YGK1_YEAST
ID YGK1_YEAST Reviewed; 215 AA.
AC P53144; D6VU44;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=5'-deoxynucleotidase YGK1 {ECO:0000305};
DE EC=3.1.3.89 {ECO:0000269|PubMed:29752939};
GN Name=YGK1 {ECO:0000303|PubMed:29752939, ECO:0000312|SGD:S000003069};
GN OrderedLocusNames=YGL101W {ECO:0000312|SGD:S000003069};
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=9290212;
RX DOI=10.1002/(sici)1097-0061(19970915)13:11<1077::aid-yea152>3.0.co;2-y;
RA Rieger M., Brueckner M., Schaefer M., Mueller-Auer S.;
RT "Sequence analysis of 203 kilobases from Saccharomyces cerevisiae
RT chromosome VII.";
RL Yeast 13:1077-1090(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169869;
RA Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J.,
RA Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M.,
RA Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L.,
RA Coblenz A., Coglievina M., Coissac E., Defoor E., Del Bino S., Delius H.,
RA Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P.,
RA Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M.,
RA Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A.,
RA Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K.,
RA Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P.,
RA Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E.,
RA Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
RA Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A.,
RA Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S.,
RA Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M.,
RA Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C.,
RA Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M.,
RA Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M.,
RA Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y.,
RA Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L.,
RA Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D.,
RA Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F.,
RA Zaccaria P., Zimmermann M., Zollner A., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
RL Nature 387:81-84(1997).
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 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 X-RAY CRYSTALLOGRAPHY (2.61 ANGSTROMS) IN COMPLEX WITH ZINC, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP MUTAGENESIS OF HIS-89; ASP-90; GLU-93; HIS-111; GLU-114 AND GLU-145.
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 -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.18 mM for dGMP {ECO:0000269|PubMed:29752939};
CC KM=0.23 mM for dTMP {ECO:0000269|PubMed:29752939};
CC KM=0.32 mM for dAMP {ECO:0000269|PubMed:29752939};
CC KM=0.36 mM for dCMP {ECO:0000269|PubMed:29752939};
CC Vmax=0.18 umol/min/mg enzyme toward dGMP
CC {ECO:0000269|PubMed:29752939};
CC Vmax=0.17 umol/min/mg enzyme toward dTMP
CC {ECO:0000269|PubMed:29752939};
CC Vmax=0.15 umol/min/mg enzyme toward dAMP
CC {ECO:0000269|PubMed:29752939};
CC Vmax=0.085 umol/min/mg enzyme toward dCMP
CC {ECO:0000269|PubMed:29752939};
CC Note=kcat is 1.2 sec(-1) with dGMP as substrate. kcat is 1.1 sec(-1)
CC with dTMP as substrate. kcat is 1.0 sec(-1) with dAMP as substrate.
CC kcat is 0.28 sec(-1) with dCMP as substrate.
CC {ECO:0000269|PubMed:29752939};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:29752939}.
CC -!- MISCELLANEOUS: Present with 1500 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the HDDC2 family. {ECO:0000305}.
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DR EMBL; Z72623; CAA96807.1; -; Genomic_DNA.
DR EMBL; BK006941; DAA08005.1; -; Genomic_DNA.
DR PIR; S64108; S64108.
DR RefSeq; NP_011414.1; NM_001180966.1.
DR PDB; 5YOX; X-ray; 2.61 A; A/B/C/D/E/F/G/H=1-215.
DR PDBsum; 5YOX; -.
DR AlphaFoldDB; P53144; -.
DR SMR; P53144; -.
DR BioGRID; 33148; 50.
DR IntAct; P53144; 1.
DR STRING; 4932.YGL101W; -.
DR iPTMnet; P53144; -.
DR MaxQB; P53144; -.
DR PaxDb; P53144; -.
DR PRIDE; P53144; -.
DR EnsemblFungi; YGL101W_mRNA; YGL101W; YGL101W.
DR GeneID; 852777; -.
DR KEGG; sce:YGL101W; -.
DR SGD; S000003069; YGK1.
DR VEuPathDB; FungiDB:YGL101W; -.
DR eggNOG; KOG3197; Eukaryota.
DR GeneTree; ENSGT00390000009937; -.
DR HOGENOM; CLU_039453_2_0_1; -.
DR InParanoid; P53144; -.
DR OMA; YEKRDNI; -.
DR BioCyc; YEAST:G3O-30601-MON; -.
DR BRENDA; 3.1.3.89; 984.
DR PRO; PR:P53144; -.
DR Proteomes; UP000002311; Chromosome VII.
DR RNAct; P53144; 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 3D-structure; Cobalt; Hydrolase; Magnesium; Manganese; Metal-binding;
KW Reference proteome.
FT CHAIN 1..215
FT /note="5'-deoxynucleotidase YGK1"
FT /id="PRO_0000202754"
FT DOMAIN 58..164
FT /note="HD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01175"
FT BINDING 61
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:29752939,
FT ECO:0007744|PDB:5YOX"
FT BINDING 89
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:29752939,
FT ECO:0007744|PDB:5YOX"
FT BINDING 90
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:29752939,
FT ECO:0007744|PDB:5YOX"
FT BINDING 93
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q7Z4H3"
FT BINDING 98
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q7Z4H3"
FT BINDING 99
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q7Z4H3"
FT BINDING 159
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:29752939,
FT ECO:0007744|PDB:5YOX"
FT MUTAGEN 89
FT /note="H->A: Abolishes activity."
FT /evidence="ECO:0000269|PubMed:29752939"
FT MUTAGEN 90
FT /note="D->A: Abolishes activity."
FT /evidence="ECO:0000269|PubMed:29752939"
FT MUTAGEN 93
FT /note="E->A: Abolishes activity."
FT /evidence="ECO:0000269|PubMed:29752939"
FT MUTAGEN 111
FT /note="H->A: No effect on activity."
FT /evidence="ECO:0000269|PubMed:29752939"
FT MUTAGEN 114
FT /note="E->A: Abolishes activity."
FT /evidence="ECO:0000269|PubMed:29752939"
FT MUTAGEN 145
FT /note="E->A: Abolishes activity."
FT /evidence="ECO:0000269|PubMed:29752939"
FT HELIX 9..12
FT /evidence="ECO:0007829|PDB:5YOX"
FT HELIX 15..21
FT /evidence="ECO:0007829|PDB:5YOX"
FT STRAND 22..25
FT /evidence="ECO:0007829|PDB:5YOX"
FT HELIX 28..37
FT /evidence="ECO:0007829|PDB:5YOX"
FT HELIX 58..69
FT /evidence="ECO:0007829|PDB:5YOX"
FT HELIX 79..89
FT /evidence="ECO:0007829|PDB:5YOX"
FT HELIX 109..125
FT /evidence="ECO:0007829|PDB:5YOX"
FT TURN 126..129
FT /evidence="ECO:0007829|PDB:5YOX"
FT HELIX 131..145
FT /evidence="ECO:0007829|PDB:5YOX"
FT HELIX 150..172
FT /evidence="ECO:0007829|PDB:5YOX"
FT STRAND 174..176
FT /evidence="ECO:0007829|PDB:5YOX"
FT TURN 181..185
FT /evidence="ECO:0007829|PDB:5YOX"
FT HELIX 193..210
FT /evidence="ECO:0007829|PDB:5YOX"
SQ SEQUENCE 215 AA; 25297 MW; 399B8D818BF47D71 CRC64;
MTAVNIWKPE DNIPREILAI LSKPHPNYQL AFLNIIQLLK TQRRTGWVDH GIDPCESISD
HMYRMGLTTM LITDKNVDRN KCIRIALVHD FAESLVGDIT PNDPMTKEEK HRREFETVKY
LCESIIRPCS ESASREILDD WLAYEKQTCL EGRYVKDIDK YEMLVQCFEY EQKYNGKKDL
KQFLGAINDI KTDEVKKWTQ SLLEDRQAFF DSLKE
