NPY1_YEAST
ID NPY1_YEAST Reviewed; 384 AA.
AC P53164; D6VU74; E9P928;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 165.
DE RecName: Full=NAD-capped RNA hydrolase NPY1 {ECO:0000305};
DE Short=DeNADding enzyme NPY1 {ECO:0000305};
DE EC=3.6.1.- {ECO:0000250|UniProtKB:Q9DCN1};
DE AltName: Full=NADH pyrophosphatase;
DE EC=3.6.1.22 {ECO:0000269|PubMed:11361135};
GN Name=NPY1 {ECO:0000303|PubMed:11361135, ECO:0000312|SGD:S000003035};
GN OrderedLocusNames=YGL067W;
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=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 [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 CHARACTERIZATION.
RX PubMed=10873676; DOI=10.1006/bbrc.2000.2999;
RA Xu W., Dunn C.A., Bessman M.J.;
RT "Cloning and characterization of the NADH pyrophosphatases from
RT Caenorhabditis elegans and Saccharomyces cerevisiae, members of a Nudix
RT hydrolase subfamily.";
RL Biochem. Biophys. Res. Commun. 273:753-758(2000).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP SUBCELLULAR LOCATION.
RX PubMed=11361135; DOI=10.1006/abbi.2000.2268;
RA AbdelRaheim S.R., Cartwright J.L., Gasmi L., McLennan A.G.;
RT "The NADH diphosphatase encoded by the Saccharomyces cerevisiae NPY1 nudix
RT hydrolase gene is located in peroxisomes.";
RL Arch. Biochem. Biophys. 388:18-24(2001).
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).
CC -!- FUNCTION: mRNA decapping enzyme that specifically removes the
CC nicotinamide adenine dinucleotide (NAD) cap from a subset of mRNAs by
CC hydrolyzing the diphosphate linkage to produce nicotinamide
CC mononucleotide (NMN) and 5' monophosphate mRNA. The NAD-cap is present
CC at the 5'-end of some RNAs; in contrast to the canonical N7
CC methylguanosine (m7G) cap, the NAD cap promotes mRNA decay (By
CC similarity). Mediates the hydrolysis of some nucleoside diphosphate
CC derivatives (PubMed:11361135). {ECO:0000250|UniProtKB:Q9DCN1,
CC ECO:0000269|PubMed:11361135}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end NAD(+)-phospho-ribonucleoside in mRNA + H2O = a 5'-
CC end phospho-adenosine-phospho-ribonucleoside in mRNA + beta-
CC nicotinamide D-ribonucleotide + 2 H(+); Xref=Rhea:RHEA:60876,
CC Rhea:RHEA-COMP:15698, Rhea:RHEA-COMP:15719, ChEBI:CHEBI:14649,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:144029,
CC ChEBI:CHEBI:144051; Evidence={ECO:0000250|UniProtKB:Q9DCN1};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60877;
CC Evidence={ECO:0000250|UniProtKB:Q9DCN1};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + NAD(+) = AMP + beta-nicotinamide D-ribonucleotide + 2
CC H(+); Xref=Rhea:RHEA:11800, ChEBI:CHEBI:14649, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57540, ChEBI:CHEBI:456215;
CC EC=3.6.1.22; Evidence={ECO:0000269|PubMed:11361135};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + NADH = AMP + 2 H(+) + reduced beta-nicotinamide D-
CC ribonucleotide; Xref=Rhea:RHEA:48868, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57945, ChEBI:CHEBI:90832,
CC ChEBI:CHEBI:456215; EC=3.6.1.22;
CC Evidence={ECO:0000269|PubMed:11361135};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:Q9DCN1};
CC Note=Binds 3 Mg(2+) ions per subunit. {ECO:0000250|UniProtKB:Q9DCN1};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250|UniProtKB:Q9DCN1};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000250|UniProtKB:Q9DCN1};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.17 mM for NADH {ECO:0000269|PubMed:11361135};
CC KM=0.5 mM for NAD(+) {ECO:0000269|PubMed:11361135};
CC KM=1.3 mM for ADP-ribose {ECO:0000269|PubMed:11361135};
CC Vmax=2.0 umol/min/mg enzyme with NADH as substrate
CC {ECO:0000269|PubMed:11361135};
CC Vmax=0.85 umol/min/mg enzyme with NAD(+) as substrate
CC {ECO:0000269|PubMed:11361135};
CC Vmax=0.80 umol/min/mg enzyme with ADP-ribose as substrate
CC {ECO:0000269|PubMed:11361135};
CC Note=kcat is 1.5 sec(-1) for NADH. kcat is 0.6 sec(-1) for NAD(+).
CC kcat is 0.6 sec(-1) for ADP-ribose. {ECO:0000269|PubMed:11361135};
CC -!- SUBUNIT: Homodimer.
CC -!- SUBCELLULAR LOCATION: Peroxisome {ECO:0000269|PubMed:11361135}.
CC -!- MISCELLANEOUS: Present with 846 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. NudC subfamily.
CC {ECO:0000305}.
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DR EMBL; Z72589; CAA96771.1; -; Genomic_DNA.
DR EMBL; AY693188; AAT93207.1; -; Genomic_DNA.
DR EMBL; BK006941; DAA08035.1; -; Genomic_DNA.
DR PIR; S64074; S64074.
DR RefSeq; NP_011448.3; NM_001180932.3.
DR AlphaFoldDB; P53164; -.
DR SMR; P53164; -.
DR BioGRID; 33180; 94.
DR IntAct; P53164; 1.
DR MINT; P53164; -.
DR STRING; 4932.YGL067W; -.
DR MaxQB; P53164; -.
DR PaxDb; P53164; -.
DR PRIDE; P53164; -.
DR EnsemblFungi; YGL067W_mRNA; YGL067W; YGL067W.
DR GeneID; 852813; -.
DR KEGG; sce:YGL067W; -.
DR SGD; S000003035; NPY1.
DR VEuPathDB; FungiDB:YGL067W; -.
DR eggNOG; KOG3084; Eukaryota.
DR GeneTree; ENSGT00940000157592; -.
DR HOGENOM; CLU_037162_0_2_1; -.
DR InParanoid; P53164; -.
DR OMA; YSHAKMY; -.
DR BioCyc; YEAST:YGL067W-MON; -.
DR BRENDA; 3.6.1.22; 984.
DR Reactome; R-SCE-197264; Nicotinamide salvaging.
DR PRO; PR:P53164; -.
DR Proteomes; UP000002311; Chromosome VII.
DR RNAct; P53164; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005829; C:cytosol; HDA:SGD.
DR GO; GO:0005777; C:peroxisome; IDA:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000210; F:NAD+ diphosphatase activity; IDA:SGD.
DR GO; GO:0035529; F:NADH pyrophosphatase activity; IBA:GO_Central.
DR GO; GO:0110153; F:RNA NAD-cap (NMN-forming) hydrolase activity; IEA:RHEA.
DR GO; GO:0019677; P:NAD catabolic process; IBA:GO_Central.
DR GO; GO:0006734; P:NADH metabolic process; IDA:SGD.
DR GO; GO:0006742; P:NADP catabolic process; IBA:GO_Central.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR020084; NUDIX_hydrolase_CS.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR InterPro; IPR015376; Znr_NADH_PPase.
DR Pfam; PF00293; NUDIX; 1.
DR Pfam; PF09297; zf-NADH-PPase; 1.
DR SUPFAM; SSF55811; SSF55811; 1.
DR PROSITE; PS51462; NUDIX; 1.
DR PROSITE; PS00893; NUDIX_BOX; 1.
PE 1: Evidence at protein level;
KW Hydrolase; Magnesium; Metal-binding; NAD; Peroxisome; Reference proteome;
KW Zinc.
FT CHAIN 1..384
FT /note="NAD-capped RNA hydrolase NPY1"
FT /id="PRO_0000056961"
FT DOMAIN 219..351
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT MOTIF 257..278
FT /note="Nudix box"
FT MOTIF 378..380
FT /note="Microbody targeting signal"
FT /evidence="ECO:0000250|UniProtKB:Q9BQG2"
FT BINDING 179
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 182
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 197
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 206
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 256..258
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 256
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 272
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 272
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 272
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 276
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 276
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 276
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 322
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 322
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 322
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT CONFLICT 44
FT /note="E -> D (in Ref. 3; AAT93207)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 384 AA; 43516 MW; 96D6768CE2BC8F0B CRC64;
MSTAVTFFGQ HVLNRVSFLR CSKEFIKKSL NHDSTVFIPF IEGEALISPE NGDLVQLSNS
VKSYKNILSA IVPLYTTLLN TTRSRSDESG INVTFLGLLE GTDSAFNFEW SNISYKGTPY
FGLDIRVTES TLFKKVDFEP IFSYPKVTRD HIFKQTNEDA SLYSQGKMYL DWLAKYKFCP
GCGSPLFPVE AGTKLQCSNE NRNVYCNVRD ARINNVCFPR TDPTVIIALT NSDYSKCCLA
RSKKRYGDFV LYSTIAGFME PSETIEEACI REIWEETGIS CKNIDIVRSQ PWPYPCSLMI
GCLGIVQFNS KNEVINLNHD DELLDAQWFD TTEIIQALDK YAGGYRVPFK NDINLPGSTT
IAFQLINHVC ENYKNLRKTS SSHL
