PAD1_YEAST
ID PAD1_YEAST Reviewed; 242 AA.
AC P33751; D6VTF7;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 2.
DT 03-AUG-2022, entry version 169.
DE RecName: Full=Flavin prenyltransferase PAD1, mitochondrial {ECO:0000255|HAMAP-Rule:MF_03197, ECO:0000305};
DE EC=2.5.1.129 {ECO:0000250|UniProtKB:Q9HX08, ECO:0000255|HAMAP-Rule:MF_03197};
DE AltName: Full=Phenylacrylic acid decarboxylase 1 {ECO:0000303|PubMed:8181743};
DE Short=PAD {ECO:0000303|PubMed:8181743};
DE Flags: Precursor;
GN Name=PAD1 {ECO:0000255|HAMAP-Rule:MF_03197, ECO:0000303|PubMed:8181743};
GN Synonyms=POF1 {ECO:0000303|PubMed:16232824};
GN OrderedLocusNames=YDR538W {ECO:0000312|SGD:S000002946};
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], AND FUNCTION.
RX PubMed=8181743; DOI=10.1016/0378-1119(94)90363-8;
RA Clausen M., Lamb C.J., Megnet R., Doerner P.W.;
RT "PAD1 encodes phenylacrylic acid decarboxylase which confers resistance to
RT cinnamic acid in Saccharomyces cerevisiae.";
RL Gene 142:107-112(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(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 BIOTECHNOLOGY.
RX PubMed=16232824; DOI=10.1016/s1389-1723(00)80040-7;
RA Shinohara T., Kubodera S., Yanagida F.;
RT "Distribution of phenolic yeasts and production of phenolic off-flavors in
RT wine fermentation.";
RL J. Biosci. Bioeng. 90:90-97(2000).
RN [5]
RP FUNCTION.
RX PubMed=11693915; DOI=10.1007/s002530100742;
RA Larsson S., Nilvebrant N.O., Jonsson L.J.;
RT "Effect of overexpression of Saccharomyces cerevisiae Pad1p on the
RT resistance to phenylacrylic acids and lignocellulose hydrolysates under
RT aerobic and oxygen-limited conditions.";
RL Appl. Microbiol. Biotechnol. 57:167-174(2001).
RN [6]
RP LACK OF DECARBOXYLASE ACTIVITY, AND BIOTECHNOLOGY.
RX PubMed=12903944; DOI=10.1021/jf026224d;
RA Smit A., Cordero Otero R.R., Lambrechts M.G., Pretorius I.S.,
RA Van Rensburg P.;
RT "Enhancing volatile phenol concentrations in wine by expressing various
RT phenolic acid decarboxylase genes in Saccharomyces cerevisiae.";
RL J. Agric. Food Chem. 51:4909-4915(2003).
RN [7]
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 [8]
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 [9]
RP SUBCELLULAR LOCATION.
RX PubMed=17054397; DOI=10.1371/journal.pgen.0020170;
RA Perocchi F., Jensen L.J., Gagneur J., Ahting U., von Mering C., Bork P.,
RA Prokisch H., Steinmetz L.M.;
RT "Assessing systems properties of yeast mitochondria through an interaction
RT map of the organelle.";
RL PLoS Genet. 2:E170-E170(2006).
RN [10]
RP FUNCTION.
RX PubMed=17766451; DOI=10.1128/aem.01246-07;
RA Stratford M., Plumridge A., Archer D.B.;
RT "Decarboxylation of sorbic acid by spoilage yeasts is associated with the
RT PAD1 gene.";
RL Appl. Environ. Microbiol. 73:6534-6542(2007).
RN [11]
RP FUNCTION.
RX PubMed=17889824; DOI=10.1016/j.abb.2007.08.009;
RA Gulmezian M., Hyman K.R., Marbois B.N., Clarke C.F., Javor G.T.;
RT "The role of UbiX in Escherichia coli coenzyme Q biosynthesis.";
RL Arch. Biochem. Biophys. 467:144-153(2007).
RN [12]
RP FUNCTION.
RX PubMed=20471595; DOI=10.1016/j.jbiosc.2009.11.011;
RA Mukai N., Masaki K., Fujii T., Kawamukai M., Iefuji H.;
RT "PAD1 and FDC1 are essential for the decarboxylation of phenylacrylic acids
RT in Saccharomyces cerevisiae.";
RL J. Biosci. Bioeng. 109:564-569(2010).
RN [13]
RP RNA-BINDING.
RX PubMed=20844764; DOI=10.1371/journal.pone.0012671;
RA Tsvetanova N.G., Klass D.M., Salzman J., Brown P.O.;
RT "Proteome-wide search reveals unexpected RNA-binding proteins in
RT Saccharomyces cerevisiae.";
RL PLoS ONE 5:E12671-E12671(2010).
RN [14]
RP BIOTECHNOLOGY.
RX PubMed=21547456; DOI=10.1007/s00253-011-3237-z;
RA Styger G., Jacobson D., Bauer F.F.;
RT "Identifying genes that impact on aroma profiles produced by Saccharomyces
RT cerevisiae and the production of higher alcohols.";
RL Appl. Microbiol. Biotechnol. 91:713-730(2011).
RN [15]
RP FUNCTION.
RX PubMed=23111598; DOI=10.1007/s00253-012-4522-1;
RA Styger G., Jacobson D., Prior B.A., Bauer F.F.;
RT "Genetic analysis of the metabolic pathways responsible for aroma
RT metabolite production by Saccharomyces cerevisiae.";
RL Appl. Microbiol. Biotechnol. 97:4429-4442(2013).
RN [16]
RP FUNCTION, SUBUNIT, MASS SPECTROMETRY, AND FMN-BINDING.
RX PubMed=25647642; DOI=10.1021/cb5008103;
RA Lin F., Ferguson K.L., Boyer D.R., Lin X.N., Marsh E.N.;
RT "Isofunctional enzymes PAD1 and UbiX catalyze formation of a novel cofactor
RT required by ferulic acid decarboxylase and 4-hydroxy-3-polyprenylbenzoic
RT acid decarboxylase.";
RL ACS Chem. Biol. 10:1137-1144(2015).
RN [17]
RP LACK OF DECARBOXYLASE ACTIVITY.
RX PubMed=25852989; DOI=10.1186/s13568-015-0103-x;
RA Richard P., Viljanen K., Penttila M.;
RT "Overexpression of PAD1 and FDC1 results in significant cinnamic acid
RT decarboxylase activity in Saccharomyces cerevisiae.";
RL AMB Express 5:12-12(2015).
CC -!- FUNCTION: Flavin prenyltransferase that catalyzes the synthesis of the
CC prenylated FMN cofactor (prenyl-FMN) for the ferulic acid decarboxylase
CC FDC1/ubiD (PubMed:25647642). The prenyltransferase is metal-independent
CC and links a dimethylallyl moiety from dimethylallyl monophosphate
CC (DMAP) to the flavin N5 and C6 atoms of FMN (By similarity). Involved
CC in the decarboxylation of phenylacrylic acids like ferulic acid, p-
CC coumaric acid or cinnamic acid, producing the corresponding vinyl
CC derivatives which play the role of aroma metabolites. Also involved in
CC the degradation of the food preservative sorbic acid (2,4-hexadienoic
CC acid) to a volatile hydrocarbon, 1,3-pentadiene. Not essential for
CC ubiquinone synthesis (PubMed:17889824, PubMed:20471595). Can rescue Q
CC biosynthesis in E.coli strains lacking UbiX (PubMed:17889824). Has mRNA
CC binding activity (PubMed:20844764). {ECO:0000250|UniProtKB:Q9HX08,
CC ECO:0000255|HAMAP-Rule:MF_03197, ECO:0000269|PubMed:11693915,
CC ECO:0000269|PubMed:12903944, ECO:0000269|PubMed:17766451,
CC ECO:0000269|PubMed:17889824, ECO:0000269|PubMed:20471595,
CC ECO:0000269|PubMed:20844764, ECO:0000269|PubMed:23111598,
CC ECO:0000269|PubMed:25647642, ECO:0000269|PubMed:8181743}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dimethylallyl phosphate + FMNH2 = phosphate + prenyl-FMNH2;
CC Xref=Rhea:RHEA:37743, ChEBI:CHEBI:43474, ChEBI:CHEBI:57618,
CC ChEBI:CHEBI:87467, ChEBI:CHEBI:88052; EC=2.5.1.129;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03197};
CC -!- SUBUNIT: Oligomer. {ECO:0000255|HAMAP-Rule:MF_03197,
CC ECO:0000269|PubMed:25647642}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000255|HAMAP-Rule:MF_03197,
CC ECO:0000269|PubMed:14562095, ECO:0000269|PubMed:17054397}.
CC -!- MASS SPECTROMETRY: Mass=21808; Method=Electrospray; Note=The measured
CC mass is of the truncated protein without mitochondrial targeting
CC sequence including the mass of an N-terminal hexahistidine tag,
CC expressed in E.coli.; Evidence={ECO:0000269|PubMed:25647642};
CC -!- BIOTECHNOLOGY: The activity of wine yeasts to decarboxylate
CC phenylacrylic acids is one of their biological properties related to
CC the production of phenolic off-flavors (POF) in winemaking.
CC {ECO:0000269|PubMed:12903944, ECO:0000269|PubMed:16232824,
CC ECO:0000269|PubMed:21547456}.
CC -!- MISCELLANEOUS: Present with 1750 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the UbiX/PAD1 family. {ECO:0000255|HAMAP-
CC Rule:MF_03197, ECO:0000305}.
CC -!- CAUTION: Was initially thought to be a phenylacrylic acid decarboxylase
CC (PubMed:11693915, PubMed:17766451). However, direct assays could not
CC confirm decarboxylase activity (PubMed:12903944, PubMed:25852989). It
CC has been shown that this enzyme synthesizes the essential cofactor for
CC the associated decarboxylase FDC1. It is therefore thought that
CC decarboxylation defects due to the disruption of this gene were in fact
CC a secondary effect of inactive FDC1 decarboxylase missing its essential
CC cofactor (PubMed:25647642). {ECO:0000269|PubMed:11693915,
CC ECO:0000269|PubMed:12903944, ECO:0000269|PubMed:17766451,
CC ECO:0000269|PubMed:25852989, ECO:0000305|PubMed:25647642}.
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DR EMBL; L09263; AAA20484.1; -; Genomic_DNA.
DR EMBL; U43834; AAB64980.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA12367.1; -; Genomic_DNA.
DR PIR; S62017; S62017.
DR RefSeq; NP_010827.3; NM_001180846.3.
DR AlphaFoldDB; P33751; -.
DR SMR; P33751; -.
DR BioGRID; 32585; 104.
DR DIP; DIP-5454N; -.
DR IntAct; P33751; 2.
DR MINT; P33751; -.
DR STRING; 4932.YDR538W; -.
DR MaxQB; P33751; -.
DR PaxDb; P33751; -.
DR PRIDE; P33751; -.
DR EnsemblFungi; YDR538W_mRNA; YDR538W; YDR538W.
DR GeneID; 852150; -.
DR KEGG; sce:YDR538W; -.
DR SGD; S000002946; PAD1.
DR VEuPathDB; FungiDB:YDR538W; -.
DR eggNOG; ENOG502QWR5; Eukaryota.
DR GeneTree; ENSGT00940000176404; -.
DR HOGENOM; CLU_074522_3_0_1; -.
DR InParanoid; P33751; -.
DR OMA; GATHIQD; -.
DR BioCyc; MetaCyc:YDR538W-MON; -.
DR BioCyc; YEAST:YDR538W-MON; -.
DR PRO; PR:P33751; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; P33751; protein.
DR GO; GO:0005739; C:mitochondrion; IDA:SGD.
DR GO; GO:0016831; F:carboxy-lyase activity; IMP:SGD.
DR GO; GO:0106141; F:flavin prenyltransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0003729; F:mRNA binding; IDA:SGD.
DR GO; GO:0019439; P:aromatic compound catabolic process; IMP:SGD.
DR GO; GO:0034599; P:cellular response to oxidative stress; IDA:CACAO.
DR GO; GO:0046281; P:cinnamic acid catabolic process; IMP:SGD.
DR Gene3D; 3.40.50.1950; -; 1.
DR HAMAP; MF_01984; ubiX_pad; 1.
DR InterPro; IPR036551; Flavin_trans-like.
DR InterPro; IPR003382; Flavoprotein.
DR InterPro; IPR004507; UbiX-like.
DR PANTHER; PTHR43374; PTHR43374; 2.
DR Pfam; PF02441; Flavoprotein; 1.
DR SUPFAM; SSF52507; SSF52507; 1.
DR TIGRFAMs; TIGR00421; ubiX_pad; 1.
PE 1: Evidence at protein level;
KW Flavoprotein; FMN; Mitochondrion; Prenyltransferase; Reference proteome;
KW RNA-binding; Transferase; Transit peptide.
FT TRANSIT 1..58
FT /note="Mitochondrion"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03197"
FT CHAIN 59..242
FT /note="Flavin prenyltransferase PAD1, mitochondrial"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03197"
FT /id="PRO_0000134984"
FT BINDING 63..65
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03197"
FT BINDING 89
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03197"
FT BINDING 140..143
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03197"
FT BINDING 175
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03197"
FT BINDING 205
FT /ligand="dimethylallyl phosphate"
FT /ligand_id="ChEBI:CHEBI:88052"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03197"
FT BINDING 221
FT /ligand="dimethylallyl phosphate"
FT /ligand_id="ChEBI:CHEBI:88052"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03197"
FT CONFLICT 76
FT /note="V -> L (in Ref. 1; AAA20484)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 242 AA; 26733 MW; 9EC09F1197D5C97D CRC64;
MLLFPRRTNI AFFKTTGIFA NFPLLGRTIT TSPSFLTHKL SKEVTRASTS PPRPKRIVVA
ITGATGVALG IRLLQVLKEL SVETHLVISK WGAATMKYET DWEPHDVAAL ATKTYSVRDV
SACISSGSFQ HDGMIVVPCS MKSLAAIRIG FTEDLITRAA DVSIKENRKL LLVTRETPLS
SIHLENMLSL CRAGVIIFPP VPAFYTRPKS LHDLLEQSVG RILDCFGIHA DTFPRWEGIK
SK
