RIR1_HELPJ
ID RIR1_HELPJ Reviewed; 788 AA.
AC Q9ZLF9;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 03-AUG-2022, entry version 132.
DE RecName: Full=Ribonucleoside-diphosphate reductase subunit alpha;
DE EC=1.17.4.1;
DE AltName: Full=Ribonucleotide reductase;
GN Name=nrdA; OrderedLocusNames=jhp_0621;
OS Helicobacter pylori (strain J99 / ATCC 700824) (Campylobacter pylori J99).
OC Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC Helicobacteraceae; Helicobacter.
OX NCBI_TaxID=85963;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=J99 / ATCC 700824;
RX PubMed=9923682; DOI=10.1038/16495;
RA Alm R.A., Ling L.-S.L., Moir D.T., King B.L., Brown E.D., Doig P.C.,
RA Smith D.R., Noonan B., Guild B.C., deJonge B.L., Carmel G., Tummino P.J.,
RA Caruso A., Uria-Nickelsen M., Mills D.M., Ives C., Gibson R., Merberg D.,
RA Mills S.D., Jiang Q., Taylor D.E., Vovis G.F., Trust T.J.;
RT "Genomic sequence comparison of two unrelated isolates of the human gastric
RT pathogen Helicobacter pylori.";
RL Nature 397:176-180(1999).
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; AE001439; AAD06201.1; -; Genomic_DNA.
DR PIR; F71908; F71908.
DR RefSeq; WP_000633948.1; NZ_CP011330.1.
DR AlphaFoldDB; Q9ZLF9; -.
DR SMR; Q9ZLF9; -.
DR STRING; 85963.jhp_0621; -.
DR EnsemblBacteria; AAD06201; AAD06201; jhp_0621.
DR KEGG; hpj:jhp_0621; -.
DR PATRIC; fig|85963.30.peg.363; -.
DR eggNOG; COG0209; Bacteria.
DR OMA; LEIWHID; -.
DR UniPathway; UPA00326; -.
DR Proteomes; UP000000804; 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..788
FT /note="Ribonucleoside-diphosphate reductase subunit alpha"
FT /id="PRO_0000187216"
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; 90232 MW; A98AFCBC5CC6398E CRC64;
MITVVKRNGR IEPLDITKIQ KYTKDATDNL EGVSQSELEV DARLQFRDKI TTEEIQQTLI
KTAVDKIDID TPNWSFVASR LFLYDLYHKV SGFTGYRHLK EYFENAEEKG RILKGFKEKF
DLEFLNSQIK PERDFQFNYL GIKTLYDRYL LKDANNHPIE LPQHMFMSIA MFLAQNEQEL
NKIALEFYEV LSKFEAMCAT PTLANARTTK HQLSSCYIGS TPDNIEGIFD SYKEMALLSK
YGGGIGWDFS LVRSIGSYID GHKNASAGTI PFLKIANDVA IAVDQLGTRK GAIAVYLEIW
HIDVMEFIDL RKNSGDERRR AHDLFPALWV CDLFMKRVLE DAMWTLFDPY ECKDLTELYG
QDFEKRYLEY EKDPKIIKEY INAKDLWKKI LMNYFEAGLP FLAFKDNANR CNPNAHAGII
RSSNLCTEIF QNTAPNHYYM QIEYTDGAIE FFEEKELVTT DSNITKCANK LTSTDILKGK
KIYIATKVAK DGQTAVCNLA SINLSKINTE EDIKRVVPIM VRLLDNVIDL NFYPNRKVKA
TNLQNRAIGL GVMGEAQMLA EHQIAWGSKE HLEKIDALME QISYHAIDTS ANLAKEKGVY
KDFENSEWSK GIFPIDKANN EALKLTEKGL FNHACDWQGL REKVKANGMR NGYLMAIAPT
SSISILVGTT QTIEPIYKKK WFEENLSGLI PVVVPNLNVE TWNFYTSAYD IDAKDLIKAA
AVRQKWIDQG QSINVFLRIE NASGKTLHEI YTLAWKLGLK STYYLRSESP SIDEKSVLDR
SVECFNCQ
