YBF5_YEAST
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 03-AUG-2022, entry version 151.
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}.
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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; 67.
DR MINT; P34220; -.
DR STRING; 4932.YBL055C; -.
DR MaxQB; P34220; -.
DR PaxDb; P34220; -.
DR PRIDE; P34220; -.
DR TopDownProteomics; P34220; -.
DR EnsemblFungi; YBL055C_mRNA; YBL055C; YBL055C.
DR GeneID; 852225; -.
DR KEGG; sce:YBL055C; -.
DR SGD; S000000151; YBL055C.
DR VEuPathDB; FungiDB:YBL055C; -.
DR eggNOG; KOG3020; Eukaryota.
DR GeneTree; ENSGT00940000156272; -.
DR HOGENOM; CLU_031506_1_0_1; -.
DR OMA; CNIERVA; -.
DR BioCyc; YEAST:G3O-28953-MON; -.
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'-exodeoxyribonuclease 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 InterPro; IPR018228; DNase_TatD-rel_CS.
DR InterPro; IPR032466; Metal_Hydrolase.
DR InterPro; IPR001130; TatD-like.
DR Pfam; PF01026; TatD_DNase; 1.
DR SUPFAM; SSF51556; SSF51556; 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
