Protein kinase R

Eukaryotic translation initiation factor 2-alpha kinase 2
NMR structure of the double stranded RNA binding domain of EIF2AK2 based on PDB: 1qu6​.
Available structures PDB Ortholog search: PDBe, RCSB List of PDB id codes 1QU6​, 2A19​, 2A1A​, 3UIU​
Identifiers
Symbols	EIF2AK2 ; EIF2AK1; PKR; PPP1R83; PRKR
External IDs	OMIM: 176871 MGI: 1353449 HomoloGene: 48134 ChEMBL: 5785 GeneCards: EIF2AK2 Gene
EC number	2.7.10.2, 2.7.11.1
Gene ontology Molecular function • double-stranded RNA binding • protein kinase activity • protein serine/threonine kinase activity • eukaryotic translation initiation factor 2alpha kinase activity • non-membrane spanning protein tyrosine kinase activity • protein binding • ATP binding • protein phosphatase type 2A regulator activity • poly(A) RNA binding Cellular component • nucleus • cytoplasm • cytosol • ribosome • membrane • perinuclear region of cytoplasm Biological process • activation of MAPKK activity • positive regulation of cytokine production • transcription, DNA-templated • translation • protein phosphorylation • negative regulation of cell proliferation • response to virus • regulation of translational initiation by eIF2 alpha phosphorylation • negative regulation of translation • peptidyl-tyrosine phosphorylation • modulation by virus of host morphology or physiology • modulation by virus of host process • viral life cycle • evasion or tolerance by virus of host immune response • endoplasmic reticulum unfolded protein response • positive regulation of chemokine production • positive regulation of stress-activated MAPK cascade • negative regulation of osteoblast proliferation • regulation of protein phosphatase type 2A activity • response to interferon-alpha • negative regulation of apoptotic process • negative regulation of viral genome replication • innate immune response • protein autophosphorylation • positive regulation of NF-kappaB transcription factor activity • defense response to virus • regulation of NLRP3 inflammasome complex assembly • positive regulation of NIK/NF-kappaB signaling • regulation of hematopoietic progenitor cell differentiation • regulation of hematopoietic stem cell proliferation • regulation of hematopoietic stem cell differentiation Sources: Amigo / QuickGO
RNA expression pattern
More reference expression data
Orthologs
Species	Human	Mouse
Entrez	5610	19106
Ensembl	ENSG00000055332	ENSMUSG00000024079
UniProt	P19525	Q03963
RefSeq (mRNA)	NM_001135651	NM_011163
RefSeq (protein)	NP_001129123	NP_035293
Location (UCSC)	Chr 2: 37.1 – 37.16 Mb	Chr 17: 78.85 – 78.88 Mb
PubMed search

Protein kinase RNA-activated also known as protein kinase R (PKR), interferon-induced, double-stranded RNA-activated protein kinase, or eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) is an enzyme that in humans is encoded by the EIF2AK2 gene.^[1][2]

PKR protects against viral infections.

Mechanism of action

Protein kinase-R is activated by double-stranded RNA (dsRNA), introduced to the cells by a viral infection. PKR can also be activated by the protein PACT or by heparin. PKR contains an N-terminal dsRNA binding domain (dsRBD) and a C-terminal kinase domain, that gives it pro-apoptotic (cell-killing) functions. The dsRBD consists of two tandem copies of a conserved double stranded RNA binding motif, dsRBM1 and dsRBM2. PKR is induced by interferon in a latent state. Binding to dsRNA is believed to activate PKR by inducing dimerization and subsequent auto-phosphorylation reactions. In situations of viral infection, the dsRNA created by viral replication and gene expression binds to the N-terminal domain, activating the protein. Once active, PKR is able to phosphorylate the eukaryotic translation initiation factor eIF2α. This inhibits further cellular mRNA translation, thereby preventing viral protein synthesis. Since ElF2α is involved in the commonly initiation translation from an AUG codon, the alternative non-AUG initiation takes place instead. An example of mRNAs using non-AUG initiation are mRNAs for the heat shock proteins. Active PKR is also able to mediate the activation of the transcription factor NFkB, by phosphorylating its inhibitory subunit, IkB. Activated NFkB upregulates the expression of Interferon cytokines, which work to spread the antiviral signal locally. Active PKR is also able to activate tumor suppressor PP2A which regulates the cell cycle and the metabolism. Through complex mechanisms, active PKR is also able to induce cellular apoptosis, to prevent further viral spread.

PKR stress pathway

PKR is in the center of cellular response to different stress signals such as pathogens, lack of nutrients, cytokines, irradiation, mechanical stress or stress of endoplasmic reticulum (ER). PKR pathway leads to stress response through activation of other stress pathway such as JNK, p38, NFkB, PP2A and phosphorylation of eIF2α. ER stress caused by excess of unfolded proteins leads to inflammatory responses. PKR contributes to this response by interacting with several inflammatory kinases such as IKK, JNK, ElF2α, insulin receptor and others. This metabolically activated inflammatory complex is called metabolic inflammasome or metaflammasome.^[3][4]

Viral defense

Viruses have developed many mechanisms to counteract the PKR mechanism. It may be done by Decoy dsRNA, degradation, hiding of virus dsRNA, dimerization block, dephosphorylation of substrate or by a pseudosubstrate.

For instance, Epstein-Barr Virus (EBV) uses the gene EBER-1 to produce decoy dsRNA. This leads to cancers such as Burkitt's lymphoma, Hodgkin's Disease, nasopharyngeal carcinoma and various leukemias.

Viral defence mechanisms against PKR

Defence type	Virus	Molecule
Decoy dsRNA	Adenovirus	VAI RNA
	Epstein-Barr virus	EBER
	HIV	TAR
PKR degradation	Poliovirus	2A^pro
hide viral dsRNA	Vaccinia virus	E3L
	Reovirus	σ3
	Influenza virus	NS1
Dimerization block	Influenza virus	p58^IPK
	Hepatitis C virus	NS5A
Pseudosubstrate	Vaccinia virus	K3L
	HIV	Tat
Dephosphorylation of substrate	Herpes simplex virus	ICP34.5

Memory and learning

PKR knockout mice or inhibition of PKR in mice enhances memory and learning.^[5]

Fetal alcohol syndrome

PKR also mediates ethanol-induced protein synthesis inhibition and apoptosis which is linked to fetal alcohol syndrome.^[6]

Interactions

Protein kinase R has been shown to interact with:

• ASK1,^[7]
• DNAJC3,^[8][8]
• ILF3,^{[9][10][11][12]}
• METAP2,^[13]
• P53,^[14]
• PPP1CA,^[15]
• PRKRA,^[16][17]
• STAT1,^[18][19] and
• TARBP2.^[20][21]

References

1. "Entrez Gene: EIF2AK2 eukaryotic translation initiation factor 2-alpha kinase 2".
2. Feng GS, Chong K, Kumar A, Williams BR (June 1992). "Identification of double-stranded RNA-binding domains in the interferon-induced double-stranded RNA-activated p68 kinase". Proc. Natl. Acad. Sci. U.S.A. 89 (12): 5447–51. doi:10.1073/pnas.89.12.5447. PMC 49309. PMID 1351683.
3. García MA, Gil J, Ventoso I, Guerra S, Domingo E, Rivas C, Esteban M (December 2006). "Impact of protein kinase PKR in cell biology: from antiviral to antiproliferative action". Microbiol. Mol. Biol. Rev. 70 (4): 1032–60. doi:10.1128/MMBR.00027-06. PMC 1698511. PMID 17158706.
4. Hotamisligil GS (2010). "Endoplasmic reticulum stress and the inflammatory basis of metabolic disease.". Cell 140 (6): 900–17. doi:10.1016/j.cell.2010.02.034. PMC 2887297. PMID 20303879.
5. Zhu PJ, Huang W, Kalikulov D, Yoo JW, Placzek AN, Stoica L, Zhou H, Bell JC, Friedlander MJ, Krnjević K, Noebels JL, Costa-Mattioli M (December 2011). "Suppression of PKR Promotes Network Excitability and Enhanced Cognition by Interferon-γ-Mediated Disinhibition". Cell 147 (6): 1384–96. doi:10.1016/j.cell.2011.11.029. PMC 3569515. PMID 22153080. Lay summary – canada.com.
6. Chen G, Ma C, Bower KA, Ke Z, Luo J (June 2006). "Interaction between RAX and PKR modulates the effect of ethanol on protein synthesis and survival of neurons". J. Biol. Chem. 281 (23): 15909–15. doi:10.1074/jbc.M600612200. PMID 16574643.
7. Takizawa T, Tatematsu C, Nakanishi Y (December 2002). "Double-stranded RNA-activated protein kinase interacts with apoptosis signal-regulating kinase 1. Implications for apoptosis signaling pathways". Eur. J. Biochem. 269 (24): 6126–32. doi:10.1046/j.1432-1033.2002.03325.x. PMID 12473108.
8. Polyak SJ, Tang N, Wambach M, Barber GN, Katze MG (January 1996). "The P58 cellular inhibitor complexes with the interferon-induced, double-stranded RNA-dependent protein kinase, PKR, to regulate its autophosphorylation and activity". J. Biol. Chem. 271 (3): 1702–7. doi:10.1074/jbc.271.3.1702. PMID 8576172.
9. Saunders LR, Perkins DJ, Balachandran S, Michaels R, Ford R, Mayeda A, Barber GN (August 2001). "Characterization of two evolutionarily conserved, alternatively spliced nuclear phosphoproteins, NFAR-1 and -2, that function in mRNA processing and interact with the double-stranded RNA-dependent protein kinase, PKR". J. Biol. Chem. 276 (34): 32300–12. doi:10.1074/jbc.M104207200. PMID 11438536.
10. Langland JO, Kao PN, Jacobs BL (May 1999). "Nuclear factor-90 of activated T-cells: A double-stranded RNA-binding protein and substrate for the double-stranded RNA-dependent protein kinase, PKR". Biochemistry 38 (19): 6361–8. doi:10.1021/bi982410u. PMID 10320367.
11. Parker LM, Fierro-Monti I, Mathews MB (August 2001). "Nuclear factor 90 is a substrate and regulator of the eukaryotic initiation factor 2 kinase double-stranded RNA-activated protein kinase". J. Biol. Chem. 276 (35): 32522–30. doi:10.1074/jbc.M104408200. PMID 11438540.
12. Patel RC, Vestal DJ, Xu Z, Bandyopadhyay S, Guo W, Erme SM, Williams BR, Sen GC (July 1999). "DRBP76, a double-stranded RNA-binding nuclear protein, is phosphorylated by the interferon-induced protein kinase, PKR". J. Biol. Chem. 274 (29): 20432–7. doi:10.1074/jbc.274.29.20432. PMID 10400669.
13. Gil J, Esteban M, Roth D (December 2000). "In vivo regulation of the dsRNA-dependent protein kinase PKR by the cellular glycoprotein p67". Biochemistry 39 (51): 16016–25. doi:10.1021/bi001754t. PMID 11123929.
14. Cuddihy AR, Wong AH, Tam NW, Li S, Koromilas AE (April 1999). "The double-stranded RNA activated protein kinase PKR physically associates with the tumor suppressor p53 protein and phosphorylates human p53 on serine 392 in vitro". Oncogene 18 (17): 2690–702. doi:10.1038/sj.onc.1202620. PMID 10348343.
15. Tan SL, Tareen SU, Melville MW, Blakely CM, Katze MG (September 2002). "The direct binding of the catalytic subunit of protein phosphatase 1 to the PKR protein kinase is necessary but not sufficient for inactivation and disruption of enzyme dimer formation". J. Biol. Chem. 277 (39): 36109–17. doi:10.1074/jbc.M205109200. PMID 12138106.
16. Huang X, Hutchins B, Patel RC (August 2002). "The C-terminal, third conserved motif of the protein activator PACT plays an essential role in the activation of double-stranded-RNA-dependent protein kinase (PKR)". Biochem. J. 366 (Pt 1): 175–86. doi:10.1042/BJ20020204. PMC 1222748. PMID 11985496.
17. Patel RC, Sen GC (August 1998). "PACT, a protein activator of the interferon-induced protein kinase, PKR". EMBO J. 17 (15): 4379–90. doi:10.1093/emboj/17.15.4379. PMC 1170771. PMID 9687506.
18. Wong AH, Tam NW, Yang YL, Cuddihy AR, Li S, Kirchhoff S, Hauser H, Decker T, Koromilas AE (March 1997). "Physical association between STAT1 and the interferon-inducible protein kinase PKR and implications for interferon and double-stranded RNA signaling pathways". EMBO J. 16 (6): 1291–304. doi:10.1093/emboj/16.6.1291. PMC 1169727. PMID 9135145.
19. Wong AH, Durbin JE, Li S, Dever TE, Decker T, Koromilas AE (April 2001). "Enhanced antiviral and antiproliferative properties of a STAT1 mutant unable to interact with the protein kinase PKR". J. Biol. Chem. 276 (17): 13727–37. doi:10.1074/jbc.M011240200. PMID 11278865.
20. Cosentino GP, Venkatesan S, Serluca FC, Green SR, Mathews MB, Sonenberg N (October 1995). "Double-stranded-RNA-dependent protein kinase and TAR RNA-binding protein form homo- and heterodimers in vivo". Proc. Natl. Acad. Sci. U.S.A. 92 (21): 9445–9. doi:10.1073/pnas.92.21.9445. PMC 40818. PMID 7568151.
21. Daher A, Longuet M, Dorin D, Bois F, Segeral E, Bannwarth S, Battisti PL, Purcell DF, Benarous R, Vaquero C, Meurs EF, Gatignol A (September 2001). "Two dimerization domains in the trans-activation response RNA-binding protein (TRBP) individually reverse the protein kinase R inhibition of HIV-1 long terminal repeat expression". J. Biol. Chem. 276 (36): 33899–905. doi:10.1074/jbc.M103584200. PMID 11438532.

Further reading

• Williams BR (1999). "PKR; a sentinel kinase for cellular stress.". Oncogene 18 (45): 6112–20. doi:10.1038/sj.onc.1203127. PMID 10557102.
• García MA, Meurs EF, Esteban M (2007). "The dsRNA protein kinase PKR: virus and cell control.". Biochimie 89 (6-7): 799–811. doi:10.1016/j.biochi.2007.03.001. PMID 17451862.
• Thomis DC, Doohan JP, Samuel CE (1992). "Mechanism of interferon action: cDNA structure, expression, and regulation of the interferon-induced, RNA-dependent P1/eIF-2 alpha protein kinase from human cells.". Virology 188 (1): 33–46. doi:10.1016/0042-6822(92)90732-5. PMID 1373553.
• McCormack SJ, Thomis DC, Samuel CE (1992). "Mechanism of interferon action: identification of a RNA binding domain within the N-terminal region of the human RNA-dependent P1/eIF-2 alpha protein kinase.". Virology 188 (1): 47–56. doi:10.1016/0042-6822(92)90733-6. PMID 1373554.
• Mellor H, Proud CG (1991). "A synthetic peptide substrate for initiation factor-2 kinases.". Biochem. Biophys. Res. Commun. 178 (2): 430–7. doi:10.1016/0006-291X(91)90125-Q. PMID 1677563.
• Meurs E, Chong K, Galabru J, Thomas NS, Kerr IM, Williams BR, Hovanessian AG (1990). "Molecular cloning and characterization of the human double-stranded RNA-activated protein kinase induced by interferon.". Cell 62 (2): 379–90. doi:10.1016/0092-8674(90)90374-N. PMID 1695551.
• Silverman RH, Sengupta DN (1991). "Translational regulation by HIV leader RNA, TAT, and interferon-inducible enzymes.". J. Exp. Pathol. 5 (2): 69–77. PMID 1708818.
• Roy S, Katze MG, Parkin NT, Edery I, Hovanessian AG, Sonenberg N (1990). "Control of the interferon-induced 68-kilodalton protein kinase by the HIV-1 tat gene product.". Science 247 (4947): 1216–9. doi:10.1126/science.2180064. PMID 2180064.
• McMillan NA, Chun RF, Siderovski DP, Galabru J, Toone WM, Samuel CE, Mak TW, Hovanessian AG, Jeang KT, Williams BR (1996). "HIV-1 Tat directly interacts with the interferon-induced, double-stranded RNA-dependent kinase, PKR.". Virology 213 (2): 413–24. doi:10.1006/viro.1995.0014. PMID 7491766.
• Barber GN, Edelhoff S, Katze MG, Disteche CM (1993). "Chromosomal assignment of the interferon-inducible double-stranded RNA-dependent protein kinase (PRKR) to human chromosome 2p21-p22 and mouse chromosome 17 E2.". Genomics 16 (3): 765–7. doi:10.1006/geno.1993.1262. PMID 7686883.
• Squire J, Meurs EF, Chong KL, McMillan NA, Hovanessian AG, Williams BR (1993). "Localization of the human interferon-induced, ds-RNA activated p68 kinase gene (PRKR) to chromosome 2p21-p22.". Genomics 16 (3): 768–70. doi:10.1006/geno.1993.1263. PMID 7686884.
• Prigmore E, Ahmed S, Best A, Kozma R, Manser E, Segal AW, Lim L (1995). "A 68-kDa kinase and NADPH oxidase component p67phox are targets for Cdc42Hs and Rac1 in neutrophils.". J. Biol. Chem. 270 (18): 10717–22. doi:10.1074/jbc.270.18.10717. PMID 7738010.
• Barber GN, Wambach M, Wong ML, Dever TE, Hinnebusch AG, Katze MG (1993). "Translational regulation by the interferon-induced double-stranded-RNA-activated 68-kDa protein kinase.". Proc. Natl. Acad. Sci. U.S.A. 90 (10): 4621–5. doi:10.1073/pnas.90.10.4621. PMC 46564. PMID 8099444.
• Chen ZJ, Parent L, Maniatis T (1996). "Site-specific phosphorylation of IkappaBalpha by a novel ubiquitination-dependent protein kinase activity.". Cell 84 (6): 853–62. doi:10.1016/S0092-8674(00)81064-8. PMID 8601309.
• Kuhen KL, Shen X, Carlisle ER, Richardson AL, Weier HU, Tanaka H, Samuel CE (1997). "Structural organization of the human gene (PKR) encoding an interferon-inducible RNA-dependent protein kinase (PKR) and differences from its mouse homolog.". Genomics 36 (1): 197–201. doi:10.1006/geno.1996.0446. PMID 8812437.
• Taylor DR, Lee SB, Romano PR, Marshak DR, Hinnebusch AG, Esteban M, Mathews MB (1996). "Autophosphorylation sites participate in the activation of the double-stranded-RNA-activated protein kinase PKR.". Mol. Cell. Biol. 16 (11): 6295–302. PMC 231632. PMID 8887659.
• Kuhen KL, Shen X, Samuel CE (1996). "Mechanism of interferon action sequence of the human interferon-inducible RNA-dependent protein kinase (PKR) deduced from genomic clones.". Gene 178 (1-2): 191–3. doi:10.1016/0378-1119(96)00314-9. PMID 8921913.