ID   RIR1_TREPA              Reviewed;         845 AA.
AC   O83972;
DT   15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1998, sequence version 1.
DT   27-MAR-2024, entry version 140.
DE   RecName: Full=Ribonucleoside-diphosphate reductase subunit alpha;
DE            EC=1.17.4.1;
DE   AltName: Full=Ribonucleotide reductase;
GN   Name=nrdA; OrderedLocusNames=TP_1008;
OS   Treponema pallidum (strain Nichols).
OC   Bacteria; Spirochaetota; Spirochaetia; Spirochaetales; Treponemataceae;
OC   Treponema.
OX   NCBI_TaxID=243276;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Nichols;
RX   PubMed=9665876; DOI=10.1126/science.281.5375.375;
RA   Fraser C.M., Norris S.J., Weinstock G.M., White O., Sutton G.G.,
RA   Dodson R.J., Gwinn M.L., Hickey E.K., Clayton R.A., Ketchum K.A.,
RA   Sodergren E., Hardham J.M., McLeod M.P., Salzberg S.L., Peterson J.D.,
RA   Khalak H.G., Richardson D.L., Howell J.K., Chidambaram M., Utterback T.R.,
RA   McDonald L.A., Artiach P., Bowman C., Cotton M.D., Fujii C., Garland S.A.,
RA   Hatch B., Horst K., Roberts K.M., Sandusky M., Weidman J.F., Smith H.O.,
RA   Venter J.C.;
RT   "Complete genome sequence of Treponema pallidum, the syphilis spirochete.";
RL   Science 281:375-388(1998).
CC   -!- FUNCTION: Provides the precursors necessary for DNA synthesis.
CC       Catalyzes the biosynthesis of deoxyribonucleotides from the
CC       corresponding ribonucleotides (By 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   -!- ACTIVITY REGULATION: Under complex allosteric control mediated by
CC       deoxynucleoside triphosphates and ATP binding. The type of nucleotide
CC       bound at the specificity site determines substrate preference. It seems
CC       probable that ATP makes the enzyme reduce CDP and UDP, dGTP favors ADP
CC       reduction and dTTP favors GDP reduction (By similarity). {ECO:0000250}.
CC   -!- SUBUNIT: Tetramer of two alpha and two beta subunits. {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the ribonucleoside diphosphate reductase large
CC       chain family. {ECO:0000305}.
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DR   EMBL; AE000520; AAC65956.1; -; Genomic_DNA.
DR   PIR; B71255; B71255.
DR   RefSeq; WP_010882452.1; NC_021490.2.
DR   AlphaFoldDB; O83972; -.
DR   SMR; O83972; -.
DR   IntAct; O83972; 2.
DR   STRING; 243276.TP_1008; -.
DR   EnsemblBacteria; AAC65956; AAC65956; TP_1008.
DR   GeneID; 57879519; -.
DR   KEGG; tpa:TP_1008; -.
DR   eggNOG; COG0209; Bacteria.
DR   HOGENOM; CLU_000404_3_0_12; -.
DR   OrthoDB; 9762933at2; -.
DR   Proteomes; UP000000811; Chromosome.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
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   CDD; cd01679; RNR_I; 1.
DR   Gene3D; 3.20.70.20; -; 1.
DR   InterPro; IPR005144; ATP-cone_dom.
DR   InterPro; IPR013346; NrdE_NrdA_C.
DR   InterPro; IPR000788; RNR_lg_C.
DR   InterPro; IPR013509; RNR_lsu_N.
DR   InterPro; IPR008926; RNR_R1-su_N.
DR   InterPro; IPR039718; Rrm1.
DR   NCBIfam; TIGR02506; NrdE_NrdA; 1.
DR   PANTHER; PTHR11573; RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE CHAIN; 1.
DR   PANTHER; PTHR11573:SF6; RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE SUBUNIT; 1.
DR   Pfam; PF03477; ATP-cone; 1.
DR   Pfam; PF02867; Ribonuc_red_lgC; 1.
DR   Pfam; PF00317; Ribonuc_red_lgN; 1.
DR   PRINTS; PR01183; RIBORDTASEM1.
DR   SUPFAM; SSF51998; PFL-like glycyl radical enzymes; 1.
DR   SUPFAM; SSF48168; R1 subunit of ribonucleotide reductase, N-terminal domain; 1.
DR   PROSITE; PS51161; ATP_CONE; 1.
DR   PROSITE; PS00089; RIBORED_LARGE; 1.
PE   3: Inferred from homology;
KW   Allosteric enzyme; ATP-binding; Deoxyribonucleotide synthesis;
KW   Disulfide bond; Nucleotide-binding; Oxidoreductase; Reference proteome.
FT   CHAIN           1..845
FT                   /note="Ribonucleoside-diphosphate reductase subunit alpha"
FT                   /id="PRO_0000187223"
FT   DOMAIN          1..98
FT                   /note="ATP-cone"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00492"
FT   ACT_SITE        534
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250"
FT   ACT_SITE        536
FT                   /note="Cysteine radical intermediate"
FT                   /evidence="ECO:0000250"
FT   ACT_SITE        538
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250"
FT   BINDING         303
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         318..319
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         347
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         534..538
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         725..729
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   SITE            319
FT                   /note="Important for hydrogen atom transfer"
FT                   /evidence="ECO:0000250"
FT   SITE            326
FT                   /note="Allosteric effector binding"
FT                   /evidence="ECO:0000250"
FT   SITE            356
FT                   /note="Allosteric effector binding"
FT                   /evidence="ECO:0000250"
FT   SITE            574
FT                   /note="Important for hydrogen atom transfer"
FT                   /evidence="ECO:0000250"
FT   SITE            828
FT                   /note="Important for electron transfer"
FT                   /evidence="ECO:0000250"
FT   SITE            829
FT                   /note="Important for electron transfer"
FT                   /evidence="ECO:0000250"
FT   SITE            840
FT                   /note="Interacts with thioredoxin/glutaredoxin"
FT                   /evidence="ECO:0000250"
FT   SITE            843
FT                   /note="Interacts with thioredoxin/glutaredoxin"
FT                   /evidence="ECO:0000250"
FT   DISULFID        319..574
FT                   /note="Redox-active"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   845 AA;  95987 MW;  47DC688E4D0B356C CRC64;
     MHIIKRNGEP QPYMREKIIV AISAAFRSVQ NPLAPEVPAI ITDLAAEVER QLFEMNRAGV
     PVHVEKIQDF VEKTLTKYNH SDEVKSFILY RDDRTKKRIA REQIACCFTD SSVLGVLKEI
     QQDFPFPEYS LDALASKFLL FKKEVTDERR SMQLLIKAAV ELTAQEAPQW ELIAARLLML
     DFSLALGTSL EKLNIHSFYE KITYLEEAGL YGVYIRTHYS RAEIEEAATY LECSRDKLFT
     YSSLDMILRR YVIRTRAHVP LETPQEMFLG IALHLAMNET QDRMQWVKRF YTVLSKLQVT
     VATPTLSNAR KPFHQLSSCF VDTVPDSLDG IYRSIDNFSQ VSKFGGGMGL YFGKVRAVGA
     PIRGFQGAAG GILRWIKLAN DTAVAVDQLG VRQGSVAVYL DVWHKDIPEF LQLRTNNGDD
     RMKAHDVFPA VCYPDLFWKT VRDNLGASWY LMCPHEILTV KGYALEDFYA EEWEKRYWDC
     VKDARISKRT IPIKELVRLV LKSVVETGTP FAFYRDHANR ANPNGHRGII YCSNLCTEIA
     QNMSAINLVS VKITEVDGQK VVVQTTRPGD FVVCNLASLV LSNIDLSDDK ELREVVRVAV
     RALDNVIDLT YYPVPYAQVT NAYYRAIGLG VSGYHHVLAQ QGIDWESDEH LAFADRIFER
     INRAAIEASM TIAREKGAYG CFTGSDWCTG AYFRKRGYVS EDWQRLQREV ATHGMRNGYL
     LAVAPTSSTS IIAGTTAGVD PIMKQYFLEE KKGMLMPRVA PSLSQKTCPL YKSAHAVEQR
     WSIRAAGLRQ RHIDQAQSVN LYITTDFTLK QVLDLYVYAW EVGMKSLYYV RSQSLEIDLC
     GYCAS
//