YB92_YEAST
ID YB92_YEAST Reviewed; 238 AA.
AC P38331; D6VQN8;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1994, sequence version 1.
DT 03-AUG-2022, entry version 149.
DE RecName: Full=5'-deoxynucleotidase YBR242W {ECO:0000305};
DE EC=3.1.3.89 {ECO:0000269|PubMed:29752939};
GN OrderedLocusNames=YBR242W; ORFNames=YBR1627;
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 [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 [2]
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 [3]
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 [4]
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 [5]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND SUBUNIT.
RX PubMed=29752939; DOI=10.1016/j.bbrc.2018.05.047;
RA Yang J., Wang F., Yang D., Zhou K., Liu M., Gao Z., Liu P., Dong Y.,
RA Zhang J., Liu Q.;
RT "Structural and biochemical characterization of the yeast HD domain
RT containing protein YGK1 reveals a metal-dependent nucleoside 5'-
RT monophosphatase.";
RL Biochem. Biophys. Res. Commun. 501:674-681(2018).
CC -!- FUNCTION: Catalyzes the dephosphorylation of the nucleoside 5'-
CC monophosphates deoxyadenosine monophosphate (dAMP), deoxycytidine
CC monophosphate (dCMP), deoxyguanosine monophosphate (dGMP) and
CC deoxythymidine monophosphate (dTMP). {ECO:0000269|PubMed:29752939}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-phosphate + H2O = a 2'-
CC deoxyribonucleoside + phosphate; Xref=Rhea:RHEA:36167,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:18274, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:65317; EC=3.1.3.89;
CC Evidence={ECO:0000269|PubMed:29752939};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:29752939};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:29752939};
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:29752939};
CC Note=Binds 2 divalent metal cations (By similarity). Shows activity
CC with Mn(2+), Co(2+) and Mg(2+) but shows no activity with Zn(2+)
CC (PubMed:29752939). {ECO:0000250|UniProtKB:Q7Z4H3,
CC ECO:0000269|PubMed:29752939};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:29752939}.
CC -!- MISCELLANEOUS: Present with 2730 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the HDDC2 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; Z36111; CAA85205.1; -; Genomic_DNA.
DR EMBL; AY692615; AAT92634.1; -; Genomic_DNA.
DR EMBL; BK006936; DAA07358.1; -; Genomic_DNA.
DR PIR; S46119; S46119.
DR RefSeq; NP_009801.1; NM_001178590.1.
DR AlphaFoldDB; P38331; -.
DR SMR; P38331; -.
DR BioGRID; 32937; 39.
DR DIP; DIP-4887N; -.
DR IntAct; P38331; 2.
DR STRING; 4932.YBR242W; -.
DR MaxQB; P38331; -.
DR PaxDb; P38331; -.
DR PRIDE; P38331; -.
DR EnsemblFungi; YBR242W_mRNA; YBR242W; YBR242W.
DR GeneID; 852544; -.
DR KEGG; sce:YBR242W; -.
DR SGD; S000000446; YBR242W.
DR VEuPathDB; FungiDB:YBR242W; -.
DR eggNOG; KOG3197; Eukaryota.
DR GeneTree; ENSGT00390000009937; -.
DR HOGENOM; CLU_039453_2_0_1; -.
DR InParanoid; P38331; -.
DR OMA; VWQEYED; -.
DR BioCyc; YEAST:G3O-29173-MON; -.
DR PRO; PR:P38331; -.
DR Proteomes; UP000002311; Chromosome II.
DR RNAct; P38331; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0002953; F:5'-deoxynucleotidase activity; IDA:SGD.
DR GO; GO:0050484; F:GMP 5'-nucleotidase activity; IDA:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0009159; P:deoxyribonucleoside monophosphate catabolic process; IDA:SGD.
DR CDD; cd00077; HDc; 1.
DR InterPro; IPR003607; HD/PDEase_dom.
DR InterPro; IPR006674; HD_domain.
DR InterPro; IPR039356; YfbR/HDDC2.
DR PANTHER; PTHR11845; PTHR11845; 1.
DR Pfam; PF13023; HD_3; 1.
DR SMART; SM00471; HDc; 1.
DR PROSITE; PS51831; HD; 1.
PE 1: Evidence at protein level;
KW Cobalt; Hydrolase; Magnesium; Manganese; Metal-binding; Reference proteome.
FT CHAIN 1..238
FT /note="5'-deoxynucleotidase YBR242W"
FT /id="PRO_0000202522"
FT DOMAIN 77..183
FT /note="HD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01175"
FT BINDING 80
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P53144"
FT BINDING 108
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P53144"
FT BINDING 109
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P53144"
FT BINDING 112
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q7Z4H3"
FT BINDING 117
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q7Z4H3"
FT BINDING 118
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q7Z4H3"
FT BINDING 178
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P53144"
SQ SEQUENCE 238 AA; 27577 MW; CDE8283134B6F48F CRC64;
MTATITNKKS CSGSVEAGKT RLTTEWKPES QVPQYVKNEL SKPHPNYILA FLNVVQQLKI
QRRTGYLDLG IKECESISDH MYRLSIITML IKDSRVNRDK CVRIALVHDI AESLVGDITP
VDPIGKEEKH RREWETIKYL CNALIKPYNE IAAKEIMDDW LAYENVTSLE ARYVKDIDKY
EMLVQCFEYE REYKGTKNFD DFFGAVASIK TDEVKGWTSD LVVQRQKYFA DLTQSITK
