ID Y079_DEIRA Reviewed; 171 AA.
AC Q9RY71;
DT 10-JAN-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 27-MAR-2024, entry version 124.
DE RecName: Full=Nudix hydrolase DR_0079;
DE EC=3.6.1.-;
GN OrderedLocusNames=DR_0079;
OS Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG
OS 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1).
OC Bacteria; Deinococcota; Deinococci; Deinococcales; Deinococcaceae;
OC Deinococcus.
OX NCBI_TaxID=243230;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC
RC 15346 / NCIMB 9279 / VKM B-1422 / R1;
RX PubMed=10567266; DOI=10.1126/science.286.5444.1571;
RA White O., Eisen J.A., Heidelberg J.F., Hickey E.K., Peterson J.D.,
RA Dodson R.J., Haft D.H., Gwinn M.L., Nelson W.C., Richardson D.L.,
RA Moffat K.S., Qin H., Jiang L., Pamphile W., Crosby M., Shen M.,
RA Vamathevan J.J., Lam P., McDonald L.A., Utterback T.R., Zalewski C.,
RA Makarova K.S., Aravind L., Daly M.J., Minton K.W., Fleischmann R.D.,
RA Ketchum K.A., Nelson K.E., Salzberg S.L., Smith H.O., Venter J.C.,
RA Fraser C.M.;
RT "Genome sequence of the radioresistant bacterium Deinococcus radiodurans
RT R1.";
RL Science 286:1571-1577(1999).
RN [2]
RP SUBUNIT, AND CRYSTALLIZATION.
RX PubMed=12657797; DOI=10.1107/s0907444903002671;
RA Holbrook E.L., Schulze-Gahmen U., Buchko G.W., Ni S., Kennedy M.A.,
RA Holbrook S.R.;
RT "Purification, crystallization and preliminary X-ray analysis of two nudix
RT hydrolases from Deinococcus radiodurans.";
RL Acta Crystallogr. D 59:737-740(2003).
RN [3]
RP STRUCTURE BY NMR, FUNCTION, AND COFACTOR.
RX PubMed=15162484; DOI=10.1002/prot.20082;
RA Buchko G.W., Ni S., Holbrook S.R., Kennedy M.A.;
RT "Solution structure of hypothetical Nudix hydrolase DR0079 from extremely
RT radiation-resistant Deinococcus radiodurans bacterium.";
RL Proteins 56:28-39(2004).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
RP COFACTOR, SUBUNIT, ACTIVITY REGULATION, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=18512963; DOI=10.1021/bi800099d;
RA Buchko G.W., Litvinova O., Robinson H., Yakunin A.F., Kennedy M.A.;
RT "Functional and structural characterization of DR_0079 from Deinococcus
RT radiodurans, a novel Nudix hydrolase with a preference for cytosine
RT (deoxy)ribonucleoside 5'-di- and triphosphates.";
RL Biochemistry 47:6571-6582(2008).
CC -!- FUNCTION: Hydrolase that converts various nucleotide triphosphates
CC (NTPs) to the corresponding nucleotide monophosphates and diphosphate,
CC and nucleotide diphosphates to nucleotide monophosphates and inorganic
CC phosphate. Has a marked preference for cytosine ribonucleoside 5'-
CC diphosphate (CDP) and cytosine ribonucleoside 5'-triphosphate (CTP).
CC Has lower activity towards the deoxyribose nucleotides dCDP and dCTP,
CC and towards dGDP, TDP and UDP. {ECO:0000269|PubMed:15162484,
CC ECO:0000269|PubMed:18512963}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:15162484, ECO:0000269|PubMed:18512963};
CC -!- ACTIVITY REGULATION: Inhibited by zinc, calcium or copper ions.
CC {ECO:0000269|PubMed:18512963}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.082 mM for CDP {ECO:0000269|PubMed:18512963};
CC KM=0.034 mM for CTP {ECO:0000269|PubMed:18512963};
CC KM=0.092 mM for dCDP {ECO:0000269|PubMed:18512963};
CC KM=0.105 mM for TDP {ECO:0000269|PubMed:18512963};
CC KM=0.137 mM for UDP {ECO:0000269|PubMed:18512963};
CC KM=0.092 mM for GDP {ECO:0000269|PubMed:18512963};
CC KM=0.051 mM for dGDP {ECO:0000269|PubMed:18512963};
CC KM=0.046 mM for IDP {ECO:0000269|PubMed:18512963};
CC pH dependence:
CC Optimum pH is 9.0-9.5. {ECO:0000269|PubMed:18512963};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:12657797,
CC ECO:0000269|PubMed:18512963}.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. {ECO:0000305}.
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DR EMBL; AE000513; AAF09672.1; -; Genomic_DNA.
DR PIR; E75562; E75562.
DR RefSeq; NP_293805.1; NC_001263.1.
DR RefSeq; WP_010886727.1; NZ_JMLF01000020.1.
DR PDB; 1Q27; NMR; -; A=1-171.
DR PDB; 2O5F; X-ray; 1.90 A; A/B=1-171.
DR PDBsum; 1Q27; -.
DR PDBsum; 2O5F; -.
DR AlphaFoldDB; Q9RY71; -.
DR BMRB; Q9RY71; -.
DR SMR; Q9RY71; -.
DR STRING; 243230.DR_0079; -.
DR PaxDb; 243230-DR_0079; -.
DR EnsemblBacteria; AAF09672; AAF09672; DR_0079.
DR GeneID; 69516309; -.
DR KEGG; dra:DR_0079; -.
DR PATRIC; fig|243230.17.peg.242; -.
DR eggNOG; COG0494; Bacteria.
DR HOGENOM; CLU_060552_3_1_0; -.
DR InParanoid; Q9RY71; -.
DR OrthoDB; 67499at2; -.
DR EvolutionaryTrace; Q9RY71; -.
DR Proteomes; UP000002524; Chromosome I.
DR GO; GO:0016787; F:hydrolase activity; IDA:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0009117; P:nucleotide metabolic process; IDA:UniProtKB.
DR Gene3D; 3.90.79.10; Nucleoside Triphosphate Pyrophosphohydrolase; 1.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR020084; NUDIX_hydrolase_CS.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR PANTHER; PTHR10885; ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE; 1.
DR PANTHER; PTHR10885:SF20; NUDIX HYDROLASE DOMAIN-CONTAINING PROTEIN; 1.
DR Pfam; PF00293; NUDIX; 1.
DR SUPFAM; SSF55811; Nudix; 1.
DR PROSITE; PS51462; NUDIX; 1.
DR PROSITE; PS00893; NUDIX_BOX; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Magnesium; Metal-binding; Nucleotide-binding;
KW Reference proteome.
FT CHAIN 1..171
FT /note="Nudix hydrolase DR_0079"
FT /id="PRO_0000057076"
FT DOMAIN 32..162
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT MOTIF 69..91
FT /note="Nudix box"
FT BINDING 85
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000305"
FT BINDING 89
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000305"
FT STRAND 8..12
FT /evidence="ECO:0007829|PDB:2O5F"
FT STRAND 18..23
FT /evidence="ECO:0007829|PDB:2O5F"
FT HELIX 31..33
FT /evidence="ECO:0007829|PDB:2O5F"
FT STRAND 34..42
FT /evidence="ECO:0007829|PDB:2O5F"
FT TURN 44..46
FT /evidence="ECO:0007829|PDB:1Q27"
FT STRAND 48..52
FT /evidence="ECO:0007829|PDB:2O5F"
FT STRAND 58..60
FT /evidence="ECO:0007829|PDB:2O5F"
FT STRAND 67..71
FT /evidence="ECO:0007829|PDB:2O5F"
FT STRAND 73..76
FT /evidence="ECO:0007829|PDB:1Q27"
FT HELIX 78..90
FT /evidence="ECO:0007829|PDB:2O5F"
FT HELIX 94..96
FT /evidence="ECO:0007829|PDB:2O5F"
FT STRAND 97..105
FT /evidence="ECO:0007829|PDB:2O5F"
FT TURN 107..109
FT /evidence="ECO:0007829|PDB:2O5F"
FT STRAND 113..122
FT /evidence="ECO:0007829|PDB:2O5F"
FT TURN 131..133
FT /evidence="ECO:0007829|PDB:2O5F"
FT STRAND 135..140
FT /evidence="ECO:0007829|PDB:2O5F"
FT HELIX 142..151
FT /evidence="ECO:0007829|PDB:2O5F"
FT HELIX 159..166
FT /evidence="ECO:0007829|PDB:2O5F"
SQ SEQUENCE 171 AA; 19283 MW; 254C737BB2A0276E CRC64;
MGGVSDERLD LVNERDEVVG QILRTDPALR WERVRVVNAF LRNSQGQLWI PRRSPSKSLF
PNALDVSVGG AVQSGETYEE AFRREAREEL NVEIDALSWR PLASFSPFQT TLSSFMCVYE
LRSDATPIFN PNDISGGEWL TPEHLLARIA AGEAAKGDLA ELVRRCYREE E
//
