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    PRKD1 protein kinase D1 [ Homo sapiens (human) ]

    Gene ID: 5587, updated on 11-Sep-2019

    Summary

    Official Symbol
    PRKD1provided by HGNC
    Official Full Name
    protein kinase D1provided by HGNC
    Primary source
    HGNC:HGNC:9407
    See related
    Ensembl:ENSG00000184304 MIM:605435
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PKD; PKCM; CHDED; PRKCM; PKC-MU
    Summary
    The protein encoded by this gene is a serine/threonine protein kinase involved in many cellular processes, including Golgi body membrane integrity and transport, cell migration and differentiation, MAPK8/JNK1 and Ras pathway signaling, MAPK1/3 (ERK1/2) pathway signaling, cell survival, and regulation of cell shape and adhesion. [provided by RefSeq, Jan 2017]
    Expression
    Broad expression in testis (RPKM 3.2), prostate (RPKM 2.7) and 22 other tissues See more
    Orthologs

    Genomic context

    See PRKD1 in Genome Data Viewer
    Location:
    14q12
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    109.20190905 current GRCh38.p13 (GCF_000001405.39) 14 NC_000014.9 (29576479..29927847, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (30045685..30396899, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs598 Neighboring gene RNA, U11 small nuclear 5, pseudogene Neighboring gene RNA, U6 small nuclear 1234, pseudogene Neighboring gene uncharacterized LOC105370429 Neighboring gene ribosomal protein S6 pseudogene 24

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Congenital heart defects and ectodermal dysplasia
    MedGen: C4479250 OMIM: 617364 GeneReviews: Not available
    not available

    NHGRI GWAS Catalog

    Description
    Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
    NHGRI GWA Catalog
    Biological insights from 108 schizophrenia-associated genetic loci.
    NHGRI GWA Catalog
    Genome-wide analysis of BMI in adolescents and young adults reveals additional insight into the effects of genetic loci over the life course.
    NHGRI GWA Catalog
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    NHGRI GWA Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    NHGRI GWA Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Screening in Jurkat T-cells with a short-hairpin-RNA (shRNA) library identifies protein kinase D1, a member of the protein kinase C family (cytosolic serine/threonine kinase), is important for HIV-1 replication PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Sulfated polymannuroguluronate (SPMG) potently arrests HIV-1 Tat-triggered protein kinase C (PKC)-dependent PKC-mu activation PubMed
    tat Phospholipase C/protein kinase C signaling pathway-dependent phosphorylation of p44/42 and JNK MAP kinases participates partially in IL-1beta induction by TAT PubMed
    tat Protein kinase C is required for HIV-1 Tat-mediated transactivation of the viral LTR promoter, indicating protein kinase C regulates the process of HIV-1 transactivation and may play a role in the transition of HIV from latency to productive growth PubMed
    tat Protein kinase C phosphorylates HIV-1 Tat on serine residue 46 PubMed
    tat HIV-1 Tat activates protein kinase C, resulting in the induction of TNF-alpha, IL-6 and IL-10 expression and the secretion of MCP-1 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from BioSystems

    • Aldosterone synthesis and secretion, organism-specific biosystem (from KEGG)
      Aldosterone synthesis and secretion, organism-specific biosystemAldosterone is a steroid hormone synthesized in and secreted from the outer layer of the adrenal cortex, the zona glomerulosa. Aldosterone plays an important role in the regulation of systemic blood ...
    • Aldosterone synthesis and secretion, conserved biosystem (from KEGG)
      Aldosterone synthesis and secretion, conserved biosystemAldosterone is a steroid hormone synthesized in and secreted from the outer layer of the adrenal cortex, the zona glomerulosa. Aldosterone plays an important role in the regulation of systemic blood ...
    • Apoptosis Modulation and Signaling, organism-specific biosystem (from WikiPathways)
      Apoptosis Modulation and Signaling, organism-specific biosystemApoptosis, or cell death program, can be activated by various mechanisms within the extrinsic and the intrinsic pathway. While activation of cell death receptors leads to the engagement of the extrin...
    • Calcium Regulation in the Cardiac Cell, organism-specific biosystem (from WikiPathways)
      Calcium Regulation in the Cardiac Cell, organism-specific biosystemCalcium is a common signaling mechanism, as once it enters the cytoplasm it exerts allosteric regulatory affects on many enzymes and proteins. Calcium can act in signal transduction after influx resu...
    • Cardiac Hypertrophic Response, organism-specific biosystem (from WikiPathways)
      Cardiac Hypertrophic Response, organism-specific biosystemIntegrated schematic of the more extensively characterized intracellular signal-transduction pathways that coordinate the cardiac hypertrophic response. During development and in response to physiolo...
    • G Protein Signaling Pathways, organism-specific biosystem (from WikiPathways)
      G Protein Signaling Pathways, organism-specific biosystemG proteins, short for guanine nucleotide-binding proteins, are a family of proteins involved in second messenger cascades. G proteins are so called because they function as "molecular switches". They...
    • IGF1 pathway, organism-specific biosystem (from Pathway Interaction Database)
      IGF1 pathway, organism-specific biosystem
      IGF1 pathway
    • LPA receptor mediated events, organism-specific biosystem (from Pathway Interaction Database)
      LPA receptor mediated events, organism-specific biosystem
      LPA receptor mediated events
    • Metabolism, organism-specific biosystem (from REACTOME)
      Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
    • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
      Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
    • Myometrial Relaxation and Contraction Pathways, organism-specific biosystem (from WikiPathways)
      Myometrial Relaxation and Contraction Pathways, organism-specific biosystemThis pathway illustrates signaling networks implicated in uterine muscle contraction at labor and quiescence throughout gestation (pregnancy). The muscle of the uterus, responsible for contractile ac...
    • Rap1 signaling pathway, organism-specific biosystem (from KEGG)
      Rap1 signaling pathway, organism-specific biosystemRap1 is a small GTPase that controls diverse processes, such as cell adhesion, cell-cell junction formation and cell polarity. Like all G proteins, Rap1 cycles between an inactive GDP-bound and an ac...
    • Rap1 signaling pathway, conserved biosystem (from KEGG)
      Rap1 signaling pathway, conserved biosystemRap1 is a small GTPase that controls diverse processes, such as cell adhesion, cell-cell junction formation and cell polarity. Like all G proteins, Rap1 cycles between an inactive GDP-bound and an ac...
    • Sphingolipid de novo biosynthesis, organism-specific biosystem (from REACTOME)
      Sphingolipid de novo biosynthesis, organism-specific biosystemThe main steps involved in de novo sphingolipid synthesis are annotated here (Merrill 2002, Gault et al. 2010).
    • Sphingolipid metabolism, organism-specific biosystem (from REACTOME)
      Sphingolipid metabolism, organism-specific biosystemSphingolipids are derivatives of long chain sphingoid bases such as sphingosine (trans-1,3-dihydroxy 2-amino-4-octadecene), an 18-carbon unsaturated amino alcohol which is the most abundant sphingoid...
    • Wnt Signaling Pathway, organism-specific biosystem (from WikiPathways)
      Wnt Signaling Pathway, organism-specific biosystemWnt proteins are secreted morphogens that are required for basic developmental processes, such as cell-fate specification, progenitor-cell proliferation and the control of asymmetric cell division, i...
    • Wnt Signaling Pathway and Pluripotency, organism-specific biosystem (from WikiPathways)
      Wnt Signaling Pathway and Pluripotency, organism-specific biosystemThis pathway was adapted from several resources and is designed to provide a theoretical frame-work for examining Wnt signaling and interacting components in the context of embryonic stem-cell plurip...
    • miRs in Muscle Cell Differentiation, organism-specific biosystem (from WikiPathways)
      miRs in Muscle Cell Differentiation, organism-specific biosystem
      miRs in Muscle Cell Differentiation

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    kinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein kinase C activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein serine/threonine kinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein serine/threonine kinase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein serine/threonine kinase activity TAS
    Traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    Golgi organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Golgi vesicle transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Ras protein signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    angiogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to amino acid starvation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cellular response to hydroperoxide IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cellular response to oxidative stress IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cellular response to vascular endothelial growth factor stimulus IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    cellular response to vascular endothelial growth factor stimulus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    inflammatory response IEA
    Inferred from Electronic Annotation
    more info
     
    innate immune response IEA
    Inferred from Electronic Annotation
    more info
     
    integrin-mediated signaling pathway TAS
    Traceable Author Statement
    more info
    PubMed 
    intracellular signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of cell death IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of endocytosis TAS
    Traceable Author Statement
    more info
    PubMed 
    peptidyl-serine phosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    peptidyl-serine phosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    peptidyl-threonine phosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    peptidyl-threonine phosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of CREB transcription factor activity IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of I-kappaB kinase/NF-kappaB signaling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of NF-kappaB transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of angiogenesis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of angiogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of autophagy IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of blood vessel endothelial cell migration IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of blood vessel endothelial cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of endothelial cell chemotaxis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of endothelial cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of endothelial cell proliferation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of histone deacetylase activity IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of neuron projection development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of osteoblast differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of peptidyl-serine phosphorylation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of phosphatidylinositol 3-kinase activity IC
    Inferred by Curator
    more info
    PubMed 
    positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein autophosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein autophosphorylation TAS
    Traceable Author Statement
    more info
    PubMed 
    protein kinase D signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein kinase D signaling IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    protein phosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of integrin-mediated signaling pathway TAS
    Traceable Author Statement
    more info
    PubMed 
    regulation of keratinocyte proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of protein stability IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    signal transduction TAS
    Traceable Author Statement
    more info
    PubMed 
    sphingolipid biosynthetic process TAS
    Traceable Author Statement
    more info
     
    vascular endothelial growth factor receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    autophagosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cytosol TAS
    Traceable Author Statement
    more info
     
    plasma membrane IDA
    Inferred from Direct Assay
    more info
     
    trans-Golgi network IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    serine/threonine-protein kinase D1
    Names
    nPKC-D1
    nPKC-mu
    protein kinase C mu type
    protein kinase C, mu
    protein kinase D
    NP_001316998.1
    NP_001335319.1
    NP_002733.2
    XP_011535267.1
    XP_016876951.1

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_052879.1 RefSeqGene

      Range
      4847..356215
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001330069.2NP_001316998.1  serine/threonine-protein kinase D1 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL135858, AL355053, AL356756
      Consensus CDS
      CCDS81796.1
      UniProtKB/TrEMBL
      F8WBA3
      Related
      ENSP00000390535.2, ENST00000415220.6
      Conserved Domains (5) summary
      smart00220
      Location:595847
      S_TKc; Serine/Threonine protein kinases, catalytic domain
      cd00029
      Location:279328
      C1; Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second ...
      cd01239
      Location:424551
      PH_PKD; Protein kinase D (PKD/PKCmu) pleckstrin homology (PH) domain
      cd14082
      Location:587846
      STKc_PKD; Catalytic domain of the Serine/Threonine kinase, Protein Kinase D
      pfam00130
      Location:147196
      C1_1; Phorbol esters/diacylglycerol binding domain (C1 domain)
    2. NM_001348390.1NP_001335319.1  serine/threonine-protein kinase D1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AL135858, AL355053, AL356756
      Conserved Domains (4) summary
      cd00029
      Location:183232
      C1; Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second ...
      cd01239
      Location:328455
      PH_PKD; Protein kinase D (PKD/PKCmu) pleckstrin homology (PH) domain
      cd14082
      Location:491750
      STKc_PKD; Catalytic domain of the Serine/Threonine kinase, Protein Kinase D
      pfam00130
      Location:51100
      C1_1; Phorbol esters/diacylglycerol binding domain (C1 domain)
    3. NM_002742.3NP_002733.2  serine/threonine-protein kinase D1 isoform 2

      See identical proteins and their annotated locations for NP_002733.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 2
      Source sequence(s)
      AL355053, BX645735, CN412379, X75756
      Consensus CDS
      CCDS9637.1
      UniProtKB/Swiss-Prot
      Q15139
      Related
      ENSP00000333568.5, ENST00000331968.10
      Conserved Domains (5) summary
      smart00220
      Location:587839
      S_TKc; Serine/Threonine protein kinases, catalytic domain
      cd00029
      Location:271320
      C1; Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second ...
      cd01239
      Location:416543
      PH_PKD; Protein kinase D (PKD/PKCmu) pleckstrin homology (PH) domain
      cd14082
      Location:579838
      STKc_PKD; Catalytic domain of the Serine/Threonine kinase, Protein Kinase D
      pfam00130
      Location:147196
      C1_1; Phorbol esters/diacylglycerol binding domain (C1 domain)

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p13 Primary Assembly

      Range
      29576479..29927847 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017021462.1XP_016876951.1  serine/threonine-protein kinase D1 isoform X2

    2. XM_011536965.2XP_011535267.1  serine/threonine-protein kinase D1 isoform X1

      Conserved Domains (4) summary
      cd00029
      Location:183232
      C1; Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second ...
      cd01239
      Location:328455
      PH_PKD; Protein kinase D (PKD/PKCmu) pleckstrin homology (PH) domain
      cd14082
      Location:491750
      STKc_PKD; Catalytic domain of the Serine/Threonine kinase, Protein Kinase D
      pfam00130
      Location:51100
      C1_1; Phorbol esters/diacylglycerol binding domain (C1 domain)

    RNA

    1. XR_943493.2 RNA Sequence

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