PRPD_YARLI
ID PRPD_YARLI Reviewed; 520 AA.
AC Q6C354;
DT 24-JUN-2015, integrated into UniProtKB/Swiss-Prot.
DT 16-AUG-2004, sequence version 1.
DT 25-MAY-2022, entry version 84.
DE RecName: Full=2-methylcitrate dehydratase, mitochondrial {ECO:0000303|Ref.2, ECO:0000303|Ref.3};
DE EC=4.2.1.79 {ECO:0000269|PubMed:7117251, ECO:0000269|Ref.2, ECO:0000269|Ref.3};
DE Flags: Precursor;
GN Name=PDH1 {ECO:0000303|PubMed:24432372}; OrderedLocusNames=YALI0F02497g;
OS Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Dipodascaceae; Yarrowia.
OX NCBI_TaxID=284591;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CLIB 122 / E 150;
RX PubMed=15229592; DOI=10.1038/nature02579;
RA Dujon B., Sherman D., Fischer G., Durrens P., Casaregola S., Lafontaine I.,
RA de Montigny J., Marck C., Neuveglise C., Talla E., Goffard N., Frangeul L.,
RA Aigle M., Anthouard V., Babour A., Barbe V., Barnay S., Blanchin S.,
RA Beckerich J.-M., Beyne E., Bleykasten C., Boisrame A., Boyer J.,
RA Cattolico L., Confanioleri F., de Daruvar A., Despons L., Fabre E.,
RA Fairhead C., Ferry-Dumazet H., Groppi A., Hantraye F., Hennequin C.,
RA Jauniaux N., Joyet P., Kachouri R., Kerrest A., Koszul R., Lemaire M.,
RA Lesur I., Ma L., Muller H., Nicaud J.-M., Nikolski M., Oztas S.,
RA Ozier-Kalogeropoulos O., Pellenz S., Potier S., Richard G.-F.,
RA Straub M.-L., Suleau A., Swennen D., Tekaia F., Wesolowski-Louvel M.,
RA Westhof E., Wirth B., Zeniou-Meyer M., Zivanovic Y., Bolotin-Fukuhara M.,
RA Thierry A., Bouchier C., Caudron B., Scarpelli C., Gaillardin C.,
RA Weissenbach J., Wincker P., Souciet J.-L.;
RT "Genome evolution in yeasts.";
RL Nature 430:35-44(2004).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND INDUCTION.
RX DOI=10.1271/bbb1961.45.2823;
RA Tabuchi T., Aoki H., Uchiyama H., Nakahara T.;
RT "2-methylcitrate dehydratase, a new enzyme functioning at the methylcitric
RT acid cycle of propionate metabolism.";
RL Agric. Biol. Chem. 45:2823-2829(1981).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND SUBUNIT.
RX DOI=10.1271/bbb1961.45.2831;
RA Aoki H., Tabuchi T.;
RT "Purification and properties of 2-methylcitrate dehydratase from Yarrowia
RT lipolytica.";
RL Agric. Biol. Chem. 45:2831-2837(1981).
RN [4]
RP SUBCELLULAR LOCATION, FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=7117251; DOI=10.1111/j.1432-1033.1982.tb06713.x;
RA Uchiyama H., Ando M., Toyonaka Y., Tabuchi T.;
RT "Subcellular localization of the methylcitric-acid-cycle enzymes in
RT propionate metabolism of Yarrowia lipolytica.";
RL Eur. J. Biochem. 125:523-527(1982).
RN [5]
RP FUNCTION.
RX DOI=10.1271/bbb.59.2013;
RA Tabuchi T., Umetsua H., Aokiab H., Uchiyamaac H.;
RT "Characteristics of 2-methylisocitrate dehydratase, isolated from Yallowia
RT lipolytica, in comparison with aconitase.";
RL Biosci. Biotechnol. Biochem. 59:2013-2017(1995).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=24432372; DOI=10.1016/j.jbiotec.2013.10.025;
RA Papanikolaou S., Beopoulos A., Koletti A., Thevenieau F., Koutinas A.A.,
RA Nicaud J.M., Aggelis G.;
RT "Importance of the methyl-citrate cycle on glycerol metabolism in the yeast
RT Yarrowia lipolytica.";
RL J. Biotechnol. 168:303-314(2013).
CC -!- FUNCTION: Component of the methylcitrate cycle that catalyzes the
CC dehydration of 2-methylcitrate to 2-methyl-cis-aconitate. The
CC methylcitrate cycle is a metabolic pathway for the consumption of
CC propionic acid. {ECO:0000269|PubMed:24432372,
CC ECO:0000269|PubMed:7117251, ECO:0000269|Ref.2, ECO:0000269|Ref.3,
CC ECO:0000269|Ref.5}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2S,3S)-2-methylcitrate = 2-methyl-cis-aconitate + H2O;
CC Xref=Rhea:RHEA:17725, ChEBI:CHEBI:15377, ChEBI:CHEBI:57872,
CC ChEBI:CHEBI:58853; EC=4.2.1.79; Evidence={ECO:0000269|PubMed:7117251,
CC ECO:0000269|Ref.2, ECO:0000269|Ref.3};
CC -!- ACTIVITY REGULATION: Several bivalent metal ions, such as nickel,
CC copper, zinc, mercury, and lead, inhibit the activity to some extent.
CC Inhibited by structural analogs such as citrate, cis-aconitate,
CC isocitrate, 2-methylisocitrate, tricarballylate and fluorocitrate, but
CC not by trans-aconitate or adipate. {ECO:0000269|Ref.3}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.19 mM for 2-methylcitrate {ECO:0000269|Ref.3};
CC pH dependence:
CC Optimum pH is 6.5-7.0. {ECO:0000269|Ref.2};
CC Temperature dependence:
CC Optimum temperature is 25-40 degrees Celsius. {ECO:0000269|Ref.2};
CC -!- PATHWAY: Organic acid metabolism; propanoate degradation.
CC {ECO:0000269|Ref.2, ECO:0000269|Ref.3}.
CC -!- SUBUNIT: Monomer. {ECO:0000269|Ref.3}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:7117251}.
CC -!- INDUCTION: Slightly repressed by glucose. {ECO:0000269|Ref.2}.
CC -!- DISRUPTION PHENOTYPE: Leads to lipid accumulation and increased citrate
CC production when biodiesel-derived waste glycerol is used as substrate.
CC {ECO:0000269|PubMed:24432372}.
CC -!- SIMILARITY: Belongs to the PrpD 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; CR382132; CAG77711.1; -; Genomic_DNA.
DR RefSeq; XP_504908.1; XM_504908.1.
DR AlphaFoldDB; Q6C354; -.
DR SMR; Q6C354; -.
DR STRING; 4952.CAG77711; -.
DR EnsemblFungi; CAG77711; CAG77711; YALI0_F02497g.
DR GeneID; 2908117; -.
DR KEGG; yli:YALI0F02497g; -.
DR VEuPathDB; FungiDB:YALI0_F02497g; -.
DR HOGENOM; CLU_021803_1_0_1; -.
DR InParanoid; Q6C354; -.
DR OMA; ECTKHLG; -.
DR UniPathway; UPA00946; -.
DR Proteomes; UP000001300; Chromosome F.
DR GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:InterPro.
DR GO; GO:0047547; F:2-methylcitrate dehydratase activity; IEA:UniProtKB-EC.
DR GO; GO:0019679; P:propionate metabolic process, methylcitrate cycle; IEA:InterPro.
DR Gene3D; 1.10.4100.10; -; 1.
DR Gene3D; 3.30.1330.120; -; 1.
DR InterPro; IPR012705; 2Me_IsoCit_deHydtase_PrpD.
DR InterPro; IPR036148; MmgE/PrpD_sf.
DR InterPro; IPR042183; MmgE/PrpD_sf_1.
DR InterPro; IPR042188; MmgE/PrpD_sf_2.
DR InterPro; IPR005656; MmgE_PrpD.
DR InterPro; IPR045337; MmgE_PrpD_C.
DR InterPro; IPR045336; MmgE_PrpD_N.
DR PANTHER; PTHR16943; PTHR16943; 1.
DR Pfam; PF03972; MmgE_PrpD; 1.
DR Pfam; PF19305; MmgE_PrpD_C; 1.
DR SUPFAM; SSF103378; SSF103378; 1.
DR TIGRFAMs; TIGR02330; prpD; 1.
PE 1: Evidence at protein level;
KW Lyase; Mitochondrion; Reference proteome; Transit peptide.
FT TRANSIT 1..37
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 38..520
FT /note="2-methylcitrate dehydratase, mitochondrial"
FT /evidence="ECO:0000255"
FT /id="PRO_0000433358"
SQ SEQUENCE 520 AA; 57737 MW; D1470C1F5F5DC7B5 CRC64;
MRAFRSAANF GAASNIYRKS FTPASIASNR FVSARMSSIM TDNARPNTDK VVQDIADYIH
DYKIDSSVAM ETARLCFLDT LGCGLEGLKY QQCANIVGPV VPGTIVPNGT KVPGTDYQVD
PVRGAFNIGT IIRWLDFNDC WLAAEWGHPS DNLGGILAVA DWQTRSAKAG LEGKVFKVKD
VLEGMIKAHE IQGGLAIENS FNRVGLDHVV LVKIASTAVV SGMLGLSREQ TADAISQAFV
DGQSLRTYRH APNTMSRKSW AAGDATSRAV NLALLVKKGE GGMPSILTAK TWGFYDVLFG
GKEFKFQRPY GSYVMENVLF KISFPAEFHA QTACESAMLL HEELKKLGKT SDDIASIKIR
TQEAAMRIID KKGPLHNYAD RDHCIQYMVA IPLIHGRLTA DDYTDEIASD PRIDALREKM
ECVEDKRFSE EYHAPDKRYI GNAIEITLKD GTVLDEIEVN YPIGHRQRRE EGTPVLLEKF
ARHLRGRFPE GQVEKILAAS NQDIVNMDID EYVDLYVKKD
