PDP1_HUMAN
ID PDP1_HUMAN Reviewed; 537 AA.
AC Q9P0J1; B3KX71; J3KPU0; Q5U5K1;
DT 24-JAN-2001, integrated into UniProtKB/Swiss-Prot.
DT 25-OCT-2005, sequence version 3.
DT 03-AUG-2022, entry version 186.
DE RecName: Full=[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial;
DE Short=PDP 1;
DE EC=3.1.3.43;
DE AltName: Full=Protein phosphatase 2C;
DE AltName: Full=Pyruvate dehydrogenase phosphatase catalytic subunit 1;
DE Short=PDPC 1;
DE Flags: Precursor;
GN Name=PDP1; Synonyms=PDP, PPM2C;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Adrenal gland;
RX PubMed=10931946; DOI=10.1073/pnas.160270997;
RA Hu R.-M., Han Z.-G., Song H.-D., Peng Y.-D., Huang Q.-H., Ren S.-X.,
RA Gu Y.-J., Huang C.-H., Li Y.-B., Jiang C.-L., Fu G., Zhang Q.-H., Gu B.-W.,
RA Dai M., Mao Y.-F., Gao G.-F., Rong R., Ye M., Zhou J., Xu S.-H., Gu J.,
RA Shi J.-X., Jin W.-R., Zhang C.-K., Wu T.-M., Huang G.-Y., Chen Z.,
RA Chen M.-D., Chen J.-L.;
RT "Gene expression profiling in the human hypothalamus-pituitary-adrenal axis
RT and full-length cDNA cloning.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:9543-9548(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), AND NUCLEOTIDE SEQUENCE
RP [LARGE SCALE MRNA] OF 1-101 (ISOFORM 2).
RC TISSUE=Amygdala, and Fetal brain;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16421571; DOI=10.1038/nature04406;
RA Nusbaum C., Mikkelsen T.S., Zody M.C., Asakawa S., Taudien S., Garber M.,
RA Kodira C.D., Schueler M.G., Shimizu A., Whittaker C.A., Chang J.L.,
RA Cuomo C.A., Dewar K., FitzGerald M.G., Yang X., Allen N.R., Anderson S.,
RA Asakawa T., Blechschmidt K., Bloom T., Borowsky M.L., Butler J., Cook A.,
RA Corum B., DeArellano K., DeCaprio D., Dooley K.T., Dorris L. III,
RA Engels R., Gloeckner G., Hafez N., Hagopian D.S., Hall J.L., Ishikawa S.K.,
RA Jaffe D.B., Kamat A., Kudoh J., Lehmann R., Lokitsang T., Macdonald P.,
RA Major J.E., Matthews C.D., Mauceli E., Menzel U., Mihalev A.H.,
RA Minoshima S., Murayama Y., Naylor J.W., Nicol R., Nguyen C., O'Leary S.B.,
RA O'Neill K., Parker S.C.J., Polley A., Raymond C.K., Reichwald K.,
RA Rodriguez J., Sasaki T., Schilhabel M., Siddiqui R., Smith C.L.,
RA Sneddon T.P., Talamas J.A., Tenzin P., Topham K., Venkataraman V., Wen G.,
RA Yamazaki S., Young S.K., Zeng Q., Zimmer A.R., Rosenthal A., Birren B.W.,
RA Platzer M., Shimizu N., Lander E.S.;
RT "DNA sequence and analysis of human chromosome 8.";
RL Nature 439:331-335(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Testis;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [6]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-202, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19608861; DOI=10.1126/science.1175371;
RA Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C.,
RA Olsen J.V., Mann M.;
RT "Lysine acetylation targets protein complexes and co-regulates major
RT cellular functions.";
RL Science 325:834-840(2009).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=25944712; DOI=10.1002/pmic.201400617;
RA Vaca Jacome A.S., Rabilloud T., Schaeffer-Reiss C., Rompais M., Ayoub D.,
RA Lane L., Bairoch A., Van Dorsselaer A., Carapito C.;
RT "N-terminome analysis of the human mitochondrial proteome.";
RL Proteomics 15:2519-2524(2015).
RN [8]
RP VARIANT PDP DEFICIENCY LEU-284 DEL, AND CHARACTERIZATION OF VARIANT PDP
RP DEFICIENCY LEU-284 DEL.
RX PubMed=15855260; DOI=10.1210/jc.2005-0123;
RA Maj M.C., MacKay N., Levandovskiy V., Addis J., Baumgartner E.R.,
RA Baumgartner M.R., Robinson B.H., Cameron J.M.;
RT "Pyruvate dehydrogenase phosphatase deficiency: identification of the first
RT mutation in two brothers and restoration of activity by protein
RT complementation.";
RL J. Clin. Endocrinol. Metab. 90:4101-4107(2005).
CC -!- FUNCTION: Catalyzes the dephosphorylation and concomitant reactivation
CC of the alpha subunit of the E1 component of the pyruvate dehydrogenase
CC complex. {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + O-phospho-L-seryl-[pyruvate dehydrogenase E1 alpha
CC subunit] = L-seryl-[pyruvate dehydrogenase E1 alpha subunit] +
CC phosphate; Xref=Rhea:RHEA:12669, Rhea:RHEA-COMP:13689, Rhea:RHEA-
CC COMP:13690, ChEBI:CHEBI:15377, ChEBI:CHEBI:29999, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:83421; EC=3.1.3.43;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Note=Binds 2 magnesium ions per subunit. {ECO:0000250};
CC -!- SUBUNIT: Heterodimer of a catalytic (PDP1) and a regulatory (PDPR)
CC subunit. {ECO:0000250}.
CC -!- INTERACTION:
CC Q9P0J1; O43439: CBFA2T2; NbExp=3; IntAct=EBI-2861634, EBI-748628;
CC Q9P0J1; Q0VD86: INCA1; NbExp=3; IntAct=EBI-2861634, EBI-6509505;
CC Q9P0J1; Q3LI66: KRTAP6-2; NbExp=3; IntAct=EBI-2861634, EBI-11962084;
CC Q9P0J1; Q6FHY5: MEOX2; NbExp=3; IntAct=EBI-2861634, EBI-16439278;
CC -!- SUBCELLULAR LOCATION: Mitochondrion matrix {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9P0J1-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9P0J1-2; Sequence=VSP_046869;
CC -!- DISEASE: Pyruvate dehydrogenase phosphatase deficiency (PDP deficiency)
CC [MIM:608782]: Results in lactic acidosis leading to neurological
CC dysfunction. {ECO:0000269|PubMed:15855260}. Note=The disease is caused
CC by variants affecting the gene represented in this entry.
CC -!- SIMILARITY: Belongs to the PP2C family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF67480.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AF155661; AAF67480.1; ALT_INIT; mRNA.
DR EMBL; AK126862; BAG54383.1; -; mRNA.
DR EMBL; DA769567; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; AC084346; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH471060; EAW91704.1; -; Genomic_DNA.
DR EMBL; BC047619; AAH47619.1; -; mRNA.
DR EMBL; BC098343; AAH98343.1; -; mRNA.
DR CCDS; CCDS55262.1; -. [Q9P0J1-2]
DR CCDS; CCDS6259.1; -. [Q9P0J1-1]
DR RefSeq; NP_001155251.1; NM_001161779.1. [Q9P0J1-2]
DR RefSeq; NP_001155252.1; NM_001161780.1. [Q9P0J1-2]
DR RefSeq; NP_001155253.1; NM_001161781.1. [Q9P0J1-1]
DR RefSeq; NP_060914.2; NM_018444.3. [Q9P0J1-1]
DR RefSeq; XP_011515438.1; XM_011517136.1. [Q9P0J1-1]
DR AlphaFoldDB; Q9P0J1; -.
DR SMR; Q9P0J1; -.
DR BioGRID; 120103; 103.
DR ComplexPortal; CPX-6261; Mitochondrial pyruvate dehydrogenase serine/threonine phosphatase complex.
DR IntAct; Q9P0J1; 29.
DR MINT; Q9P0J1; -.
DR STRING; 9606.ENSP00000379503; -.
DR DEPOD; PDP1; -.
DR GlyGen; Q9P0J1; 1 site, 1 O-linked glycan (1 site).
DR iPTMnet; Q9P0J1; -.
DR PhosphoSitePlus; Q9P0J1; -.
DR BioMuta; PDP1; -.
DR DMDM; 78099789; -.
DR EPD; Q9P0J1; -.
DR jPOST; Q9P0J1; -.
DR MassIVE; Q9P0J1; -.
DR MaxQB; Q9P0J1; -.
DR PaxDb; Q9P0J1; -.
DR PeptideAtlas; Q9P0J1; -.
DR PRIDE; Q9P0J1; -.
DR ProteomicsDB; 83553; -. [Q9P0J1-1]
DR Antibodypedia; 12838; 279 antibodies from 32 providers.
DR DNASU; 54704; -.
DR Ensembl; ENST00000297598.5; ENSP00000297598.4; ENSG00000164951.16. [Q9P0J1-1]
DR Ensembl; ENST00000396200.3; ENSP00000379503.3; ENSG00000164951.16. [Q9P0J1-2]
DR Ensembl; ENST00000517764.1; ENSP00000430380.1; ENSG00000164951.16. [Q9P0J1-1]
DR Ensembl; ENST00000520728.5; ENSP00000428317.1; ENSG00000164951.16. [Q9P0J1-1]
DR GeneID; 54704; -.
DR KEGG; hsa:54704; -.
DR MANE-Select; ENST00000297598.5; ENSP00000297598.4; NM_018444.4; NP_060914.2.
DR UCSC; uc003yge.4; human. [Q9P0J1-1]
DR CTD; 54704; -.
DR DisGeNET; 54704; -.
DR GeneCards; PDP1; -.
DR HGNC; HGNC:9279; PDP1.
DR HPA; ENSG00000164951; Low tissue specificity.
DR MalaCards; PDP1; -.
DR MIM; 605993; gene.
DR MIM; 608782; phenotype.
DR neXtProt; NX_Q9P0J1; -.
DR OpenTargets; ENSG00000164951; -.
DR Orphanet; 79246; Pyruvate dehydrogenase phosphatase deficiency.
DR PharmGKB; PA33607; -.
DR VEuPathDB; HostDB:ENSG00000164951; -.
DR eggNOG; KOG0700; Eukaryota.
DR GeneTree; ENSGT00940000156368; -.
DR HOGENOM; CLU_021928_0_0_1; -.
DR InParanoid; Q9P0J1; -.
DR OMA; SHFRYAP; -.
DR OrthoDB; 461546at2759; -.
DR PhylomeDB; Q9P0J1; -.
DR TreeFam; TF313505; -.
DR BRENDA; 3.1.3.43; 2681.
DR PathwayCommons; Q9P0J1; -.
DR Reactome; R-HSA-204174; Regulation of pyruvate dehydrogenase (PDH) complex.
DR SignaLink; Q9P0J1; -.
DR SIGNOR; Q9P0J1; -.
DR BioGRID-ORCS; 54704; 13 hits in 1072 CRISPR screens.
DR ChiTaRS; PDP1; human.
DR GeneWiki; Pyruvate_dehydrogenase_phosphatase; -.
DR GenomeRNAi; 54704; -.
DR Pharos; Q9P0J1; Tbio.
DR PRO; PR:Q9P0J1; -.
DR Proteomes; UP000005640; Chromosome 8.
DR RNAct; Q9P0J1; protein.
DR Bgee; ENSG00000164951; Expressed in lateral nuclear group of thalamus and 200 other tissues.
DR ExpressionAtlas; Q9P0J1; baseline and differential.
DR Genevisible; Q9P0J1; HS.
DR GO; GO:0005759; C:mitochondrial matrix; TAS:Reactome.
DR GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
DR GO; GO:0045253; C:pyruvate dehydrogenase (lipoamide) phosphatase complex; IC:ComplexPortal.
DR GO; GO:0004741; F:[pyruvate dehydrogenase (lipoamide)] phosphatase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004722; F:protein serine/threonine phosphatase activity; IDA:UniProtKB.
DR GO; GO:0035970; P:peptidyl-threonine dephosphorylation; IDA:UniProtKB.
DR GO; GO:1904184; P:positive regulation of pyruvate dehydrogenase activity; IBA:GO_Central.
DR GO; GO:0006470; P:protein dephosphorylation; IBA:GO_Central.
DR CDD; cd00143; PP2Cc; 1.
DR Gene3D; 3.60.40.10; -; 1.
DR InterPro; IPR015655; PP2C.
DR InterPro; IPR000222; PP2C_BS.
DR InterPro; IPR036457; PPM-type_dom_sf.
DR InterPro; IPR001932; PPM-type_phosphatase_dom.
DR PANTHER; PTHR13832; PTHR13832; 1.
DR Pfam; PF00481; PP2C; 1.
DR SMART; SM00332; PP2Cc; 1.
DR SUPFAM; SSF81606; SSF81606; 1.
DR PROSITE; PS01032; PPM_1; 1.
DR PROSITE; PS51746; PPM_2; 1.
PE 1: Evidence at protein level;
KW Acetylation; Alternative splicing; Calcium; Disease variant; Hydrolase;
KW Magnesium; Metal-binding; Mitochondrion; Protein phosphatase;
KW Reference proteome; Transit peptide.
FT TRANSIT 1..71
FT /note="Mitochondrion"
FT /evidence="ECO:0000250"
FT CHAIN 72..537
FT /note="[Pyruvate dehydrogenase [acetyl-transferring]]-
FT phosphatase 1, mitochondrial"
FT /id="PRO_0000025419"
FT DOMAIN 109..525
FT /note="PPM-type phosphatase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01082"
FT BINDING 144
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 144
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 145
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 418
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 516
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT MOD_RES 202
FT /note="N6-acetyllysine"
FT /evidence="ECO:0007744|PubMed:19608861"
FT VAR_SEQ 1
FT /note="M -> MCVCPGPRRIGIPVRSSSLPLFSDAM (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_046869"
FT VARIANT 284
FT /note="Missing (in PDP deficiency; low activity)"
FT /evidence="ECO:0000269|PubMed:15855260"
FT /id="VAR_029882"
FT CONFLICT 105..116
FT /note="NVSSILGFDSNQ -> MSVLSLDLTAIK (in Ref. 1; AAF67480)"
FT /evidence="ECO:0000305"
FT CONFLICT 151
FT /note="C -> W (in Ref. 1; AAF67480)"
FT /evidence="ECO:0000305"
FT CONFLICT 165
FT /note="V -> G (in Ref. 1; AAF67480)"
FT /evidence="ECO:0000305"
FT CONFLICT 168
FT /note="L -> V (in Ref. 1; AAF67480)"
FT /evidence="ECO:0000305"
FT CONFLICT 537
FT /note="E -> EK (in Ref. 1; AAF67480)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 537 AA; 61054 MW; 818B0064CA7961A0 CRC64;
MPAPTQLFFP LIRNCELSRI YGTACYCHHK HLCCSSSYIP QSRLRYTPHP AYATFCRPKE
NWWQYTQGRR YASTPQKFYL TPPQVNSILK ANEYSFKVPE FDGKNVSSIL GFDSNQLPAN
APIEDRRSAA TCLQTRGMLL GVFDGHAGCA CSQAVSERLF YYIAVSLLPH ETLLEIENAV
ESGRALLPIL QWHKHPNDYF SKEASKLYFN SLRTYWQELI DLNTGESTDI DVKEALINAF
KRLDNDISLE AQVGDPNSFL NYLVLRVAFS GATACVAHVD GVDLHVANTG DSRAMLGVQE
EDGSWSAVTL SNDHNAQNER ELERLKLEHP KSEAKSVVKQ DRLLGLLMPF RAFGDVKFKW
SIDLQKRVIE SGPDQLNDNE YTKFIPPNYH TPPYLTAEPE VTYHRLRPQD KFLVLATDGL
WETMHRQDVV RIVGEYLTGM HHQQPIAVGG YKVTLGQMHG LLTERRTKMS SVFEDQNAAT
HLIRHAVGNN EFGTVDHERL SKMLSLPEEL ARMYRDDITI IVVQFNSHVV GAYQNQE
