PDPK1 3-phosphoinositide dependent protein kinase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PDPK1provided by HGNC
Official Full Name: 3-phosphoinositide dependent protein kinase 1provided by HGNC
Primary source: HGNC:HGNC:8816
See related: Ensembl:ENSG00000140992 MIM:605213; AllianceGenome:HGNC:8816
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PDK1; PDPK2; PDPK2P; PRO0461
Summary: Enables 3-phosphoinositide-dependent protein kinase activity; phospholipase activator activity; and phospholipase binding activity. Involved in several processes, including cell surface receptor signaling pathway; regulation of protein kinase activity; and regulation of signal transduction. Acts upstream of or within intracellular signal transduction. Located in cell projection; cytosol; and plasma membrane. Implicated in prostate cancer. Biomarker of lung non-small cell carcinoma. [provided by Alliance of Genome Resources, Nov 2024]
Annotation information: Note: PDK1 (Gene ID: 5163) and PDPK1 (Gene ID: 5170) share the PDK1 symbol/alias in common. PDK1 is a widely used alternative name for 3-phosphoinositide dependent protein kinase 1 (PDPK1). [01 Jun 2018]
Expression: Ubiquitous expression in brain (RPKM 5.6), testis (RPKM 5.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16p13.3

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (2538021..2603188)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (2560174..2625339)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (2588022..2653189)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Mitotic gene regulation by the N-MYC-WDR5-PDPK1 nexus.
Title: Mitotic gene regulation by the N-MYC-WDR5-PDPK1 nexus.
KLK10 promotes the progression of KRAS mutant colorectal cancer via PAR1-PDK1-AKT signaling pathway.
Title: KLK10 promotes the progression of KRAS mutant colorectal cancer via PAR1-PDK1-AKT signaling pathway.
CPT1A mediates the succinylation of SP5 which activates transcription of PDPK1 to promote the viability and glycolysis of prostate cancer cells.
Title: CPT1A mediates the succinylation of SP5 which activates transcription of PDPK1 to promote the viability and glycolysis of prostate cancer cells.
SDC2 Stabilization by USP14 Promotes Gastric Cancer Progression through Co-option of PDK1.
Title: SDC2 Stabilization by USP14 Promotes Gastric Cancer Progression through Co-option of PDK1.
Cooperative activation of PDK1 and AKT by MAPK4 enhances cancer growth and resistance to therapy.
Title: Cooperative activation of PDK1 and AKT by MAPK4 enhances cancer growth and resistance to therapy.
Hsa_circ_0000851 promotes PDK1/p-AKT-mediated cell proliferation and migration by regulating miR-1183 in triple-negative breast cancer.
Title: Hsa_circ_0000851 promotes PDK1/p-AKT-mediated cell proliferation and migration by regulating miR-1183 in triple-negative breast cancer.
Hsa_circ_0000081 promotes the function of gastric cancer through sponging hsa-miR-423-5p to influence 3-phosphoinositide-dependent kinase 1 expression.
Title: Hsa_circ_0000081 promotes the function of gastric cancer through sponging hsa-miR-423-5p to influence 3-phosphoinositide-dependent kinase 1 expression.
MiR-34b-3p Impaired HUVECs Viability and Migration via Targeting PDK1 in an In Vitro Model of Gestational Diabetes Mellitus.
Title: MiR-34b-3p Impaired HUVECs Viability and Migration via Targeting PDK1 in an In Vitro Model of Gestational Diabetes Mellitus.
TMEM116 is required for lung cancer cell motility and metastasis through PDK1 signaling pathway.
Title: TMEM116 is required for lung cancer cell motility and metastasis through PDK1 signaling pathway.
Copper Promotes Tumorigenesis by Activating the PDK1-AKT Oncogenic Pathway in a Copper Transporter 1 Dependent Manner.
Title: Copper Promotes Tumorigenesis by Activating the PDK1-AKT Oncogenic Pathway in a Copper Transporter 1 Dependent Manner.

Submit: New GeneRIF Correction See all GeneRIFs (147)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	A Coumarin derivative BPRHIV001 modulates HIV-1 Tat function through a reduction of the phosphorylated PDPK1 protein level	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH78462 (e-PCR)
- UniSTS:48236

D16S426E (e-PCR)
- UniSTS:147333

PDPK1_7852 (e-PCR)
- UniSTS:471709

GDB:176413 (e-PCR)
- UniSTS:154809

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 3-phosphoinositide-dependent protein kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables 3-phosphoinositide-dependent protein kinase activity	IEA Inferred from Electronic Annotation more info
enables AMP-activated protein kinase activity	IEA Inferred from Electronic Annotation more info
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables DNA-dependent protein kinase activity	IEA Inferred from Electronic Annotation more info
enables Rho-dependent protein serine/threonine kinase activity	IEA Inferred from Electronic Annotation more info
enables eukaryotic translation initiation factor 2alpha kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AS1 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AS121 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AT120 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AXS139 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2BS14 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2BS36 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3S10 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3S28 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3S57 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T11 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T3 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T45 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T6 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H4S1 kinase activity	IEA Inferred from Electronic Annotation more info
enables phospholipase activator activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables phospholipase binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein serine kinase activity	IEA Inferred from Electronic Annotation more info
enables protein serine/threonine kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein serine/threonine kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein serine/threonine kinase activity	TAS Traceable Author Statement more info
enables ribosomal protein S6 kinase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in T cell costimulation	TAS Traceable Author Statement more info
involved_in actin cytoskeleton organization	TAS Traceable Author Statement more info	PubMed
involved_in activation of protein kinase B activity	IDA Inferred from Direct Assay more info	PubMed
involved_in calcium-mediated signaling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to epidermal growth factor stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to insulin stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in epidermal growth factor receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in extrinsic apoptotic signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in hyperosmotic response	IEA Inferred from Electronic Annotation more info
involved_in insulin receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in insulin-like growth factor receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in intracellular signal transduction	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within intracellular signal transduction	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cardiac muscle cell apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of endothelial cell apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of protein kinase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of toll-like receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transforming growth factor beta receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in peptidyl-threonine phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of blood vessel endothelial cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	TAS Traceable Author Statement more info
involved_in positive regulation of phospholipase activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein localization to plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of release of sequestered calcium ion into cytosol	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of sprouting angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of vascular endothelial cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein autophosphorylation	TAS Traceable Author Statement more info	PubMed
involved_in protein phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of canonical NF-kappaB signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mast cell degranulation	IEA Inferred from Electronic Annotation more info
involved_in type B pancreatic cell development	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cell projection	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasmic vesicle	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in focal adhesion	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in postsynaptic density	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: 3-phosphoinositide-dependent protein kinase 1

Names: 3-phosphoinositide-dependent protein kinase 2 pseudogene; PkB kinase like gene 1; Putative 3-phosphoinositide-dependent protein kinase 2

NP_001248745.1

EC 2.7.11.1

NP_002604.1

EC 2.7.11.1

NP_112558.2

EC 2.7.11.1

XP_011520823.1

EC 2.7.11.1

XP_011520825.1

EC 2.7.11.1

XP_024306064.1

EC 2.7.11.1

XP_047290154.1

EC 2.7.11.1

XP_047290155.1

EC 2.7.11.1

XP_047290156.1

EC 2.7.11.1

XP_047290157.1

EC 2.7.11.1

XP_047290158.1

EC 2.7.11.1

XP_054236418.1

EC 2.7.11.1

XP_054236419.1

EC 2.7.11.1

XP_054236420.1

EC 2.7.11.1

XP_054236421.1

EC 2.7.11.1

XP_054236422.1

EC 2.7.11.1

XP_054236423.1

EC 2.7.11.1

XP_054236424.1

EC 2.7.11.1

XP_054236425.1

EC 2.7.11.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001261816.2 → NP_001248745.1 3-phosphoinositide-dependent protein kinase 1 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks two consecutive exons in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AB209835, AC141586

Consensus CDS

CCDS58411.1

UniProtKB/TrEMBL

Q9UPJ8

Related

ENSP00000395357.3, ENST00000441549.7

Conserved Domains (1) summary

cd05581
Location:80 → 342

STKc_PDK1; Catalytic domain of the Serine/Threonine Kinase, Phosphoinositide-dependent kinase 1
NM_002613.5 → NP_002604.1 3-phosphoinositide-dependent protein kinase 1 isoform 1

See identical proteins and their annotated locations for NP_002604.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AC141586, BC012103

Consensus CDS

CCDS10472.1

UniProtKB/Swiss-Prot

H0Y4Z0, O15530, Q59EH6, Q6FI20, Q8IV52, Q9BRD5

UniProtKB/TrEMBL

Q53HJ9

Related

ENSP00000344220.4, ENST00000342085.9

Conserved Domains (2) summary

cd01262
Location:441 → 547

PH_PDK1; 3-Phosphoinositide dependent protein kinase 1 (PDK1) pleckstrin homology (PH) domain

cd05581
Location:80 → 342

STKc_PDK1; Catalytic domain of the Serine/Threonine Kinase, Phosphoinositide-dependent kinase 1
NM_031268.6 → NP_112558.2 3-phosphoinositide-dependent protein kinase 1 isoform 2

See identical proteins and their annotated locations for NP_112558.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks three consecutive exons in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AC093525, AC141586, BC033494

Consensus CDS

CCDS10473.1

UniProtKB/Swiss-Prot

O15530

Related

ENSP00000268673.7, ENST00000268673.12

Conserved Domains (2) summary

cd01262
Location:314 → 420

PH_PDK1; 3-Phosphoinositide dependent protein kinase 1 (PDK1) pleckstrin homology (PH) domain

cl21453
Location:81 → 215

PKc_like; Protein Kinases, catalytic domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

2538021..2603188

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047434200.1 → XP_047290156.1 3-phosphoinositide-dependent protein kinase 1 isoform X3

UniProtKB/TrEMBL

E9PER6
XM_024450296.2 → XP_024306064.1 3-phosphoinositide-dependent protein kinase 1 isoform X3

UniProtKB/TrEMBL

E9PER6, Q53HJ9

Related

ENSP00000373876.3, ENST00000389224.7

Conserved Domains (2) summary

cd01262
Location:414 → 520

PH_PDK1; 3-Phosphoinositide dependent protein kinase 1 (PDK1) pleckstrin homology (PH) domain

cd05581
Location:53 → 315

STKc_PDK1; Catalytic domain of the Serine/Threonine Kinase, Phosphoinositide-dependent kinase 1
XM_047434199.1 → XP_047290155.1 3-phosphoinositide-dependent protein kinase 1 isoform X3

UniProtKB/TrEMBL

E9PER6
XM_047434202.1 → XP_047290158.1 3-phosphoinositide-dependent protein kinase 1 isoform X6
XM_011522523.4 → XP_011520825.1 3-phosphoinositide-dependent protein kinase 1 isoform X4

Conserved Domains (2) summary

cd01262
Location:348 → 454

PH_PDK1; 3-Phosphoinositide dependent protein kinase 1 (PDK1) pleckstrin homology (PH) domain

cl21453
Location:115 → 249

PKc_like; Protein Kinases, catalytic domain
XM_011522521.4 → XP_011520823.1 3-phosphoinositide-dependent protein kinase 1 isoform X1

UniProtKB/TrEMBL

Q53HJ9

Conserved Domains (3) summary

smart00220
Location:116 → 376

S_TKc; Serine/Threonine protein kinases, catalytic domain

cd01262
Location:475 → 581

PH_PDK1; 3-Phosphoinositide dependent protein kinase 1 (PDK1) pleckstrin homology (PH) domain

cd05581
Location:114 → 376

STKc_PDK1; Catalytic domain of the Serine/Threonine Kinase, Phosphoinositide-dependent kinase 1
XM_047434198.1 → XP_047290154.1 3-phosphoinositide-dependent protein kinase 1 isoform X2
XM_047434201.1 → XP_047290157.1 3-phosphoinositide-dependent protein kinase 1 isoform X5

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

2560174..2625339

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054380447.1 → XP_054236422.1 3-phosphoinositide-dependent protein kinase 1 isoform X3

UniProtKB/TrEMBL

E9PER6
XM_054380446.1 → XP_054236421.1 3-phosphoinositide-dependent protein kinase 1 isoform X3

UniProtKB/TrEMBL

E9PER6
XM_054380445.1 → XP_054236420.1 3-phosphoinositide-dependent protein kinase 1 isoform X3

UniProtKB/TrEMBL

E9PER6
XM_054380444.1 → XP_054236419.1 3-phosphoinositide-dependent protein kinase 1 isoform X2
XM_054380443.1 → XP_054236418.1 3-phosphoinositide-dependent protein kinase 1 isoform X1
XM_054380448.1 → XP_054236423.1 3-phosphoinositide-dependent protein kinase 1 isoform X4
XM_054380450.1 → XP_054236425.1 3-phosphoinositide-dependent protein kinase 1 isoform X6
XM_054380449.1 → XP_054236424.1 3-phosphoinositide-dependent protein kinase 1 isoform X5