RIR1_HELPY
ID RIR1_HELPY Reviewed; 788 AA.
AC P55982;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=Ribonucleoside-diphosphate reductase subunit alpha;
DE EC=1.17.4.1;
DE AltName: Full=Ribonucleotide reductase;
GN Name=nrdA; OrderedLocusNames=HP_0680;
OS Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori).
OC Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC Helicobacteraceae; Helicobacter.
OX NCBI_TaxID=85962;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700392 / 26695;
RX PubMed=9252185; DOI=10.1038/41483;
RA Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G.,
RA Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A.,
RA Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N.,
RA Loftus B.J., Richardson D.L., Dodson R.J., Khalak H.G., Glodek A.,
RA McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E.,
RA Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D.,
RA Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S.,
RA Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C.;
RT "The complete genome sequence of the gastric pathogen Helicobacter
RT pylori.";
RL Nature 388:539-547(1997).
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; AE000511; AAD14884.1; -; Genomic_DNA.
DR PIR; H64604; H64604.
DR RefSeq; NP_207474.1; NC_000915.1.
DR RefSeq; WP_000633984.1; NC_018939.1.
DR AlphaFoldDB; P55982; -.
DR SMR; P55982; -.
DR DIP; DIP-3151N; -.
DR IntAct; P55982; 5.
DR MINT; P55982; -.
DR STRING; 85962.C694_03505; -.
DR PaxDb; P55982; -.
DR EnsemblBacteria; AAD14884; AAD14884; HP_0680.
DR KEGG; hpy:HP_0680; -.
DR PATRIC; fig|85962.47.peg.728; -.
DR eggNOG; COG0209; Bacteria.
DR OMA; LEIWHID; -.
DR PhylomeDB; P55982; -.
DR UniPathway; UPA00326; -.
DR Proteomes; UP000000429; Chromosome.
DR GO; GO:0005971; C:ribonucleoside-diphosphate reductase complex; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IBA:GO_Central.
DR GO; GO:0004748; F:ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor; IBA:GO_Central.
DR GO; GO:0009263; P:deoxyribonucleotide biosynthetic process; IBA:GO_Central.
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; Reference proteome.
FT CHAIN 1..788
FT /note="Ribonucleoside-diphosphate reductase subunit alpha"
FT /id="PRO_0000187215"
FT DOMAIN 2..92
FT /note="ATP-cone"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00492"
FT ACT_SITE 424
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 426
FT /note="Cysteine radical intermediate"
FT /evidence="ECO:0000250"
FT ACT_SITE 428
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 6
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="allosteric activator"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 12..18
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="allosteric activator"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 52
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="allosteric activator"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 200
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 223..225
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 253
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 424
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 428
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 661..663
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT SITE 216
FT /note="Important for hydrogen atom transfer"
FT /evidence="ECO:0000250"
FT SITE 497
FT /note="Important for hydrogen atom transfer"
FT /evidence="ECO:0000250"
FT SITE 763
FT /note="Important for electron transfer"
FT /evidence="ECO:0000250"
FT SITE 764
FT /note="Important for electron transfer"
FT /evidence="ECO:0000250"
FT SITE 784
FT /note="Interacts with thioredoxin/glutaredoxin"
FT /evidence="ECO:0000250"
FT SITE 787
FT /note="Interacts with thioredoxin/glutaredoxin"
FT /evidence="ECO:0000250"
FT DISULFID 216..497
FT /note="Redox-active"
FT /evidence="ECO:0000250"
SQ SEQUENCE 788 AA; 90160 MW; BF22559D3D3796D4 CRC64;
MITVVKRNGR IEPLDITKIQ KYTKDATDNL EGVSQSELEV DARLQFRDKI TTEEIQQTLI
KTAVDKIDID TPNWSFVASR LFLYDLYHKV SGFTGYRHLK EYFENAEEKG RILKGFKEKF
DLEFLNSQIK PERDFQFNYL GIKTLYDRYL LKDANNNPIE LPQHMFMSIA MFLAQNEQEP
NKIALEFYEV LSKFEAMCAT PTLANARTTK HQLSSCYIGS TPDNIEGIFD SYKEMALLSK
YGGGIGWDFS LVRSIGSYID GHKNASAGTI PFLKIANDVA IAVDQLGTRK GAIAVYLEIW
HIDVMEFIDL RKNSGDERRR AHDLFPALWV CDLFLKRVLE DAMWTLFDPY ECKDLTELYG
QDFEKRYLEY EKDPKIIKEY INAKDLWKKI LMNYFEAGLP FLAFKDNANR CNPNAHAGII
RSSNLCTEIF QNTAPNHYYM QIEYTDGTIE FFEEKELVTT DSNITKCANK LTSTDILKGK
PIYIATKVAK DGQTAVCNLA SINLSKINTE EDIKRVVPIM VRLLDNVIDL NFYPNRKVKA
TNLQNRAIGL GVMGEAQMLA EHQIAWGSKE HLEKIDALME QISYHAIDTS ANLAKEKGVY
KDFENSEWSK GIFPIDKANN EALKLTEKGL FNHACDWQGL REKVKANGMR NGYLMAIAPT
SSISILVGTT QTIEPIYKKK WFEENLSGLI PVVVPNLNVE TWNFYTSAYD IDAKDLIKAA
AVRQKWIDQG QSLNVFLRIE NASGKTLHDI YTLAWKLGLK STYYLRSESP SIDEKSVLDR
SVECFNCQ