Y1025_DEIRA
ID Y1025_DEIRA Reviewed; 159 AA.
AC Q9RVK2;
DT 25-MAY-2022, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=Nudix hydrolase DR_1025 {ECO:0000303|PubMed:15123424, ECO:0000303|PubMed:23481913};
DE EC=3.6.1.61 {ECO:0000269|PubMed:23481913};
DE EC=3.6.1.69 {ECO:0000269|PubMed:23481913};
DE AltName: Full=MutT-like DR_1025 {ECO:0000303|PubMed:15123424};
DE AltName: Full=MutT/nudix family protein {ECO:0000312|EMBL:AAF10599.1};
GN OrderedLocusNames=DR_1025 {ECO:0000312|EMBL:AAF10599.1};
OS Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG
OS 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422).
OC Bacteria; Deinococcus-Thermus; Deinococci; Deinococcales; Deinococcaceae;
OC Deinococcus.
OX NCBI_TaxID=243230 {ECO:0000312|EMBL:AAF10599.1, ECO:0000312|Proteomes:UP000002524};
RN [1] {ECO:0000312|EMBL:AAF10599.1, ECO:0000312|Proteomes:UP000002524}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422 {ECO:0000312|Proteomes:UP000002524};
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 FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBSTRATE
RP SPECIFICITY.
RX PubMed=23481913; DOI=10.1016/j.ab.2013.02.023;
RA Xu A., Desai A.M., Brenner S.E., Kirsch J.F.;
RT "A continuous fluorescence assay for the characterization of Nudix
RT hydrolases.";
RL Anal. Biochem. 437:178-184(2013).
RN [4] {ECO:0007744|PDB:1SJY, ECO:0007744|PDB:1SOI, ECO:0007744|PDB:1SU2, ECO:0007744|PDB:1SZ3}
RP X-RAY CRYSTALLOGRAPHY (1.39 ANGSTROMS) AND IN COMPLEXES WITH ATP; GTP
RP ANALOG; MAGNESIUM AND SAMARIUM, COFACTOR, AND SUBUNIT.
RX PubMed=15123424; DOI=10.1016/j.jmb.2004.01.065;
RA Ranatunga W., Hill E.E., Mooster J.L., Holbrook E.L., Schulze-Gahmen U.,
RA Xu W., Bessman M.J., Brenner S.E., Holbrook S.R.;
RT "Structural studies of the Nudix hydrolase DR1025 from Deinococcus
RT radiodurans and its ligand complexes.";
RL J. Mol. Biol. 339:103-116(2004).
CC -!- FUNCTION: Hydrolase that can act as a nucleoside triphosphatase and a
CC dinucleoside polyphosphate pyrophosphatase. The best substrates are 8-
CC oxo-dGTP and 8-oxo-GTP. Other substrates include Ap4A, dGTP and GTP.
CC May be involved in protection from damage caused by radiation.
CC {ECO:0000269|PubMed:23481913}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=8-oxo-dGTP + H2O = 8-oxo-dGDP + H(+) + phosphate;
CC Xref=Rhea:RHEA:59980, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:63715, ChEBI:CHEBI:77896; EC=3.6.1.69;
CC Evidence={ECO:0000269|PubMed:23481913};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=8-oxo-GTP + H2O = 8-oxo-GDP + H(+) + phosphate;
CC Xref=Rhea:RHEA:60032, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:143553, ChEBI:CHEBI:143554;
CC EC=3.6.1.69; Evidence={ECO:0000269|PubMed:23481913};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + P(1),P(4)-bis(5'-adenosyl) tetraphosphate = AMP + ATP +
CC 2 H(+); Xref=Rhea:RHEA:32039, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:58141, ChEBI:CHEBI:456215;
CC EC=3.6.1.61; Evidence={ECO:0000269|PubMed:23481913};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:15123424};
CC Note=Binds 3 Mg(2+) ions per subunit. {ECO:0000269|PubMed:23481913};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=26 uM for 8-oxo-dGTP (at pH 7.6 and 37 degrees Celsius as measured
CC by the Pi sensor assay) {ECO:0000269|PubMed:23481913};
CC KM=28 uM for 8-oxo-dGTP (at pH 7.6 and 37 degrees Celsius as measured
CC by the Fiske-SubbaRow assay) {ECO:0000269|PubMed:23481913};
CC KM=22 uM for 8-oxo-GTP (at pH 7.6 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:23481913};
CC Note=kcat is 0.18 sec(-1) with 8-oxo-dGTP as substrate measured by
CC the Pi sensor assay. kcat is 0.29 sec(-1) with 8-oxo-dGTP as
CC substrate measured by the Fiske-SubbaRow assay. kcat is 0.13 sec(-1)
CC with 8-oxo-GTP as substrate. {ECO:0000269|PubMed:23481913};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:12657797,
CC ECO:0000269|PubMed:15123424}.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family.
CC {ECO:0000255|RuleBase:RU003476}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AE000513; AAF10599.1; -; Genomic_DNA.
DR PIR; C75446; C75446.
DR RefSeq; NP_294749.1; NC_001263.1.
DR RefSeq; WP_010887668.1; NZ_CP015081.1.
DR PDB; 1SJY; X-ray; 1.39 A; A=1-159.
DR PDB; 1SOI; X-ray; 1.80 A; A=1-159.
DR PDB; 1SU2; X-ray; 1.60 A; A/B=1-159.
DR PDB; 1SZ3; X-ray; 1.60 A; A/B=1-159.
DR PDBsum; 1SJY; -.
DR PDBsum; 1SOI; -.
DR PDBsum; 1SU2; -.
DR PDBsum; 1SZ3; -.
DR SMR; Q9RVK2; -.
DR STRING; 243230.DR_1025; -.
DR EnsemblBacteria; AAF10599; AAF10599; DR_1025.
DR KEGG; dra:DR_1025; -.
DR PATRIC; fig|243230.17.peg.1217; -.
DR eggNOG; COG1051; Bacteria.
DR HOGENOM; CLU_1692614_0_0_0; -.
DR InParanoid; Q9RVK2; -.
DR OMA; THRAAGM; -.
DR OrthoDB; 1846332at2; -.
DR EvolutionaryTrace; Q9RVK2; -.
DR Proteomes; UP000002524; Chromosome I.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR InterPro; IPR020476; Nudix_hydrolase.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR020084; NUDIX_hydrolase_CS.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR Pfam; PF00293; NUDIX; 1.
DR PRINTS; PR00502; NUDIXFAMILY.
DR SUPFAM; SSF55811; SSF55811; 1.
DR PROSITE; PS51462; NUDIX; 1.
DR PROSITE; PS00893; NUDIX_BOX; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Hydrolase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome.
FT CHAIN 1..159
FT /note="Nudix hydrolase DR_1025"
FT /id="PRO_0000455561"
FT DOMAIN 11..144
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT MOTIF 50..71
FT /note="Nudix box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794,
FT ECO:0000305|PubMed:15123424"
FT BINDING 1..6
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:15123424,
FT ECO:0007744|PDB:1SU2, ECO:0007744|PDB:1SZ3"
FT BINDING 1
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:15123424,
FT ECO:0007744|PDB:1SU2"
FT BINDING 14
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /evidence="ECO:0000269|PubMed:15123424,
FT ECO:0007744|PDB:1SU2"
FT BINDING 49
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:15123424,
FT ECO:0007744|PDB:1SU2"
FT BINDING 50..51
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:15123424,
FT ECO:0007744|PDB:1SU2, ECO:0007744|PDB:1SZ3"
FT BINDING 53
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:15123424,
FT ECO:0007744|PDB:1SU2"
FT BINDING 65
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:15123424,
FT ECO:0007744|PDB:1SU2, ECO:0007744|PDB:1SZ3"
FT BINDING 87..89
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:15123424,
FT ECO:0007744|PDB:1SU2, ECO:0007744|PDB:1SZ3"
FT BINDING 95
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:15123424,
FT ECO:0007744|PDB:1SU2"
SQ SEQUENCE 159 AA; 17569 MW; 2D209C7DFC972D82 CRC64;
MEHDERTHVP VELRAAGVVL LNERGDILLV QEKGIPGHPE KAGLWHIPSG AVEDGENPQD
AAVREACEET GLRVRPVKFL GAYLGRFPDG VLILRHVWLA EPEPGQTLAP AFTDEIAEAS
FVSREDFAQL YAAGQIRMYQ TKLFYADALR EKGFPALPV
