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Protein

3-phosphoinositide-dependent protein kinase 1

Gene

PDPK1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

May couple lipid signals to the activation-loop phosphorylation of several protein kinases of the so-called AGC kinase family. Interacts via its pleckstrin homology domain with phosphatidic acid, PtdIns3P and PtdIns(3,4)P2 and to a lesser extent with PtdIns(4,5)P2 and PtdIns4P. May play a general role in signaling processes controlling the pathogen/stress response, polar auxin transport and development. Transphosphorylates the AGC protein kinases OXI1/AGC2-1, PK1/S6K1, PK19/S6K2 and PID resulting in their activation.5 Publications

Catalytic activityi

ATP + a protein = ADP + a phosphoprotein.1 Publication

Enzyme regulationi

Activated by phosphatidic acid (PA) and in response to the fungal elicitor xylanase.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei73ATPBy similarity1
Binding sitei128ATPBy similarity1
Active sitei167Proton acceptorPROSITE-ProRule annotation1
Binding sitei171ATP; via carbonyl oxygenBy similarity1
Binding sitei185ATPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi54 – 56ATPBy similarity3
Nucleotide bindingi122 – 124ATPBy similarity3

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • kinase activity Source: TAIR
  • phosphatidic acid binding Source: UniProtKB
  • phosphatidylinositol binding Source: TAIR
  • protein kinase activity Source: UniProtKB
  • protein serine/threonine kinase activity Source: TAIR

GO - Biological processi

  • intracellular signal transduction Source: GO_Central
  • peptidyl-serine phosphorylation Source: GO_Central
  • positive regulation of protein kinase activity Source: TAIR
  • protein autophosphorylation Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Serine/threonine-protein kinase, Transferase

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-ATH-1257604. PIP3 activates AKT signaling.
R-ATH-165158. Activation of AKT2.
R-ATH-202424. Downstream TCR signaling.
R-ATH-2730905. Role of LAT2/NTAL/LAB on calcium mobilization.
R-ATH-389357. CD28 dependent PI3K/Akt signaling.
R-ATH-5218920. VEGFR2 mediated vascular permeability.

Names & Taxonomyi

Protein namesi
Recommended name:
3-phosphoinositide-dependent protein kinase 1 (EC:2.7.11.1)
Short name:
AtPDK1
Gene namesi
Name:PDPK1
Synonyms:PDK1
Ordered Locus Names:At5g04510
ORF Names:T32M21.110
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G04510.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi167D → A: Abolishes autophosphorylation. 1 Publication1
Mutagenesisi176T → A: Strongly reduces autophosphorylation. 1 Publication1
Mutagenesisi177S → A: Reduces autophosphorylation. 1 Publication1
Mutagenesisi211T → A: Strongly reduces autophosphorylation. 1 Publication1
Mutagenesisi276S → A: Abolishes autophosphorylation. 1 Publication1
Mutagenesisi382S → A: Slightly reduces autophosphorylation. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003999021 – 4913-phosphoinositide-dependent protein kinase 1Add BLAST491

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei177Phosphoserine1 Publication1
Modified residuei211Phosphothreonine; by autocatalysis1 Publication1
Modified residuei276Phosphoserine1 Publication1
Modified residuei337PhosphoserineCombined sources1
Modified residuei382Phosphoserine1 Publication1

Post-translational modificationi

Phosphorylation on Thr-211 in the activation loop is required for full activity. PDK1 itself can autophosphorylate Thr-211, leading to its own activation.1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ9XF67.

PTM databases

iPTMnetiQ9XF67.

Expressioni

Tissue specificityi

Ubiquitous.1 Publication

Gene expression databases

ExpressionAtlasiQ9XF67. baseline and differential.
GenevisibleiQ9XF67. AT.

Interactioni

Subunit structurei

Interacts with AGC1-5 and AGC1-7 (PubMed:16973627). Interacts with the C-terminal PIF domain of the protein kinases D6PK/AGC1-1, OXI1/AGC2-1 and PID (PubMed:14749726, PubMed:16601102).3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
AGC1-5Q9LTW53EBI-1103587,EBI-1103747
AGC1-7Q1PFB92EBI-1103587,EBI-1103730
At2g36350Q9SJM32EBI-1103587,EBI-1103882
At2g44830Q8RY372EBI-1103587,EBI-1103670
At5g40030Q9LUK32EBI-1103587,EBI-1103691
D6PKQ9FG742EBI-1103587,EBI-1103570
D6PKL1Q9SUA33EBI-1103587,EBI-1103605
D6PKL2Q391834EBI-1103587,EBI-1103628
D6PKL3Q059992EBI-1103587,EBI-1103648
PIDO646823EBI-1103587,EBI-1393382
PID2Q64FQ22EBI-1103587,EBI-1103769
RHS3F4I4F22EBI-1103587,EBI-1103713
T18B22.10Q9M1P32EBI-1103587,EBI-1103792

Protein-protein interaction databases

BioGridi15609. 7 interactors.
DIPiDIP-39596N.
IntActiQ9XF67. 16 interactors.
STRINGi3702.AT5G04510.1.

Structurei

3D structure databases

ProteinModelPortaliQ9XF67.
SMRiQ9XF67.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini44 – 311Protein kinasePROSITE-ProRule annotationAdd BLAST268
Domaini386 – 491PHAdd BLAST106

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni75 – 119PIF-pocketBy similarityAdd BLAST45
Regioni77 – 112PIF-bindingSequence analysisAdd BLAST36
Regioni185 – 222Activation loopAdd BLAST38

Domaini

The PH domain is responsible for the interaction with the 3-phosphoinositides. The activation loop within the kinase domain is the target of phosphorylation. The PIF-binding region in the kinase domain of PDK1 acts as a docking site, enabling it to interact with and enhance the phosphorylation of substrates containing the PIF motif.
The PIF-pocket is a small lobe in the catalytic domain required by the enzyme for the binding to the hydrophobic motif of its substrates. It is an allosteric regulatory site that can accommodate small compounds acting as allosteric inhibitors.By similarity

Sequence similaritiesi

Contains 1 PH domain.Curated
Contains 1 protein kinase domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0592. Eukaryota.
ENOG410XRT8. LUCA.
HOGENOMiHOG000233026.
InParanoidiQ9XF67.
KOiK06276.
OMAiQENFTSH.
OrthoDBiEOG093607T4.
PhylomeDBiQ9XF67.

Family and domain databases

Gene3Di2.30.29.30. 1 hit.
InterProiIPR011009. Kinase-like_dom.
IPR033931. PDK1-typ_PH.
IPR011993. PH_dom-like.
IPR000719. Prot_kinase_dom.
IPR008271. Ser/Thr_kinase_AS.
[Graphical view]
PfamiPF14593. PH_3. 1 hit.
PF00069. Pkinase. 1 hit.
[Graphical view]
SMARTiSM00220. S_TKc. 1 hit.
[Graphical view]
SUPFAMiSSF50729. SSF50729. 2 hits.
SSF56112. SSF56112. 1 hit.
PROSITEiPS50011. PROTEIN_KINASE_DOM. 1 hit.
PS00108. PROTEIN_KINASE_ST. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

This entry describes 1 isoform i produced by alternative splicing. AlignAdd to basket

Note: A number of isoforms are produced. According to EST sequences.
Isoform 1 (identifier: Q9XF67-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MLAMEKEFDS KLVLQGNSSN GANVSRSKSF SFKAPQENFT SHDFEFGKIY
60 70 80 90 100
GVGSYSKVVR AKKKETGTVY ALKIMDKKFI TKENKTAYVK LERIVLDQLE
110 120 130 140 150
HPGIIKLYFT FQDTSSLYMA LESCEGGELF DQITRKGRLS EDEARFYTAE
160 170 180 190 200
VVDALEYIHS MGLIHRDIKP ENLLLTSDGH IKIADFGSVK PMQDSQITVL
210 220 230 240 250
PNAASDDKAC TFVGTAAYVP PEVLNSSPAT FGNDLWALGC TLYQMLSGTS
260 270 280 290 300
PFKDASEWLI FQRIIARDIK FPNHFSEAAR DLIDRLLDTE PSRRPGAGSE
310 320 330 340 350
GYVALKRHPF FNGVDWKNLR SQTPPKLAPD PASQTASPER DDTHGSPWNL
360 370 380 390 400
THIGDSLATQ NEGHSAPPTS SESSGSITRL ASIDSFDSRW QQFLEPGESV
410 420 430 440 450
LMISAVKKLQ KITSKKVQLI LTNKPKLIYV DPSKLVVKGN IIWSDNSNDL
460 470 480 490
NVVVTSPSHF KICTPKKVLS FEDAKQRASV WKKAIETLQN R
Length:491
Mass (Da):54,711
Last modified:November 1, 1999 - v1
Checksum:i2319EE69CDB5CB38
GO

Sequence cautioni

The sequence CAB85557 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF132742 mRNA. Translation: AAD37165.1.
AL162875 Genomic DNA. Translation: CAB85557.1. Different initiation.
CP002688 Genomic DNA. Translation: AED90755.1.
AF360326 mRNA. Translation: AAK26036.1.
AY056336 mRNA. Translation: AAL07185.1.
PIRiT48447.
RefSeqiNP_568138.1. NM_120533.5. [Q9XF67-1]
UniGeneiAt.4924.

Genome annotation databases

EnsemblPlantsiAT5G04510.1; AT5G04510.1; AT5G04510. [Q9XF67-1]
GeneIDi830330.
GrameneiAT5G04510.1; AT5G04510.1; AT5G04510.
KEGGiath:AT5G04510.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF132742 mRNA. Translation: AAD37165.1.
AL162875 Genomic DNA. Translation: CAB85557.1. Different initiation.
CP002688 Genomic DNA. Translation: AED90755.1.
AF360326 mRNA. Translation: AAK26036.1.
AY056336 mRNA. Translation: AAL07185.1.
PIRiT48447.
RefSeqiNP_568138.1. NM_120533.5. [Q9XF67-1]
UniGeneiAt.4924.

3D structure databases

ProteinModelPortaliQ9XF67.
SMRiQ9XF67.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi15609. 7 interactors.
DIPiDIP-39596N.
IntActiQ9XF67. 16 interactors.
STRINGi3702.AT5G04510.1.

PTM databases

iPTMnetiQ9XF67.

Proteomic databases

PaxDbiQ9XF67.

Protocols and materials databases

DNASUi830330.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G04510.1; AT5G04510.1; AT5G04510. [Q9XF67-1]
GeneIDi830330.
GrameneiAT5G04510.1; AT5G04510.1; AT5G04510.
KEGGiath:AT5G04510.

Organism-specific databases

TAIRiAT5G04510.

Phylogenomic databases

eggNOGiKOG0592. Eukaryota.
ENOG410XRT8. LUCA.
HOGENOMiHOG000233026.
InParanoidiQ9XF67.
KOiK06276.
OMAiQENFTSH.
OrthoDBiEOG093607T4.
PhylomeDBiQ9XF67.

Enzyme and pathway databases

ReactomeiR-ATH-1257604. PIP3 activates AKT signaling.
R-ATH-165158. Activation of AKT2.
R-ATH-202424. Downstream TCR signaling.
R-ATH-2730905. Role of LAT2/NTAL/LAB on calcium mobilization.
R-ATH-389357. CD28 dependent PI3K/Akt signaling.
R-ATH-5218920. VEGFR2 mediated vascular permeability.

Miscellaneous databases

PROiQ9XF67.

Gene expression databases

ExpressionAtlasiQ9XF67. baseline and differential.
GenevisibleiQ9XF67. AT.

Family and domain databases

Gene3Di2.30.29.30. 1 hit.
InterProiIPR011009. Kinase-like_dom.
IPR033931. PDK1-typ_PH.
IPR011993. PH_dom-like.
IPR000719. Prot_kinase_dom.
IPR008271. Ser/Thr_kinase_AS.
[Graphical view]
PfamiPF14593. PH_3. 1 hit.
PF00069. Pkinase. 1 hit.
[Graphical view]
SMARTiSM00220. S_TKc. 1 hit.
[Graphical view]
SUPFAMiSSF50729. SSF50729. 2 hits.
SSF56112. SSF56112. 1 hit.
PROSITEiPS50011. PROTEIN_KINASE_DOM. 1 hit.
PS00108. PROTEIN_KINASE_ST. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPDPK1_ARATH
AccessioniPrimary (citable) accession number: Q9XF67
Secondary accession number(s): Q9LZ74
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 2, 2010
Last sequence update: November 1, 1999
Last modified: November 30, 2016
This is version 125 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.