PDK_ARATH
ID PDK_ARATH Reviewed; 366 AA.
AC Q9SBJ1; O82657; Q9C8Z0; Q9SQV2;
DT 03-OCT-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=[Pyruvate dehydrogenase (acetyl-transferring)] kinase, mitochondrial;
DE Short=AtPDHK;
DE Short=Pyruvate dehydrogenase kinase;
DE EC=2.7.11.2;
GN Name=PDK; Synonyms=PDHK, YA5; OrderedLocusNames=At3g06483;
GN ORFNames=F24P17.1, F5E6.19;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Columbia;
RA Thelen J.J., Miernyk J.A., Randall D.D.;
RT "Nucleotide and deduced amino acid sequences of the pyruvate dehydrogenase
RT kinase from Arabidopsis thaliana.";
RL (er) Plant Gene Register PGR98-192(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY, DISRUPTION
RP PHENOTYPE, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=10737148; DOI=10.1023/a:1006393726018;
RA Zou J., Qi Q., Katavic V., Marillia E.-F., Taylor D.C.;
RT "Effects of antisense repression of an Arabidopsis thaliana pyruvate
RT dehydrogenase kinase cDNA on plant development.";
RL Plant Mol. Biol. 41:837-849(1999).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [6]
RP FUNCTION, MUTAGENESIS OF HIS-121, AND PHOSPHORYLATION AT HIS-121.
RX PubMed=10861228; DOI=10.1042/0264-6021:3490195;
RA Thelen J.J., Miernyk J.A., Randall D.D.;
RT "Pyruvate dehydrogenase kinase from Arabidopsis thaliana: a protein
RT histidine kinase that phosphorylates serine residues.";
RL Biochem. J. 349:195-201(2000).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, AND AUTOPHOSPHORYLATION.
RX PubMed=10631090; DOI=10.1006/bbrc.1999.1994;
RA Mooney B.P., David N.R., Thelen J.J., Miernyk J.A., Randall D.D.;
RT "Histidine modifying agents abolish pyruvate dehydrogenase kinase
RT activity.";
RL Biochem. Biophys. Res. Commun. 267:500-503(2000).
RN [8]
RP MUTAGENESIS OF HIS-121 AND HIS-168.
RX PubMed=12027899; DOI=10.1046/j.1432-1033.2002.02933.x;
RA Tovar-Mendez A., Miernyk J.A., Randall D.D.;
RT "Histidine mutagenesis of Arabidopsis thaliana pyruvate dehydrogenase
RT kinase.";
RL Eur. J. Biochem. 269:2601-2606(2002).
RN [9]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=12493853; DOI=10.1093/jxb/erg020;
RA Marillia E.-F., Micallef B.J., Micallef M., Weninger A., Pedersen K.K.,
RA Zou J., Taylor D.C.;
RT "Biochemical and physiological studies of Arabidopsis thaliana transgenic
RT lines with repressed expression of the mitochondrial pyruvate dehydrogenase
RT kinase.";
RL J. Exp. Bot. 54:259-270(2003).
RN [10]
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND MUTAGENESIS OF GLU-238 AND
RP LYS-241.
RX PubMed=15629119; DOI=10.1016/j.abb.2004.10.017;
RA Tovar-Mendez A., Hirani T.A., Miernyk J.A., Randall D.D.;
RT "Analysis of the catalytic mechanism of pyruvate dehydrogenase kinase.";
RL Arch. Biochem. Biophys. 434:159-168(2005).
CC -!- FUNCTION: Serine protein kinase that inhibits the mitochondrial
CC pyruvate dehydrogenase (PDH) complex (mtPDC) by phosphorylation of the
CC E1 alpha subunit on Ser residues, thus contributing to the regulation
CC of glucose metabolism. {ECO:0000269|PubMed:10631090,
CC ECO:0000269|PubMed:10737148, ECO:0000269|PubMed:10861228,
CC ECO:0000269|PubMed:12493853}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-seryl-[pyruvate dehydrogenase E1 alpha subunit] = ADP
CC + H(+) + O-phospho-L-seryl-[pyruvate dehydrogenase E1 alpha subunit];
CC Xref=Rhea:RHEA:23052, Rhea:RHEA-COMP:13689, Rhea:RHEA-COMP:13690,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:29999, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:83421, ChEBI:CHEBI:456216; EC=2.7.11.2;
CC Evidence={ECO:0000269|PubMed:10631090, ECO:0000269|PubMed:10737148};
CC -!- ACTIVITY REGULATION: Treatment with the His-directed reagents diethyl
CC pyrocarbonate (DEPC) and dichloro-(2,2*:6*,2(-terpyridine))-
CC platinum(II) dihydrate inhibits kinase activity, including
CC autophosphorylation. {ECO:0000269|PubMed:10631090}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=50 uM for ATP (at pH 7.5) {ECO:0000269|PubMed:15629119};
CC Note=kcat is 0.55 sec(-1) with ATP as substrate (at pH 7.5, in
CC PubMed:15629119).;
CC pH dependence:
CC Optimum pH is 7-7.5. {ECO:0000269|PubMed:15629119};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:15629119}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000250}.
CC -!- TISSUE SPECIFICITY: Expressed constitutively and ubiquitously.
CC {ECO:0000269|PubMed:10737148}.
CC -!- PTM: Autophosphorylated on Ser residues near N-terminus.
CC {ECO:0000269|PubMed:10861228}.
CC -!- DISRUPTION PHENOTYPE: Elevation of the mitochondrial pyruvate
CC dehydrogenase (PDH) complex (mtPDC) activity. Altered vegetative growth
CC with reduced accumulation of vegetative tissues, early flower
CC development and shorter generation time. Increased seed oil content and
CC seed weight at maturity. {ECO:0000269|PubMed:10737148,
CC ECO:0000269|PubMed:12493853}.
CC -!- SIMILARITY: Belongs to the PDK/BCKDK protein kinase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF08568.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF039406; AAC97601.1; -; mRNA.
DR EMBL; AJ007312; CAA07447.1; -; mRNA.
DR EMBL; AC011623; AAF08568.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC020580; AAG51324.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE74401.1; -; Genomic_DNA.
DR EMBL; AY035017; AAK59522.1; -; mRNA.
DR EMBL; AY059083; AAL15189.1; -; mRNA.
DR PIR; T51626; T51626.
DR RefSeq; NP_187300.3; NM_111524.4.
DR AlphaFoldDB; Q9SBJ1; -.
DR SMR; Q9SBJ1; -.
DR STRING; 3702.AT3G06483.1; -.
DR iPTMnet; Q9SBJ1; -.
DR PaxDb; Q9SBJ1; -.
DR PRIDE; Q9SBJ1; -.
DR ProteomicsDB; 236720; -.
DR EnsemblPlants; AT3G06483.1; AT3G06483.1; AT3G06483.
DR GeneID; 819826; -.
DR Gramene; AT3G06483.1; AT3G06483.1; AT3G06483.
DR KEGG; ath:AT3G06483; -.
DR Araport; AT3G06483; -.
DR TAIR; locus:2081031; AT3G06483.
DR eggNOG; KOG0787; Eukaryota.
DR HOGENOM; CLU_023861_5_0_1; -.
DR InParanoid; Q9SBJ1; -.
DR OMA; TIKHYSN; -.
DR OrthoDB; 1242599at2759; -.
DR PhylomeDB; Q9SBJ1; -.
DR BRENDA; 2.7.11.2; 399.
DR PRO; PR:Q9SBJ1; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9SBJ1; baseline and differential.
DR Genevisible; Q9SBJ1; AT.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IDA:TAIR.
DR GO; GO:0009927; F:histidine phosphotransfer kinase activity; IDA:TAIR.
DR GO; GO:0042803; F:protein homodimerization activity; IPI:UniProtKB.
DR GO; GO:0004740; F:pyruvate dehydrogenase (acetyl-transferring) kinase activity; IBA:GO_Central.
DR GO; GO:0046777; P:protein autophosphorylation; IDA:UniProtKB.
DR GO; GO:0006468; P:protein phosphorylation; IBA:GO_Central.
DR GO; GO:0010906; P:regulation of glucose metabolic process; IBA:GO_Central.
DR Gene3D; 1.20.140.20; -; 1.
DR Gene3D; 3.30.565.10; -; 1.
DR InterPro; IPR036784; AK/P_DHK_N_sf.
DR InterPro; IPR018955; BCDHK/PDK_N.
DR InterPro; IPR039028; BCKD/PDK.
DR InterPro; IPR003594; HATPase_C.
DR InterPro; IPR036890; HATPase_C_sf.
DR InterPro; IPR005467; His_kinase_dom.
DR InterPro; IPR004358; Sig_transdc_His_kin-like_C.
DR PANTHER; PTHR11947; PTHR11947; 1.
DR Pfam; PF10436; BCDHK_Adom3; 1.
DR Pfam; PF02518; HATPase_c; 1.
DR PRINTS; PR00344; BCTRLSENSOR.
DR SMART; SM00387; HATPase_c; 1.
DR SUPFAM; SSF55874; SSF55874; 1.
DR SUPFAM; SSF69012; SSF69012; 1.
DR PROSITE; PS50109; HIS_KIN; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Kinase; Mitochondrion; Nucleotide-binding; Phosphoprotein;
KW Pyruvate; Reference proteome; Transferase.
FT CHAIN 1..366
FT /note="[Pyruvate dehydrogenase (acetyl-transferring)]
FT kinase, mitochondrial"
FT /id="PRO_0000419693"
FT DOMAIN 122..359
FT /note="Histidine kinase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00107"
FT BINDING 238..245
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 278
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 297..298
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 320..325
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT MOD_RES 121
FT /note="Phosphohistidine; by autocatalysis"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00107,
FT ECO:0000269|PubMed:10861228"
FT MUTAGEN 121
FT /note="H->A,Q: Reduced autophosphorylation and slower
FT kinase activity toward the mitochondrial pyruvate
FT dehydrogenase complex (PDC)."
FT /evidence="ECO:0000269|PubMed:10861228,
FT ECO:0000269|PubMed:12027899"
FT MUTAGEN 168
FT /note="H->Q: Reduced autophosphorylation and slower kinase
FT activity toward the mitochondrial pyruvate dehydrogenase
FT complex (PDC); when associated with H-121."
FT /evidence="ECO:0000269|PubMed:12027899"
FT MUTAGEN 238
FT /note="E->A,H,Q: Reduced activity."
FT /evidence="ECO:0000269|PubMed:15629119"
FT MUTAGEN 241
FT /note="K->A: Reduced activity."
FT /evidence="ECO:0000269|PubMed:15629119"
FT CONFLICT 233
FT /note="H -> D (in Ref. 2; CAA07447)"
FT /evidence="ECO:0000305"
FT CONFLICT 316..319
FT /note="VTMA -> GTMG (in Ref. 2; CAA07447)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 366 AA; 41447 MW; E0957597276F0215 CRC64;
MAVKKACEMF PKSLIEDVHK WGCMKQTGVS LRYMMEFGSK PTERNLLISA QFLHKELPIR
VARRAIELQT LPYGLSDKPA VLKVRDWYLE SFRDMRAFPE IKDSGDEKDF TQMIKAVKVR
HNNVVPMMAL GVNQLKKGMN SGNLDEIHQF LDRFYLSRIG IRMLIGQHVE LHNPNPPLHT
VGYIHTKMSP MEVARNASED ARSICFREYG SAPEINIYGD PSFTFPYVPT HLHLMMYELV
KNSLRAVQER FVDSDRVAPP IRIIVADGIE DVTIKVSDEG GGIARSGLPR IFTYLYSTAR
NPLEEDVDLG IADVPVTMAG YGYGLPISRL YARYFGGDLQ IISMEGYGTD AYLHLSRLGD
SQEPLP
