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

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: mouse all
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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_000008.11 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
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?

Identification of MCM4 and PRKDC as new regulators of osteosarcoma cell dormancy based on 3D cell cultures.
Title: Identification of MCM4 and PRKDC as new regulators of osteosarcoma cell dormancy based on 3D cell cultures.
Chemical inhibition of DNA-PKcs impairs the activation and cytotoxicity of CD4[+] helper and CD8[+] effector T cells.
Title: Chemical inhibition of DNA-PKcs impairs the activation and cytotoxicity of CD4(+) helper and CD8(+) effector T cells.
Up-regulation of PRKDC was associated with poor renal dysfunction after renal transplantation: A multi-centre analysis.
Title: Up-regulation of PRKDC was associated with poor renal dysfunction after renal transplantation: A multi-centre analysis.
FAP is critical for ovarian cancer cell survival by sustaining NF-kappaB activation through recruitment of PRKDC in lipid rafts.
Title: FAP is critical for ovarian cancer cell survival by sustaining NF-κB activation through recruitment of PRKDC in lipid rafts.
DNA damage repair kinase DNA-PK and cGAS synergize to induce cancer-related inflammation in glioblastoma.
Title: DNA damage repair kinase DNA-PK and cGAS synergize to induce cancer-related inflammation in glioblastoma.
DNA-PKcs and ATM modulate mitochondrial ADP-ATP exchange as an oxidative stress checkpoint mechanism.
Title: DNA-PKcs and ATM modulate mitochondrial ADP-ATP exchange as an oxidative stress checkpoint mechanism.
DNA-PK hyperactivation occurs in deletion 11q chronic lymphocytic leukemia and is both a biomarker and therapeutic target for drug-resistant disease.
Title: DNA-PK hyperactivation occurs in deletion 11q chronic lymphocytic leukemia and is both a biomarker and therapeutic target for drug-resistant disease.
Structural analysis of the basal state of the Artemis:DNA-PKcs complex.
Title: Structural analysis of the basal state of the Artemis:DNA-PKcs complex.
Potential value of PRKDC as a therapeutic target and prognostic biomarker in pan-cancer.
Title: Potential value of PRKDC as a therapeutic target and prognostic biomarker in pan-cancer.
PRKDC promotes hepatitis B virus transcription through enhancing the binding of RNA Pol II to cccDNA.
Title: PRKDC promotes hepatitis B virus transcription through enhancing the binding of RNA Pol II to cccDNA.

Submit: New GeneRIF Correction See all GeneRIFs (326)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Severe combined immunodeficiency due to DNA-PKcs deficiency MedGen: C4014833 OMIM: 615966 GeneReviews: Not available	Compare labs

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
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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-N27515 (e-PCR)
- UniSTS:32529

PMC84245P1 (e-PCR)
- UniSTS:273442

EST197660 (e-PCR)
- UniSTS:10824

G29848 (e-PCR)
- UniSTS:40531

PMC140533P4 (e-PCR)
- UniSTS:270937

PMC140533P5 (e-PCR)
- UniSTS:270938

PMC140533P6 (e-PCR)
- UniSTS:270939

PMC140533P7 (e-PCR)
- UniSTS:270940

PRKDC_2296 (e-PCR)
- UniSTS:280927

D8S485 (e-PCR)
- UniSTS:44911

D8S1353E (e-PCR)
- UniSTS:151168

RH121464 (e-PCR)
- UniSTS:134592

BCD1153 (e-PCR)
- UniSTS:10713

RH69034 (e-PCR)
- UniSTS:48378

D8S1212 (e-PCR)
- UniSTS:150269

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables DNA-dependent protein kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	HDA more info	PubMed
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables U3 snoRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables enzyme binding	IEA Inferred from Electronic Annotation more info
enables histone H2AXS139 kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein kinase activity	IMP Inferred from Mutant Phenotype 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

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 more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in membrane	HDA more info	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

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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

EC 2.7.11.1

NP_008835.5

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.

Genomic

NG_023435.1 RefSeqGene

Range

5001..192076

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_162

mRNA and Protein(s)

NM_001081640.2 → NP_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:3719 → 3984

PIKKc_DNA-PK; Catalytic domain of DNA-dependent protein kinase

pfam02259
Location:3023 → 3470

FAT; FAT domain

pfam02260
Location:4066 → 4097

FATC; FATC domain

pfam08163
Location:1815 → 2202

NUC194; NUC194 domain
NM_006904.7 → NP_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:3719 → 4015

PIKKc_DNA-PK; Catalytic domain of DNA-dependent protein kinase

pfam02259
Location:3023 → 3470

FAT; FAT domain

pfam02260
Location:4097 → 4128

FATC; FATC domain

pfam08163
Location:1816 → 2202

NUC194; NUC194 domain