG SMVRSTKGQA SGVVELIRLY DASSGMVMQG GVRRGASMGI LNIDHPEIIH
FINSKRGGDI THFNLSVGVT DAFMEALERD EDWPLVFNGE VHQTVPAREL WDLITESAHA
CGDPGIIFLD RLQRDNPVPE KKINATNPCV TGDTWVTTGA GPRQVRELVG RPFEAIVNGK
AYGTGKDGFF QTGTKPVVKL CTREGYTVRL TADHMILRVT DKTRYRLSQE WVPAADLKAG
DQIVLHNHRP LPGWPGALTE GEGYLLGLLV GDGTLKKETA ILSTWVKKQA VNGSGAGDGV
DSVMQLVLQY TGKMRHRADF TGWDPVKGRN EYRFKSAGIK VLAERMGLGP GRKTATPEIE
GASSEGYRGF LRGLFDADGT IIGEQQKGVS IRLTQSNRDL LGIVQRMLAR LGIISTIYEG
RRPAGLKSLP DGNGGNKEYH IKAQHELVIS RDNISVFAER IGFGNSEKAG RLKSLLEAYK
RDLNRERFTA TVLCVEEDGI EDVYDVQVPG INAFDANGIV AHNCGEQPLS PGESCLLGSV
NLARMLKPGR DGYVVDWELL RDTVRLGIRF LDNLIDVAEY PLEFIAEATR ATRKVGLGYT
GLHDLLIKMG LPYDAEEGRR FAGTVFKAVQ DAALAYSREL AGERGCFPEW ERSVFHPHEK
RRNAACITVA PTGSVTTIAG CEGYGIEPIF AVAYTKDTDV AGSFEVFSPL FLEACERLGV
SREVMSEVAR RGGCQGVEGV PPELARIFKG AQEISPRDHI LMQAEVQKYV CNAVSKTINL
PNSATIHDIE TCYRLAYELG LKGVTVFRDG CKQGVVTVGR KKRKPVPGEL ARGEIMPRPE
NAQGVTHRLD SGCGKIYLTV NYHPATGEIL ETFITTGSDG GCLIYTEATS RLISLAIRGG
IPLEEIIGQL QSTHACPSYQ LARGRGRQLS PGKSCASAIA RKLIEIQTEL ARRCNGGEIP
APWGVRNPDT EPGPDRCEVC GLRMNRAEGC YVCPHCGFAK C
//
