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PRKDC protein kinase, DNA-activated, catalytic subunit [ Homo sapiens (human) ]

Gene ID: 5591, updated on 5-May-2024

Summary

Official Symbol
PRKDCprovided by HGNC
Official Full Name
protein kinase, DNA-activated, catalytic subunitprovided by HGNC
Primary source
HGNC:HGNC:9413
See related
Ensembl:ENSG00000253729 MIM:600899; AllianceGenome:HGNC:9413
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
HYRC; p350; DNAPK; DNPK1; HYRC1; IMD26; XRCC7; DNAPKc; DNA-PKC; DNA-PKcs
Summary
This gene encodes the catalytic subunit of the DNA-dependent protein kinase (DNA-PK). It functions with the Ku70/Ku80 heterodimer protein in DNA double strand break repair and recombination. The protein encoded is a member of the PI3/PI4-kinase family.[provided by RefSeq, Jul 2010]
Expression
Ubiquitous expression in testis (RPKM 10.8), lymph node (RPKM 10.6) and 25 other tissues See more
Orthologs
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Genomic context

Location:
8q11.21
Exon count:
86
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (47773111..47960136, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (48149356..48336384, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (48685672..48872696, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene scaffold protein involved in DNA repair Neighboring gene RNA, U6 small nuclear 665, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:48649750-48650688 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19173 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19174 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:48664855-48665355 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27329 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:48678117-48678684 Neighboring gene CCAAT enhancer binding protein delta Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:48734487-48735248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:48737843-48738343 Neighboring gene Sharpr-MPRA regulatory region 7649 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:48770411-48770910 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27330 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:48836071-48836571 Neighboring gene uncharacterized LOC105375818 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:48867403-48867904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27331 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19176 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19177 Neighboring gene origin of replication upstream of MCM4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19178 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19179 Neighboring gene RNA, U6 small nuclear 519, pseudogene Neighboring gene minichromosome maintenance complex component 4

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?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify catalytic polypeptide of DNA-activated protein kinase (PRKDC), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify catalytic polypeptide of DNA-activated protein kinase (PRKDC), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify catalytic polypeptide of DNA-activated protein kinase (PRKDC), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Cellular biotinylated protein kinase, DNA-activated, catalytic polypeptide (PRKDC) protein is incorporated into HIV-1 Gag virus-like particles PubMed
gag Tandem affinity purification and mass spectrometry analysis identify catalytic polypeptide of DNA-activated protein kinase (PRKDC), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Rev rev HIV-1 Rev interacting protein, DNA-dependent protein kinase catalytic subunit (PRKDC), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with PRKDC is increased by RRE PubMed
Tat tat HIV-1 Tat directly binds PRKDC and forms a complex with CDK9 and Cyclin T1, which regulates HIV-1 transcription PubMed
tat Amino acids 56-101 of HIV-1 Tat mediate Tat binding to DNA-PK, an effect that augments DNA-PK-mediated phosphorylation of Sp1 during Tat transactivation of the HIV-1 LTR promoter PubMed
tat HIV-1 Tat is phosphorylated by DNA-PK at serine positions 16 and 62 and DNA-PK-induced Tat phosphorylation contributes significantly to HIV-1 replication PubMed
tat The DNA repair gene DNA-PKcs and cell cycle-related genes Cdc20, Cdc25C, KIF2C and CTS1 are downregulated in HIV-1 Tat-expressing human rhabdomyosarcoma cells PubMed
Vpu vpu HIV-1 Vpu is identified to have a physical interaction with protein kinase, DNA-activated, catalytic polypeptide (PRKDC) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
integrase gag-pol HIV-1 IN-mediated proviral DNA integration triggers cell death during HIV-1 infection. The mechanism of killing during viral integration involves activation of DNA-PK, which causes phosphorylation of p53 and histone gammaH2AX PubMed
gag-pol DNA-PK is proposed to play a role in retroviral DNA integration and protects cells against toxicity induced by HIV-1 Integrase or integration PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in B cell lineage commitment IEA
Inferred from Electronic Annotation
more info
 
involved_in DNA damage response IDA
Inferred from Direct Assay
more info
PubMed 
involved_in T cell differentiation in thymus IEA
Inferred from Electronic Annotation
more info
 
involved_in T cell lineage commitment IEA
Inferred from Electronic Annotation
more info
 
involved_in T cell receptor V(D)J recombination IEA
Inferred from Electronic Annotation
more info
 
involved_in activation of innate immune response IDA
Inferred from Direct Assay
more info
PubMed 
involved_in brain development IEA
Inferred from Electronic Annotation
more info
 
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 double-strand break repair IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in double-strand break repair IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in double-strand break repair via alternative nonhomologous end joining TAS
Traceable Author Statement
more info
PubMed 
involved_in double-strand break repair via nonhomologous end joining NAS
Non-traceable Author Statement
more info
PubMed 
involved_in double-strand break repair via nonhomologous end joining TAS
Traceable Author Statement
more info
 
involved_in ectopic germ cell programmed cell death IEA
Inferred from Electronic Annotation
more info
 
involved_in heart development IEA
Inferred from Electronic Annotation
more info
 
involved_in immature B cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in immunoglobulin V(D)J recombination IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in innate immune response IEA
Inferred from Electronic Annotation
more info
 
involved_in intrinsic apoptotic signaling pathway in response to DNA damage IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in maturation of 5.8S rRNA IDA
Inferred from Direct Assay
more info
PubMed 
involved_in mitotic G1 DNA damage checkpoint signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of cGAS/STING signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of protein phosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within peptidyl-serine phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in peptidyl-serine phosphorylation 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 apoptotic process IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of double-strand break repair via nonhomologous end joining IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of erythrocyte differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of lymphocyte differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of platelet formation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of translation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in pro-B cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in protein destabilization IEA
Inferred from Electronic Annotation
more info
 
involved_in protein modification process TAS
Traceable Author Statement
more info
PubMed 
involved_in protein phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in protein phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of circadian rhythm ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of epithelial cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of hematopoietic stem cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of smooth muscle cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in response to gamma radiation IEA
Inferred from Electronic Annotation
more info
 
involved_in rhythmic process IEA
Inferred from Electronic Annotation
more info
 
involved_in small-subunit processome assembly IDA
Inferred from Direct Assay
more info
PubMed 
involved_in somitogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in telomere capping IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in telomere maintenance IBA
Inferred from Biological aspect of Ancestor
more info
 
Component Evidence Code Pubs
part_of DNA-dependent protein kinase complex IPI
Inferred from Physical Interaction
more info
PubMed 
part_of DNA-dependent protein kinase-DNA ligase 4 complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of chromatin IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromosome, telomeric region HDA PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in membrane HDA PubMed 
part_of nonhomologous end joining complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
part_of protein-DNA complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of protein-containing complex IMP
Inferred from Mutant Phenotype
more info
PubMed 
part_of small-subunit processome IDA
Inferred from Direct Assay
more info
PubMed 
part_of transcription regulator complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
DNA-dependent protein kinase catalytic subunit
Names
DNA-PK catalytic subunit
hyper-radiosensitivity of murine scid mutation, complementing 1
p460
protein kinase, DNA-activated, catalytic polypeptide
NP_001075109.1
NP_008835.5

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_023435.1 RefSeqGene

    Range
    5001..192076
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_162

mRNA and Protein(s)

  1. NM_001081640.2NP_001075109.1  DNA-dependent protein kinase catalytic subunit isoform 2

    See identical proteins and their annotated locations for NP_001075109.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    U34994, U47077
    Consensus CDS
    CCDS75734.1
    UniProtKB/Swiss-Prot
    P78527
    Related
    ENSP00000345182.4, ENST00000338368.7
    Conserved Domains (4) summary
    cd05172
    Location:37193984
    PIKKc_DNA-PK; Catalytic domain of DNA-dependent protein kinase
    pfam02259
    Location:30233470
    FAT; FAT domain
    pfam02260
    Location:40664097
    FATC; FATC domain
    pfam08163
    Location:18152202
    NUC194; NUC194 domain
  2. NM_006904.7NP_008835.5  DNA-dependent protein kinase catalytic subunit isoform 1

    See identical proteins and their annotated locations for NP_008835.5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    U47077
    Consensus CDS
    CCDS75735.1
    UniProtKB/Swiss-Prot
    P78527, P78528, Q13327, Q13337, Q14175, Q59H99, Q7Z611, Q96SE6, Q9UME3
    Related
    ENSP00000313420.3, ENST00000314191.7
    Conserved Domains (4) summary
    cd05172
    Location:37194015
    PIKKc_DNA-PK; Catalytic domain of DNA-dependent protein kinase
    pfam02259
    Location:30233470
    FAT; FAT domain
    pfam02260
    Location:40974128
    FATC; FATC domain
    pfam08163
    Location:18162202
    NUC194; NUC194 domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    47773111..47960136 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    48149356..48336384 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)