RIR1_BUCAP
ID RIR1_BUCAP Reviewed; 763 AA.
AC Q8K9W3;
DT 15-NOV-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=Ribonucleoside-diphosphate reductase subunit alpha;
DE EC=1.17.4.1;
DE AltName: Full=Ribonucleotide reductase;
GN Name=nrdA; OrderedLocusNames=BUsg_173;
OS Buchnera aphidicola subsp. Schizaphis graminum (strain Sg).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Erwiniaceae; Buchnera.
OX NCBI_TaxID=198804;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Sg;
RX PubMed=12089438; DOI=10.1126/science.1071278;
RA Tamas I., Klasson L., Canbaeck B., Naeslund A.K., Eriksson A.-S.,
RA Wernegreen J.J., Sandstroem J.P., Moran N.A., Andersson S.G.E.;
RT "50 million years of genomic stasis in endosymbiotic bacteria.";
RL Science 296:2376-2379(2002).
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 to separate specificity
CC and activation sites on the alpha subunit. The type of nucleotide bound
CC 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. Stimulated by ATP and
CC inhibited by dATP binding to the activity site (By similarity).
CC {ECO:0000250}.
CC -!- PATHWAY: Genetic information processing; DNA replication.
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; AE013218; AAM67739.1; -; Genomic_DNA.
DR RefSeq; WP_011053706.1; NC_004061.1.
DR AlphaFoldDB; Q8K9W3; -.
DR SMR; Q8K9W3; -.
DR STRING; 198804.BUsg_173; -.
DR EnsemblBacteria; AAM67739; AAM67739; BUsg_173.
DR KEGG; bas:BUsg_173; -.
DR eggNOG; COG0209; Bacteria.
DR HOGENOM; CLU_000404_3_0_6; -.
DR OMA; RGSIQNI; -.
DR OrthoDB; 357568at2; -.
DR UniPathway; UPA00326; -.
DR Proteomes; UP000000416; 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:0006260; P:DNA replication; IEA:UniProtKB-UniPathway.
DR InterPro; IPR005144; ATP-cone_dom.
DR InterPro; IPR013346; NrdE_NrdA.
DR InterPro; IPR000788; RNR_lg_C.
DR InterPro; IPR013509; RNR_lsu_N.
DR InterPro; IPR008926; RNR_R1-su_N.
DR InterPro; IPR039718; Rrm1.
DR PANTHER; PTHR11573; PTHR11573; 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; SSF48168; SSF48168; 1.
DR TIGRFAMs; TIGR02506; NrdE_NrdA; 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.
FT CHAIN 1..763
FT /note="Ribonucleoside-diphosphate reductase subunit alpha"
FT /id="PRO_0000187207"
FT DOMAIN 5..95
FT /note="ATP-cone"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00492"
FT ACT_SITE 437
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 439
FT /note="Cysteine radical intermediate"
FT /evidence="ECO:0000250"
FT ACT_SITE 441
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 9
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="allosteric activator"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 15..21
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="allosteric activator"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 55
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="allosteric activator"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 91
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="allosteric activator"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 209
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 232..234
FT /ligand="dTTP"
FT /ligand_id="ChEBI:CHEBI:37568"
FT /ligand_note="allosteric effector that controls substrate
FT specificity"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 262
FT /ligand="dTTP"
FT /ligand_id="ChEBI:CHEBI:37568"
FT /ligand_note="allosteric effector that controls substrate
FT specificity"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 269
FT /ligand="dTTP"
FT /ligand_id="ChEBI:CHEBI:37568"
FT /ligand_note="allosteric effector that controls substrate
FT specificity"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 437
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 441
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 623..625
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT SITE 225
FT /note="Important for hydrogen atom transfer"
FT /evidence="ECO:0000250"
FT SITE 462
FT /note="Important for hydrogen atom transfer"
FT /evidence="ECO:0000250"
FT SITE 730
FT /note="Important for electron transfer"
FT /evidence="ECO:0000250"
FT SITE 731
FT /note="Important for electron transfer"
FT /evidence="ECO:0000250"
FT SITE 756
FT /note="Interacts with thioredoxin/glutaredoxin"
FT /evidence="ECO:0000250"
FT SITE 761
FT /note="Interacts with thioredoxin/glutaredoxin"
FT /evidence="ECO:0000250"
FT DISULFID 225..462
FT /note="Redox-active"
FT /evidence="ECO:0000250"
SQ SEQUENCE 763 AA; 87471 MW; BDE02289A8CF8D3D CRC64;
MKNSLFVTKR NGKKEKINLD KIHKVLNWAA KGLENISVSQ VELRSRIQFY NNISTVNIHE
TIIKAAADLI SENTPDYQYM AARLAIFHLR KKAYGQFEPP NLYYHVKKMV QLGKYDEKLL
QNYSFEEYVE MNSFVDHRRD MNFSYAAVKQ LEAKYLLQNR VTGQIYESAQ FLYILISACL
FSKYEKKVRM NYIQRFYNAI STFKISLPTP IMSGVRTPTR QFSSCVLIEC ADNLNSINAT
TSAIVKYVSQ RAGIGINAGQ IRALGSPIRN GEAFHTGCIP FYKHFQSAVK SCSQGGVRGG
AATVFYPIWH LEIESLLVLK NNRGIEENRV RHLDYAVQIN KLMYQRMLLG QKITLFSPSD
VPKLYEFFFS DQKKFKEIYI KYEKNRNIRK KSINAIDLFC LIMRERASTG RIYIQHVDHC
NSHSAFNSKL ATIRQSNLCL EITLPTKPLN NIDDKNGEIA LCTLSALNLG LINDLHDLKE
LSTLSVRALD EILEYQNYPV VCAKKSAISR RSLGIGVINF AYYLAKNKVR YSDGSAKNLT
HKTFEAIQYY LLKASCELAK EKGSCSLFNQ TNYYLGKFPI DTYKKDIDSI CNEPLHLNWN
LLRKKIKKYG LRNSTLSALM PSETSSQISN ATNGIEPPRG FISIKSSKDG MLRQVVPEYK
KLKSEYELLW EIPNNIGYLE LVAIMQKFVD QSISANTNYD PKRFLNEKIP MKQLIYDLLV
AYKLGIKTLY YQNTRDGAED NQNLNKSIEN IKEDNCTSGS CTI
