YNCF_BACSU
ID YNCF_BACSU Reviewed; 144 AA.
AC O31801;
DT 24-NOV-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=Deoxyuridine 5'-triphosphate nucleotidohydrolase YncF;
DE Short=dUTPase;
DE EC=3.6.1.23 {ECO:0000250|UniProtKB:O34919};
DE AltName: Full=dUTP pyrophosphatase;
GN Name=yncF; OrderedLocusNames=BSU17660;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [2]
RP DISRUPTION PHENOTYPE.
RC STRAIN=168;
RX PubMed=17114254; DOI=10.1128/jb.01381-06;
RA Thomaides H.B., Davison E.J., Burston L., Johnson H., Brown D.R.,
RA Hunt A.C., Errington J., Czaplewski L.;
RT "Essential bacterial functions encoded by gene pairs.";
RL J. Bacteriol. 189:591-602(2007).
RN [3]
RP PRELIMINARY CRYSTALLIZATION.
RX PubMed=19342774; DOI=10.1107/s1744309109006228;
RA Li G.-L., Wang J., Li L.-F., Su X.-D.;
RT "Crystallization and preliminary X-ray analysis of three dUTPases from
RT Gram-positive bacteria.";
RL Acta Crystallogr. F 65:339-342(2009).
RN [4] {ECO:0007744|PDB:2XCD, ECO:0007744|PDB:2XCE}
RP X-RAY CRYSTALLOGRAPHY (1.84 ANGSTROMS) ALONE AND IN COMPLEX WITH SUBSTRATE
RP ANALOG, PROBABLE ACTIVE SITE, COFACTOR, AND SUBUNIT.
RX PubMed=20823546; DOI=10.1107/s0907444910026272;
RA Garcia-Nafria J., Burchell L., Takezawa M., Rzechorzek N.J., Fogg M.J.,
RA Wilson K.S.;
RT "The structure of the genomic Bacillus subtilis dUTPase: novel features in
RT the Phe-lid.";
RL Acta Crystallogr. D 66:953-961(2010).
RN [5] {ECO:0007744|PDB:4AOO, ECO:0007744|PDB:4AOZ, ECO:0007744|PDB:4APZ, ECO:0007744|PDB:4B0H}
RP X-RAY CRYSTALLOGRAPHY (1.18 ANGSTROMS) IN COMPLEX WITH 2'-DEOXYURIDINE;
RP DIPHOSPHATE(2-) AND PHOSPHATE(3-), PROBABLE ACTIVE SITE, SUBUNIT, AND
RP DOMAIN.
RX PubMed=23897460; DOI=10.1107/s090744491300735x;
RA Garcia-Nafria J., Timm J., Harrison C., Turkenburg J.P., Wilson K.S.;
RT "Tying down the arm in Bacillus dUTPase: structure and mechanism.";
RL Acta Crystallogr. D 69:1367-1380(2013).
CC -!- FUNCTION: Involved in nucleotide metabolism: produces dUMP, the
CC immediate precursor of thymidine nucleotides and decreases the
CC intracellular concentration of dUTP, so that uracil cannot be
CC incorporated into DNA (Probable). The Ser-64 side chain changes its
CC position upon ligand-binding to make contacts with the nucleotide
CC phosphates (PubMed:20823546). {ECO:0000269|PubMed:20823546,
CC ECO:0000305|PubMed:20823546}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dUTP + H2O = diphosphate + dUMP + H(+); Xref=Rhea:RHEA:10248,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:61555, ChEBI:CHEBI:246422; EC=3.6.1.23;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:20823546, ECO:0000269|PubMed:23897460};
CC Note=Binds 1 Mg(2+) per subunit, coordinated entirely by the nucleotide
CC and ordered water molecules. {ECO:0000269|PubMed:20823546,
CC ECO:0000269|PubMed:23897460};
CC -!- PATHWAY: Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP (dUTP
CC route): step 2/2.
CC -!- SUBUNIT: Homotrimer. {ECO:0000269|PubMed:20823546,
CC ECO:0000269|PubMed:23897460}.
CC -!- DOMAIN: The uracil deoxyribose moiety interacts with the protein
CC through Ile-81 and Tyr-85, which discriminate against the ribose form
CC of the nucleotide. {ECO:0000269|PubMed:20823546,
CC ECO:0000269|PubMed:23897460}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype; double yncF-yosS deletions
CC (both encode dUTPases) are also viable. {ECO:0000269|PubMed:17114254}.
CC -!- SIMILARITY: Belongs to the dUTPase family. {ECO:0000305}.
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; AL009126; CAB13650.1; -; Genomic_DNA.
DR PIR; H69888; H69888.
DR RefSeq; NP_389649.1; NC_000964.3.
DR RefSeq; WP_003245820.1; NZ_JNCM01000035.1.
DR PDB; 2XCD; X-ray; 1.84 A; A/B/C/D/E/F=1-144.
DR PDB; 2XCE; X-ray; 1.85 A; A/B/C/D/E/F=1-144.
DR PDB; 4AOO; X-ray; 2.30 A; A/B/C/D=1-144.
DR PDB; 4AOZ; X-ray; 2.05 A; A/B/C=1-144.
DR PDB; 4APZ; X-ray; 2.01 A; 1/2/3/4/5/6/7/8/9/A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X/Y/Z/a/b/c/d/e/f/g/h/i/j/k/l/m=1-144.
DR PDB; 4B0H; X-ray; 1.18 A; A/B/C=1-144.
DR PDBsum; 2XCD; -.
DR PDBsum; 2XCE; -.
DR PDBsum; 4AOO; -.
DR PDBsum; 4AOZ; -.
DR PDBsum; 4APZ; -.
DR PDBsum; 4B0H; -.
DR AlphaFoldDB; O31801; -.
DR SMR; O31801; -.
DR STRING; 224308.BSU17660; -.
DR PaxDb; O31801; -.
DR PRIDE; O31801; -.
DR EnsemblBacteria; CAB13650; CAB13650; BSU_17660.
DR GeneID; 939541; -.
DR KEGG; bsu:BSU17660; -.
DR PATRIC; fig|224308.179.peg.1917; -.
DR eggNOG; COG0756; Bacteria.
DR InParanoid; O31801; -.
DR OMA; ERICQFR; -.
DR PhylomeDB; O31801; -.
DR BioCyc; BSUB:BSU17660-MON; -.
DR BRENDA; 3.6.1.23; 658.
DR UniPathway; UPA00610; UER00666.
DR EvolutionaryTrace; O31801; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0004170; F:dUTP diphosphatase activity; IBA:GO_Central.
DR GO; GO:0000287; F:magnesium ion binding; IBA:GO_Central.
DR GO; GO:0006226; P:dUMP biosynthetic process; IBA:GO_Central.
DR GO; GO:0046081; P:dUTP catabolic process; IBA:GO_Central.
DR CDD; cd07557; trimeric_dUTPase; 1.
DR Gene3D; 2.70.40.10; -; 1.
DR InterPro; IPR008181; dUTPase.
DR InterPro; IPR029054; dUTPase-like.
DR InterPro; IPR036157; dUTPase-like_sf.
DR InterPro; IPR033704; dUTPase_trimeric.
DR PANTHER; PTHR11241; PTHR11241; 1.
DR Pfam; PF00692; dUTPase; 1.
DR SUPFAM; SSF51283; SSF51283; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Magnesium; Metal-binding; Nucleotide metabolism;
KW Reference proteome.
FT CHAIN 1..144
FT /note="Deoxyuridine 5'-triphosphate nucleotidohydrolase
FT YncF"
FT /id="PRO_0000389001"
FT ACT_SITE 82
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:20823546,
FT ECO:0000305|PubMed:23897460"
FT BINDING 64
FT /ligand="dUTP"
FT /ligand_id="ChEBI:CHEBI:61555"
FT /evidence="ECO:0000305|PubMed:20823546,
FT ECO:0007744|PDB:2XCE"
FT BINDING 76
FT /ligand="dUTP"
FT /ligand_id="ChEBI:CHEBI:61555"
FT /evidence="ECO:0000305|PubMed:20823546,
FT ECO:0007744|PDB:2XCE"
FT BINDING 85
FT /ligand="dUTP"
FT /ligand_id="ChEBI:CHEBI:61555"
FT /evidence="ECO:0000305|PubMed:20823546,
FT ECO:0007744|PDB:2XCE"
FT BINDING 93
FT /ligand="dUTP"
FT /ligand_id="ChEBI:CHEBI:61555"
FT /evidence="ECO:0000305|PubMed:20823546,
FT ECO:0007744|PDB:2XCE"
FT STRAND 3..11
FT /evidence="ECO:0007829|PDB:4B0H"
FT STRAND 24..29
FT /evidence="ECO:0007829|PDB:4B0H"
FT STRAND 34..36
FT /evidence="ECO:0007829|PDB:4B0H"
FT STRAND 41..45
FT /evidence="ECO:0007829|PDB:4B0H"
FT STRAND 48..51
FT /evidence="ECO:0007829|PDB:4B0H"
FT STRAND 56..62
FT /evidence="ECO:0007829|PDB:4B0H"
FT HELIX 66..70
FT /evidence="ECO:0007829|PDB:4B0H"
FT STRAND 72..74
FT /evidence="ECO:0007829|PDB:4B0H"
FT STRAND 77..81
FT /evidence="ECO:0007829|PDB:4B0H"
FT STRAND 93..100
FT /evidence="ECO:0007829|PDB:4B0H"
FT STRAND 102..104
FT /evidence="ECO:0007829|PDB:4B0H"
FT STRAND 109..117
FT /evidence="ECO:0007829|PDB:4B0H"
FT STRAND 122..126
FT /evidence="ECO:0007829|PDB:4B0H"
FT TURN 138..141
FT /evidence="ECO:0007829|PDB:4AOO"
SQ SEQUENCE 144 AA; 16410 MW; 2E15AE84170ED23B CRC64;
MTMQIKIKYL DETQTRISKI EQGDWIDLRA AEDVTIKKDE FKLVPLGVAM ELPEGYEAHV
VPRSSTYKNF GVIQTNSMGV IDESYKGDND FWFFPAYALR DTEIKKGDRI CQFRIMKKMP
AVELVEVEHL GNEDRGGLGS TGTK
