ID   YBF5_YEAST              Reviewed;         418 AA.
AC   P34220; D6VPU5; Q6B2V4;
DT   01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-1994, sequence version 1.
DT   27-MAR-2024, entry version 160.
DE   RecName: Full=Deoxyribonuclease Tat-D;
DE            EC=3.1.21.-;
GN   OrderedLocusNames=YBL055C; ORFNames=YBL0511, YBL0512;
OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC   Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX   NCBI_TaxID=559292;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=8154187; DOI=10.1002/yea.320091210;
RA   Scherens B., el Bakkoury M., Vierendeels F., Dubois E., Messenguy F.;
RT   "Sequencing and functional analysis of a 32,560 bp segment on the left arm
RT   of yeast chromosome II. Identification of 26 open reading frames, including
RT   the KIP1 and SEC17 genes.";
RL   Yeast 9:1355-1371(1993).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=7813418; DOI=10.1002/j.1460-2075.1994.tb06923.x;
RA   Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C.,
RA   Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M.,
RA   Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M.,
RA   Cziepluch C., Demolis N., Delaveau T., Doignon F., Domdey H.,
RA   Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D.,
RA   Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N.,
RA   Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J.,
RA   Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C.,
RA   Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P.,
RA   Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y.,
RA   Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F.,
RA   Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E.,
RA   Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M.,
RA   Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B.,
RA   Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L.,
RA   Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M.,
RA   Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S.,
RA   Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K.,
RA   Mewes H.-W., Kleine K.;
RT   "Complete DNA sequence of yeast chromosome II.";
RL   EMBO J. 13:5795-5809(1994).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=24374639; DOI=10.1534/g3.113.008995;
RA   Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA   Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA   Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT   "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL   G3 (Bethesda) 4:389-398(2014).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=17322287; DOI=10.1101/gr.6037607;
RA   Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA   Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA   Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA   Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA   LaBaer J.;
RT   "Approaching a complete repository of sequence-verified protein-encoding
RT   clones for Saccharomyces cerevisiae.";
RL   Genome Res. 17:536-543(2007).
RN   [5]
RP   SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX   PubMed=14562095; DOI=10.1038/nature02026;
RA   Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA   Weissman J.S., O'Shea E.K.;
RT   "Global analysis of protein localization in budding yeast.";
RL   Nature 425:686-691(2003).
RN   [6]
RP   LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX   PubMed=14562106; DOI=10.1038/nature02046;
RA   Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA   O'Shea E.K., Weissman J.S.;
RT   "Global analysis of protein expression in yeast.";
RL   Nature 425:737-741(2003).
RN   [7]
RP   FUNCTION, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF
RP   GLU-185; GLU-325 AND ASP-327.
RX   PubMed=15657035; DOI=10.1074/jbc.m413547200;
RA   Qiu J., Yoon J.H., Shen B.;
RT   "Search for apoptotic nucleases in yeast: role of Tat-D nuclease in
RT   apoptotic DNA degradation.";
RL   J. Biol. Chem. 280:15370-15379(2005).
CC   -!- FUNCTION: Has both endo- and exonuclease activities. Incises double-
CC       stranded DNA without obvious specificity via its endonuclease activity
CC       and excises the DNA from the 3'-to 5'-end by its exonuclease activity.
CC       May have a role in apoptosis. {ECO:0000269|PubMed:15657035}.
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000269|PubMed:15657035};
CC       Note=Divalent metal cations. Has optimal activity with Mg(2+).
CC       {ECO:0000269|PubMed:15657035};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       pH dependence:
CC         Optimum pH is 5. {ECO:0000269|PubMed:15657035};
CC       Temperature dependence:
CC         Optimum temperature is 30 degrees Celsius.
CC         {ECO:0000269|PubMed:15657035};
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}.
CC   -!- MISCELLANEOUS: Present with 1460 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the metallo-dependent hydrolases superfamily.
CC       TatD-type hydrolase 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; Z23261; CAA80792.1; -; Genomic_DNA.
DR   EMBL; Z35816; CAA84875.1; -; Genomic_DNA.
DR   EMBL; AY692626; AAT92645.1; -; Genomic_DNA.
DR   EMBL; BK006936; DAA07065.1; -; Genomic_DNA.
DR   PIR; S39833; S39833.
DR   RefSeq; NP_009498.1; NM_001178295.1.
DR   AlphaFoldDB; P34220; -.
DR   SMR; P34220; -.
DR   BioGRID; 32644; 71.
DR   MINT; P34220; -.
DR   STRING; 4932.YBL055C; -.
DR   MaxQB; P34220; -.
DR   PaxDb; 4932-YBL055C; -.
DR   PeptideAtlas; P34220; -.
DR   TopDownProteomics; P34220; -.
DR   EnsemblFungi; YBL055C_mRNA; YBL055C; YBL055C.
DR   GeneID; 852225; -.
DR   KEGG; sce:YBL055C; -.
DR   AGR; SGD:S000000151; -.
DR   SGD; S000000151; YBL055C.
DR   VEuPathDB; FungiDB:YBL055C; -.
DR   eggNOG; KOG3020; Eukaryota.
DR   GeneTree; ENSGT00940000156272; -.
DR   HOGENOM; CLU_031506_1_0_1; -.
DR   InParanoid; P34220; -.
DR   OMA; CSDIFFE; -.
DR   OrthoDB; 2331935at2759; -.
DR   BioCyc; YEAST:G3O-28953-MONOMER; -.
DR   BioGRID-ORCS; 852225; 8 hits in 10 CRISPR screens.
DR   PRO; PR:P34220; -.
DR   Proteomes; UP000002311; Chromosome II.
DR   RNAct; P34220; Protein.
DR   GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR   GO; GO:0008296; F:3'-5'-DNA exonuclease activity; IDA:SGD.
DR   GO; GO:0004519; F:endonuclease activity; IDA:SGD.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0006309; P:apoptotic DNA fragmentation; IMP:SGD.
DR   GO; GO:0034599; P:cellular response to oxidative stress; IMP:SGD.
DR   CDD; cd01310; TatD_DNAse; 1.
DR   Gene3D; 3.20.20.140; Metal-dependent hydrolases; 1.
DR   InterPro; IPR018228; DNase_TatD-rel_CS.
DR   InterPro; IPR032466; Metal_Hydrolase.
DR   InterPro; IPR001130; TatD-like.
DR   PANTHER; PTHR10060:SF15; DEOXYRIBONUCLEASE TATDN1; 1.
DR   PANTHER; PTHR10060; TATD FAMILY DEOXYRIBONUCLEASE; 1.
DR   Pfam; PF01026; TatD_DNase; 1.
DR   SUPFAM; SSF51556; Metallo-dependent hydrolases; 1.
DR   PROSITE; PS01090; TATD_2; 1.
DR   PROSITE; PS01091; TATD_3; 1.
PE   1: Evidence at protein level;
KW   Cytoplasm; Hydrolase; Metal-binding; Nuclease; Reference proteome.
FT   CHAIN           1..418
FT                   /note="Deoxyribonuclease Tat-D"
FT                   /id="PRO_0000201994"
FT   BINDING         185
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         185
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         226
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         277
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         327
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   MUTAGEN         185
FT                   /note="E->A: Reduces enzymatic activities by 50%."
FT                   /evidence="ECO:0000269|PubMed:15657035"
FT   MUTAGEN         325
FT                   /note="E->A: Reduces enzymatic activities by 50%."
FT                   /evidence="ECO:0000269|PubMed:15657035"
FT   MUTAGEN         327
FT                   /note="D->A: Reduces enzymatic activities by almost 95%."
FT                   /evidence="ECO:0000269|PubMed:15657035"
FT   CONFLICT        278
FT                   /note="S -> P (in Ref. 4; AAT92645)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   418 AA;  47390 MW;  F1107C1B8E94CAD1 CRC64;
     MWGILLKSSN KSCSRLWKPI LTQYYSMTST ATDSPLKYYD IGLNLTDPMF HGIYNGKQYH
     PADYVKLLER AAQRHVKNAL VTGSSIAESQ SAIELVSSVK DLSPLKLYHT IGVHPCCVNE
     FADASQGDKA SASIDNPSMD EAYNESLYAK VISNPSFAQG KLKELYDLMN QQAKPHDTSF
     RSIGEIGLDY DRFHYSSKEM QKVFFEEQLK ISCLNDKLSS YPLFLHMRSA CDDFVQILER
     FIAGFTDERD TFQLQKLGAS SSSGFYKFHP DRKLVVHSFT GSAIDLQKLL NLSPNIFIGV
     NGCSLRTEEN LAVVKQIPTE RLLLETDAPW CEIKRTHASF QYLAKYQEVR DFEYPAFKSV
     KKNKLADKLN AEELYMVKGR NEPCNMEQVA IVVSEVKDVD LATLIDTTWK TTCKIFGE
//