YKD3A_YEAST
ID YKD3A_YEAST Reviewed; 236 AA.
AC Q86ZR7; D6VXQ2;
DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2005, sequence version 2.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=Probable pseudouridine-5'-phosphatase YKL033W-A {ECO:0000305};
DE EC=3.1.3.96 {ECO:0000305|PubMed:26071590};
GN OrderedLocusNames=YKL033W-A {ECO:0000312|SGD:S000007242};
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=8203146; DOI=10.1002/yea.320100112;
RA Purnelle B., Skala J., van Dyck L., Goffeau A.;
RT "Analysis of an 11.7 kb DNA fragment of chromosome XI reveals a new tRNA
RT gene and four new open reading frames including a leucine zipper protein
RT and a homologue to the yeast mitochondrial regulator ABF2.";
RL Yeast 10:125-130(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8196765; DOI=10.1038/369371a0;
RA Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V.,
RA Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P.,
RA Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L.,
RA Daignan-Fornier B., del Rey F., Dion C., Domdey H., Duesterhoeft A.,
RA Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H.,
RA Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L.,
RA Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M.,
RA Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H.,
RA Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J.,
RA Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H.,
RA Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J.,
RA Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S.,
RA Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F.,
RA Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R.,
RA Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W.,
RA Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M.,
RA Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C.,
RA Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H.,
RA Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L.,
RA van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S.,
RA von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M.,
RA Becker I., Mewes H.-W.;
RT "Complete DNA sequence of yeast chromosome XI.";
RL Nature 369:371-378(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] OF 26-98.
RC STRAIN=ATCC 204511 / S288c / AB972;
RX PubMed=12844361; DOI=10.1186/gb-2003-4-7-r45;
RA Brachat S., Dietrich F.S., Voegeli S., Zhang Z., Stuart L., Lerch A.,
RA Gates K., Gaffney T.D., Philippsen P.;
RT "Reinvestigation of the Saccharomyces cerevisiae genome annotation by
RT comparison to the genome of a related fungus: Ashbya gossypii.";
RL Genome Biol. 4:R45.1-R45.13(2003).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=26071590; DOI=10.1074/jbc.m115.657916;
RA Kuznetsova E., Nocek B., Brown G., Makarova K.S., Flick R., Wolf Y.I.,
RA Khusnutdinova A., Evdokimova E., Jin K., Tan K., Hanson A.D., Hasnain G.,
RA Zallot R., de Crecy-Lagard V., Babu M., Savchenko A., Joachimiak A.,
RA Edwards A.M., Koonin E.V., Yakunin A.F.;
RT "Functional diversity of haloacid dehalogenase superfamily phosphatases
RT from Saccharomyces cerevisiae: Biochemical, structural, and evolutionary
RT insights.";
RL J. Biol. Chem. 290:18678-18698(2015).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=29897761; DOI=10.1021/acs.jproteome.8b00032;
RA He C., Jia C., Zhang Y., Xu P.;
RT "Enrichment-based proteogenomics identifies microproteins, missing
RT proteins, and novel smORFs in Saccharomyces cerevisiae.";
RL J. Proteome Res. 17:2335-2344(2018).
CC -!- FUNCTION: Nucleotidase with XMP as the best in vitro substrate. Low
CC catalytic efficiencies of YKL033W-A observed with XMP and other
CC substrates suggest that these could be secondary activities for this
CC protein, and its primary substrate is not yet identified. May possess
CC pseudouridine 5'-phosphatase activity and together with dTTP/UTP
CC pyrophosphatase YOR111W might constitute a pathway for the
CC detoxification of pseudouridine 5'-triphosphate (Psi-UTP) and
CC -monophosphate (Psi-UMP). {ECO:0000269|PubMed:26071590}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + XMP = phosphate + xanthosine; Xref=Rhea:RHEA:28530,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:18107, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:57464; Evidence={ECO:0000305|PubMed:26071590};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:28531;
CC Evidence={ECO:0000305|PubMed:26071590};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + psi-UMP = phosphate + pseudouridine;
CC Xref=Rhea:RHEA:10944, ChEBI:CHEBI:15377, ChEBI:CHEBI:17802,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:58380; EC=3.1.3.96;
CC Evidence={ECO:0000305|PubMed:26071590};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:10945;
CC Evidence={ECO:0000269|PubMed:26071590};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.26 mM for XMP {ECO:0000269|PubMed:26071590};
CC Note=kcat is 1.9 sec(-1) with XMP as substrate.
CC {ECO:0000269|PubMed:26071590};
CC -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=Z28033; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; X71622; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; Z28033; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AY260896; AAP21764.1; -; Genomic_DNA.
DR EMBL; BK006944; DAA09122.1; -; Genomic_DNA.
DR RefSeq; NP_012891.4; NM_001184335.3.
DR AlphaFoldDB; Q86ZR7; -.
DR SMR; Q86ZR7; -.
DR BioGRID; 34098; 66.
DR IntAct; Q86ZR7; 1.
DR STRING; 4932.YKL033W-A; -.
DR iPTMnet; Q86ZR7; -.
DR MaxQB; Q86ZR7; -.
DR PaxDb; Q86ZR7; -.
DR PRIDE; Q86ZR7; -.
DR EnsemblFungi; YKL033W-A_mRNA; YKL033W-A; YKL033W-A.
DR GeneID; 853833; -.
DR KEGG; sce:YKL033W-A; -.
DR SGD; S000007242; YKL033W-A.
DR VEuPathDB; FungiDB:YKL033W-A; -.
DR eggNOG; KOG2914; Eukaryota.
DR GeneTree; ENSGT00390000014753; -.
DR HOGENOM; CLU_045011_13_0_1; -.
DR InParanoid; Q86ZR7; -.
DR OMA; HTLDDSW; -.
DR BioCyc; YEAST:G3O-32091-MON; -.
DR Reactome; R-SCE-73614; Pyrimidine salvage.
DR PRO; PR:Q86ZR7; -.
DR Proteomes; UP000002311; Chromosome XI.
DR RNAct; Q86ZR7; protein.
DR GO; GO:0008253; F:5'-nucleotidase activity; IDA:SGD.
DR GO; GO:0016791; F:phosphatase activity; IBA:GO_Central.
DR GO; GO:1990738; F:pseudouridine 5'-phosphatase activity; IDA:SGD.
DR CDD; cd07529; HAD_AtGPP-like; 1.
DR Gene3D; 1.10.150.240; -; 1.
DR Gene3D; 3.40.50.1000; -; 1.
DR InterPro; IPR045228; Gpp1/Gpp2-like.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR006439; HAD-SF_hydro_IA.
DR InterPro; IPR041492; HAD_2.
DR InterPro; IPR023214; HAD_sf.
DR InterPro; IPR023198; PGP-like_dom2.
DR Pfam; PF13419; HAD_2; 1.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR01509; HAD-SF-IA-v3; 1.
PE 1: Evidence at protein level;
KW Hydrolase; Reference proteome.
FT CHAIN 1..236
FT /note="Probable pseudouridine-5'-phosphatase YKL033W-A"
FT /id="PRO_0000203186"
SQ SEQUENCE 236 AA; 26170 MW; 3F6BE3A774E18AC9 CRC64;
MTHPVAVKAC LFDMDGLLIN TEDIYTETLN ETLAEFGKGP LTWDVKIKLQ GLPGPEAGKR
VIEHYKLPIT LDEYDERNVA LQSLKWGTCE FLPGALNLLK YLKLKNIPIA LCTSSNKTKF
RGKTSHLEEG FDLFDTIVTG DDPRIAKGRG KPFPDIWQLG LKELNEKFHT DIKPDECIVF
EDGIPGVKSA KAFGAHVIWV PHPEAHAVLG DTEALLAGKG ELLSSLEKLE MSKYGL
