PDPK2_ARATH
ID PDPK2_ARATH Reviewed; 486 AA.
AC Q4V3C8; Q0WSV2; Q9SQY4;
DT 02-NOV-2010, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2005, sequence version 1.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=3-phosphoinositide-dependent protein kinase 2;
DE Short=AtPDK2;
DE EC=2.7.11.1;
GN Name=PDPK2; Synonyms=PDK2; OrderedLocusNames=At3g10540;
GN ORFNames=F13M14.18, F18K10.12;
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 [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 [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Kim C.J., Chen H., Cheuk R., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF Clones.";
RL Submitted (MAY-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Shinn P., Chen H., Kim C.J., Quinitio C., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (MAY-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP GENE FAMILY, AND REVIEW.
RX PubMed=13678909; DOI=10.1016/s1360-1385(03)00188-2;
RA Boegre L., Okresz L., Henriques R., Anthony R.G.;
RT "Growth signalling pathways in Arabidopsis and the AGC protein kinases.";
RL Trends Plant Sci. 8:424-431(2003).
RN [7]
RP INTERACTION WITH OXI1.
RX PubMed=14749726; DOI=10.1038/sj.emboj.7600068;
RA Anthony R.G., Henriques R., Helfer A., Meszaros T., Rios G., Testerink C.,
RA Munnik T., Deak M., Koncz C., Boegre L.;
RT "A protein kinase target of a PDK1 signalling pathway is involved in root
RT hair growth in Arabidopsis.";
RL EMBO J. 23:572-581(2004).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=17272265; DOI=10.1074/mcp.m600408-mcp200;
RA Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.;
RT "Multidimensional protein identification technology (MudPIT) analysis of
RT ubiquitinated proteins in plants.";
RL Mol. Cell. Proteomics 6:601-610(2007).
RN [9]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-
CC [protein]; Xref=Rhea:RHEA:17989, Rhea:RHEA-COMP:9863, Rhea:RHEA-
CC COMP:11604, ChEBI:CHEBI:15378, ChEBI:CHEBI:29999, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:83421, ChEBI:CHEBI:456216; EC=2.7.11.1;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-
CC threonyl-[protein]; Xref=Rhea:RHEA:46608, Rhea:RHEA-COMP:11060,
CC Rhea:RHEA-COMP:11605, ChEBI:CHEBI:15378, ChEBI:CHEBI:30013,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:61977, ChEBI:CHEBI:456216;
CC EC=2.7.11.1;
CC -!- SUBUNIT: Interacts with the C-terminal PIF domain of OXI1/AGC2-1.
CC {ECO:0000269|PubMed:14749726}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}. Membrane {ECO:0000250};
CC Peripheral membrane protein {ECO:0000250}. Note=Membrane-associated
CC after cell stimulation leading to its translocation. {ECO:0000250}.
CC -!- DOMAIN: The PH domain is responsible for the interaction with the 3-
CC phosphoinositides. The activation loop within the kinase domain is the
CC target of phosphorylation. The PIF-binding region on the kinase domain
CC of PDK2 acts as a docking site, enabling it to interact with and
CC enhance the phosphorylation of substrates containing the PIF motif (By
CC similarity). {ECO:0000250}.
CC -!- DOMAIN: The PIF-pocket is a small lobe in the catalytic domain required
CC by the enzyme for the binding to the hydrophobic motif of its
CC substrates. It is an allosteric regulatory site that can accommodate
CC small compounds acting as allosteric inhibitors.
CC {ECO:0000250|UniProtKB:O15530}.
CC -!- PTM: Phosphorylation on Thr-212 in the activation loop is required for
CC full activity. PDK2 itself can autophosphorylate Thr-212, leading to
CC its own activation (By similarity). {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the protein kinase superfamily. AGC Ser/Thr
CC protein kinase family. PDPK1 subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF76356.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=AAG51370.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AC011560; AAG51370.1; ALT_INIT; Genomic_DNA.
DR EMBL; AC013428; AAF76356.1; ALT_INIT; Genomic_DNA.
DR EMBL; CP002686; AEE74923.1; -; Genomic_DNA.
DR EMBL; BT023428; AAY56419.1; -; mRNA.
DR EMBL; BT025327; ABF57283.1; -; mRNA.
DR EMBL; AK227816; BAE99796.1; -; mRNA.
DR RefSeq; NP_187665.2; NM_111890.4.
DR AlphaFoldDB; Q4V3C8; -.
DR SMR; Q4V3C8; -.
DR BioGRID; 5553; 1.
DR STRING; 3702.AT3G10540.1; -.
DR iPTMnet; Q4V3C8; -.
DR PaxDb; Q4V3C8; -.
DR PRIDE; Q4V3C8; -.
DR ProteomicsDB; 251363; -.
DR EnsemblPlants; AT3G10540.1; AT3G10540.1; AT3G10540.
DR GeneID; 820219; -.
DR Gramene; AT3G10540.1; AT3G10540.1; AT3G10540.
DR KEGG; ath:AT3G10540; -.
DR Araport; AT3G10540; -.
DR TAIR; locus:2075740; AT3G10540.
DR eggNOG; KOG0592; Eukaryota.
DR HOGENOM; CLU_000288_63_9_1; -.
DR InParanoid; Q4V3C8; -.
DR OMA; GYPSIRA; -.
DR OrthoDB; 1157543at2759; -.
DR PhylomeDB; Q4V3C8; -.
DR PRO; PR:Q4V3C8; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q4V3C8; baseline and differential.
DR Genevisible; Q4V3C8; AT.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0016020; C:membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016301; F:kinase activity; ISS:TAIR.
DR GO; GO:0106310; F:protein serine kinase activity; IEA:RHEA.
DR GO; GO:0004674; F:protein serine/threonine kinase activity; IBA:GO_Central.
DR GO; GO:0035556; P:intracellular signal transduction; IBA:GO_Central.
DR GO; GO:0018105; P:peptidyl-serine phosphorylation; IBA:GO_Central.
DR CDD; cd05581; STKc_PDK1; 1.
DR Gene3D; 2.30.29.30; -; 1.
DR InterPro; IPR011009; Kinase-like_dom_sf.
DR InterPro; IPR033931; PDK1-typ_PH.
DR InterPro; IPR039046; PDPK1.
DR InterPro; IPR011993; PH-like_dom_sf.
DR InterPro; IPR000719; Prot_kinase_dom.
DR InterPro; IPR008271; Ser/Thr_kinase_AS.
DR Pfam; PF14593; PH_3; 1.
DR Pfam; PF00069; Pkinase; 1.
DR SMART; SM00220; S_TKc; 1.
DR SUPFAM; SSF56112; SSF56112; 1.
DR PROSITE; PS50011; PROTEIN_KINASE_DOM; 1.
DR PROSITE; PS00108; PROTEIN_KINASE_ST; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Cytoplasm; Kinase; Membrane; Nucleotide-binding;
KW Phosphoprotein; Reference proteome; Serine/threonine-protein kinase;
KW Transferase.
FT CHAIN 1..486
FT /note="3-phosphoinositide-dependent protein kinase 2"
FT /id="PRO_0000399903"
FT DOMAIN 45..312
FT /note="Protein kinase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159"
FT DOMAIN 381..486
FT /note="PH"
FT REGION 1..25
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 76..120
FT /note="PIF-pocket"
FT /evidence="ECO:0000250|UniProtKB:O15530"
FT REGION 78..113
FT /note="PIF-binding"
FT /evidence="ECO:0000255"
FT REGION 186..223
FT /note="Activation loop"
FT REGION 322..369
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 10..25
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 337..369
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 168
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159,
FT ECO:0000255|PROSITE-ProRule:PRU10027"
FT BINDING 55..57
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O15530"
FT BINDING 74
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O15530"
FT BINDING 123..125
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O15530"
FT BINDING 129
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O15530"
FT BINDING 172
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O15530"
FT BINDING 186
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O15530"
FT MOD_RES 212
FT /note="Phosphothreonine; by autocatalysis"
FT /evidence="ECO:0000250|UniProtKB:Q9XF67"
FT MOD_RES 277
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9XF67"
FT MOD_RES 338
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9XF67"
FT MOD_RES 377
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9XF67"
FT CONFLICT 271
FT /note="K -> E (in Ref. 5; BAE99796)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 486 AA; 54441 MW; F4F0F80C49CD0107 CRC64;
MLTMDKEFDS KLTLQGNSSS NGETISRSKS FAFKAPQENF TYHDFELGKI YGVGSYSKVV
RAKKKDNGTV YALKIMDKKF ITKENKTAYV KLERIVLDQL EHPGIVKLFF TFQDTQSLYM
ALESCEGGEL FDQITRKGRL SEDEARFYSA EVVDALEYIH NMGLIHRDIK PENLLLTLDG
HIKIADFGSV KPMQDSQITV LPNAASDDKA CTFVGTAAYV PPEVLNSSPA TFGNDLWALG
CTLYQMLSGT SPFKDASEWL IFQRIIARDI KFPNHFSEAA RDLIDRLLDT DPSRRPGAGS
EGYDSLKRHP FFKGVDWKNL RSQTPPKLAP DPASQSASPE RDGSPWNPTH VGDTSVLQND
GHNGLSESSG SITRLASIDS FDSRWQQFLE PGESVLMISA VKKLQKITSK KVQLILTNKP
RLIYVDPSKL VVKGNIIWSD NSNDLNVQVS SPSHFKICTP KKVLSFEDAK QRALQWKKAI
ETLQNR
