RIR1_AQUAE
ID RIR1_AQUAE Reviewed; 801 AA.
AC O66503;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, 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=aq_094;
OS Aquifex aeolicus (strain VF5).
OC Bacteria; Aquificae; Aquificales; Aquificaceae; Aquifex.
OX NCBI_TaxID=224324;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=VF5;
RX PubMed=9537320; DOI=10.1038/32831;
RA Deckert G., Warren P.V., Gaasterland T., Young W.G., Lenox A.L.,
RA Graham D.E., Overbeek R., Snead M.A., Keller M., Aujay M., Huber R.,
RA Feldman R.A., Short J.M., Olsen G.J., Swanson R.V.;
RT "The complete genome of the hyperthermophilic bacterium Aquifex aeolicus.";
RL Nature 392:353-358(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 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; AE000657; AAC06460.1; -; Genomic_DNA.
DR PIR; D70309; D70309.
DR RefSeq; NP_213062.1; NC_000918.1.
DR RefSeq; WP_010880000.1; NC_000918.1.
DR PDB; 7AGJ; X-ray; 2.70 A; A/B=1-801.
DR PDBsum; 7AGJ; -.
DR AlphaFoldDB; O66503; -.
DR SMR; O66503; -.
DR STRING; 224324.aq_094; -.
DR PRIDE; O66503; -.
DR EnsemblBacteria; AAC06460; AAC06460; aq_094.
DR KEGG; aae:aq_094; -.
DR PATRIC; fig|224324.8.peg.82; -.
DR eggNOG; COG0209; Bacteria.
DR HOGENOM; CLU_000404_3_0_0; -.
DR InParanoid; O66503; -.
DR OMA; RGSIQNI; -.
DR OrthoDB; 357568at2; -.
DR UniPathway; UPA00326; -.
DR Proteomes; UP000000798; 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 1: Evidence at protein level;
KW 3D-structure; Allosteric enzyme; ATP-binding;
KW Deoxyribonucleotide synthesis; Disulfide bond; Nucleotide-binding;
KW Oxidoreductase; Reference proteome.
FT CHAIN 1..801
FT /note="Ribonucleoside-diphosphate reductase subunit alpha"
FT /id="PRO_0000187205"
FT DOMAIN 3..92
FT /note="ATP-cone"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00492"
FT ACT_SITE 483
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 485
FT /note="Cysteine radical intermediate"
FT /evidence="ECO:0000250"
FT ACT_SITE 487
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 7
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="allosteric activator"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 13..19
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 88
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="allosteric activator"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 219
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 242..244
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 272
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 279
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 483
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 487
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT BINDING 682..684
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P00452"
FT SITE 235
FT /note="Important for hydrogen atom transfer"
FT /evidence="ECO:0000250"
FT SITE 521
FT /note="Important for hydrogen atom transfer"
FT /evidence="ECO:0000250"
FT SITE 783
FT /note="Important for electron transfer"
FT /evidence="ECO:0000250"
FT SITE 784
FT /note="Important for electron transfer"
FT /evidence="ECO:0000250"
FT SITE 796
FT /note="Interacts with thioredoxin/glutaredoxin"
FT /evidence="ECO:0000250"
FT SITE 799
FT /note="Interacts with thioredoxin/glutaredoxin"
FT /evidence="ECO:0000250"
FT DISULFID 235..521
FT /note="Redox-active"
FT /evidence="ECO:0000250"
FT STRAND 4..6
FT /evidence="ECO:0007829|PDB:7AGJ"
FT STRAND 8..10
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 17..28
FT /evidence="ECO:0007829|PDB:7AGJ"
FT STRAND 31..33
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 35..44
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 52..65
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 74..94
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 110..112
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 113..121
FT /evidence="ECO:0007829|PDB:7AGJ"
FT TURN 122..124
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 129..132
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 136..143
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 148..153
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 156..165
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 179..190
FT /evidence="ECO:0007829|PDB:7AGJ"
FT TURN 191..193
FT /evidence="ECO:0007829|PDB:7AGJ"
FT TURN 196..198
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 199..211
FT /evidence="ECO:0007829|PDB:7AGJ"
FT STRAND 214..217
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 219..224
FT /evidence="ECO:0007829|PDB:7AGJ"
FT STRAND 227..229
FT /evidence="ECO:0007829|PDB:7AGJ"
FT STRAND 235..239
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 244..260
FT /evidence="ECO:0007829|PDB:7AGJ"
FT STRAND 264..267
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 289..301
FT /evidence="ECO:0007829|PDB:7AGJ"
FT STRAND 312..317
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 323..326
FT /evidence="ECO:0007829|PDB:7AGJ"
FT TURN 327..330
FT /evidence="ECO:0007829|PDB:7AGJ"
FT STRAND 341..349
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 351..358
FT /evidence="ECO:0007829|PDB:7AGJ"
FT STRAND 362..366
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 368..377
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 418..431
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 434..436
FT /evidence="ECO:0007829|PDB:7AGJ"
FT STRAND 437..441
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 442..456
FT /evidence="ECO:0007829|PDB:7AGJ"
FT STRAND 460..463
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 464..470
FT /evidence="ECO:0007829|PDB:7AGJ"
FT TURN 472..475
FT /evidence="ECO:0007829|PDB:7AGJ"
FT STRAND 484..486
FT /evidence="ECO:0007829|PDB:7AGJ"
FT TURN 504..506
FT /evidence="ECO:0007829|PDB:7AGJ"
FT STRAND 508..514
FT /evidence="ECO:0007829|PDB:7AGJ"
FT STRAND 523..527
FT /evidence="ECO:0007829|PDB:7AGJ"
FT TURN 528..530
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 534..554
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 560..569
FT /evidence="ECO:0007829|PDB:7AGJ"
FT STRAND 573..577
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 579..584
FT /evidence="ECO:0007829|PDB:7AGJ"
FT TURN 585..587
FT /evidence="ECO:0007829|PDB:7AGJ"
FT STRAND 590..592
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 593..621
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 632..634
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 642..651
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 658..668
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 682..688
FT /evidence="ECO:0007829|PDB:7AGJ"
FT STRAND 700..702
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 718..721
FT /evidence="ECO:0007829|PDB:7AGJ"
FT TURN 722..724
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 728..730
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 734..743
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 744..746
FT /evidence="ECO:0007829|PDB:7AGJ"
FT TURN 759..761
FT /evidence="ECO:0007829|PDB:7AGJ"
FT HELIX 764..777
FT /evidence="ECO:0007829|PDB:7AGJ"
SQ SEQUENCE 801 AA; 92914 MW; FF728EDC7D97C396 CRC64;
MTMYVIKRSG RKEKLDINKI RIAIKFACEG LNVDPLELEA DAQIQFRDGI TTKEIQQLLI
KTAAEKVSAE RPDWTYTAAR LLLYDLYKDV AHLRGYSLRD DLGKYKPYNR KNFYSFVKEY
VEKGIYGEYL LENYSEEDFN KLANYIKPER DLYFTYTGIK ILYDRYLVRD EEGRVIELPQ
EMYMLIAMTL AVPEKPEERL KWAKKFYDVL SEHKVTVATP TLMNARRPFT QLSSCFVLTV
DDDLFDIFDN VKKAGMISKF AGGLGVYLGK IRATGAPIRK FKGASSGVIP VVKLINDTMT
YVDQLGMRKG SASITLDIWH KDILDFLEVK TNVGDERKKA HDIHPAVSIP DLFMKRLKNR
EDWTLIDPYW ARQYITRKIY DGKYKEVKPL PGSHYYVGIK EDGTQDILEP KGLEDFYGEE
FEKWYLELEE NLPSYAKKKV NSFELWKRLL TVAFETGEPY IFFRDEANRK NPNKHTGMVY
SSNLCHEIVQ TMSPSKHEKP VLDPETGEIT YKKEAGDLPV CNLGSVNLGK VHTEEEIKEV
LPLLVRMLDN VIEMNFYAIP EAEYTNKRYR AIGIGVSNYH YCLVKNGIKW ESEEHLKFAD
KLFELIAFYA LKGSLELAKE RGRYKLFDGS NWSKGILFGR SVEEIEENSR QNGNNLPWRE
LAEEIKKYGI RNAYLLALMP TGSTSLILGA TPSIDPIFAR FYKEENMSGI LPQVPPEVDR
FYWHYKTAYT IDHEWTIRAA AVRQKWIDQA QSLNLFVDPQ NIDGPRLSRL YELAWELGLK
TIYYLRSRSA MDIEECEACS V
