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Pseudoenzyme

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Pseudoenzymes are variants of enzymes that are catalytically-deficient (usually inactive), meaning that they perform little or no enzyme catalysis. [1] They are believed to be represented in all major enzyme families in the kingdoms of life, where they have important signaling and metabolic functions, many of which are only now coming to light.[2] Pseudoenzymes are becoming increasingly important to analyse, especially as the bioinformatic analysis of genomes reveals their ubiquity. Their important regulatory and sometimes disease-associated functions in metabolic and signalling pathways are also shedding new light on the non-catalytic functions of active enzymes, of moonlighting proteins,[3][4] the re-purposing of proteins in distinct cellular roles (Protein moonlighting). They are also suggesting new ways to target and interpret cellular signalling mechanisms using small molecules and drugs.[5] The most intensively analyzed, and certainly the best understood pseudoenzymes in terms of cellular signalling functions are probably the pseudokinases, the pseudoproteases and the pseudophosphatases. Recently, the pseudo-deubiquitylases have also begun to gain prominence.[6][7]

Structures and roles

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The difference between enzymatically active and inactive homologues has been noted (and in some cases, understood when comparing catalytically active and inactive proteins residing in recognisable families) for some time at the sequence level,[8] owing to the absence of key catalytic residues. Some pseudoenzymes have also been referred to as 'prozymes' when they were analysed in protozoan parasites.[9] The best studied pseudoenzymes reside amongst various key signalling superfamilies of enzymes, such as the proteases,[10] the protein kinases,[11][12][13][14][15][16][17] protein phosphatases[18][19] and ubiquitin modifying enzymes.[20][21] The role of pseudoenzymes as "pseudo scaffolds" has also been recognised [22] and pseudoenzymes are now beginning to be more thoroughly studied in terms of their biology and function, in large part because they are also interesting potential targets (or anti-targets) for drug design in the context of intracellular cellular signalling complexes.[23][24]

Examples classes

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Class Function Examples [25]
Pseudokinase Allosteric regulation of conventional protein kinase STRADα regulates activity of the conventional protein kinase, LKB1

JAK1-3 and TYK2 C-terminal tyrosine kinase domains are regulated by their adjacent pseudokinase domain KSR1/2 regulates activation of the conventional protein kinase, Raf

Allosteric regulation of other enzymes VRK3 regulates activity of the phosphatase, VHR
Pseudo-Histidine kinase Protein interaction domain Caulobacter DivL binds the phosphorylated response regulator, DivK, allowing DivL to negatively regulate the asymmetric cell division regulatory kinase, CckA
Pseudophosphatase Occlusion of conventional phosphatase access to substrate EGG-4/EGG-5 binds to the phosphorylated activation loop of the kinase, MBK-2

STYX competes with DUSP4 for binding to ERK1/2

Allosteric regulation of conventional phosphatases MTMR13 binds and promotes lipid phosphatase activity of MTMR2
Regulation of protein localisation in a cell STYX acts as a nuclear anchor for ERK1/2
Regulation of signalling complex assembly STYX binds the F-box protein, FBXW7, to inhibit its recruitment to the SCF Ubiquitin ligase complex
Pseudoprotease Allosteric regulator of conventional protease cFLIP binds and inhibits the cysteine protease, Caspase-8, to block extrinsic apoptosis
Regulation of protein localisation in a cell Mammalian iRhom proteins bind and regulate trafficking single pass transmembrane proteins to plasma membrane or ER-associated degradation pathway
Pseudodeubiquitinase (pseudoDUB) Allosteric regulator of conventional DUB KIAA0157 is crucial to assembly of a higher order heterotetramer with DUB, BRCC36, and DUB activity
Pseudoligase (pseudo-Ubiquitin E2) Allosteric regulator of conventional E2 ligase Mms2 is a ubiquitin E2 variant (UEV) that binds active E2, Ubc13, to direct K63 ubiquitin linkages
Regulation of protein localisation in a cell Tsg101 is a component of the ESCRT-I trafficking complex, and plays a key role in HIV-1 Gag binding and HIV budding
Pseudoligase (pseudo-Ubiquitin E3) Possible allosteric regulator of conventional RBR family E3 ligase BRcat regulates interdomain architecture in RBR family E3 Ubiquitin ligases, such as Parkin and Ariadne-1/2
Pseudonuclease Allosteric regulator of conventional nuclease CPSF-100 is a component of the pre-mRNA 3´ end processing complex containing the active counterpart, CPSF-73
PseudoATPase Allosteric regulator of conventional ATPase EccC comprises two pseudoATPase domains that regulate the N-terminal conventional ATPase domain
PseudoGTPase Allosteric regulator of conventional GTPase GTP-bound Rnd1 or Rnd3/RhoE bind p190RhoGAP to regulate the catalytic activity of the conventional GTPase, RhoA
Scaffold for assembly of signalling complexes MiD51, which is catalytically dead but binds GDP or ADP, is part of a complex that recruits Drp1 to mediate mitochondrial fission. CENP-M cannot bind GTP or switch conformations, but is essential for nucleating the CENP-I, CENP-H, CENP-K small GTPase complex to regulate kinetochore assembly
Regulation of protein localisation in a cell Yeast light intermediate domain (LIC) is a pseudoGTPase, devoid of nucleotide binding, which binds the dynein motor to cargo. Human LIC binds GDP in preference to GTP, suggesting nucleotide binding could confer stability rather than underlying a switch mechanism.
Pseudochitinase Substrate recruitment or sequestration YKL-39 binds, but does not process, chitooligosaccharides via 5 binding subsites
Pseudosialidase Scaffold for assembly of signalling complexes CyRPA nucleates assembly of the P. falciparum PfRh5/PfRipr complex that binds the erythrocyte receptor, basigin, and mediates host cell invasion
Pseudolyase Allosteric activation of conventional enzyme counterpart Prozyme heterodimerisation with S-adenosylmethionine decarboxylase (AdoMetDC) activates catalytic activity 1000-fold
Pseudotransferase Allosteric activation of cellular enzyme counterpart Viral GAT recruits cellular PFAS to deaminate RIG-I and counter host antiviral defence. T. brucei deoxyhypusine synthase (TbDHS) dead paralog, DHSp, binds to and activates DHSc >1000-fold.
Pseudo-histone acetyl transferase (pseudoHAT) Possible scaffold for assembly of signalling complexes Human O-GlcNAcase (OGA) lacks catalytic residues and acetyl CoA binding, unlike bacterial counterpart
Pseudo-phospholipase Possible scaffold for assembly of signalling complexes FAM83 family proteins presumed to have acquired new functions in preference to ancestral phospholipase D catalytic activity
Allosteric inactivation of conventional enzyme counterpart Viper phospholipase A2 inhibitor structurally resembles the human cellular protein it targets, phospholipase A2.
Pseudo-oxidoreductase Allosteric inactivation of conventional enzyme counterpart ALDH2*2 thwarts assembly of the active counterpart, ALDH2*1, into a tetramer.
Pseudo-dismutase Allosteric activation of conventional enzyme counterpart Copper chaperone for superoxide dismutase (CCS) binds and activates catalysis by its enzyme counterpart, SOD1
Pseudo-dihydroorotase Regulating folding or complex assembly of conventional enzyme Pseudomonas pDHO is required for either folding of the aspartate transcarbamoylase catalytic subunit, or its assembly into an active oligomer
Pseudo-RNase Facilitating complex assembly/stability and promoting association of catalytic paralog KREPB4 may act as a pseudoenzyme to form the noncatalytic half of an RNase III heterodimer with the editing endonuclease(s)[26]

See also

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References

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  1. ^ Ribeiro AJ, Das S, Dawson N, Zaru R, Orchard S, Thornton JM, Orengo C, Zeqiraj E, Murphy JM, Eyers PA (Aug 2019). "Emerging concepts in pseudoenzyme classification, evolution, and signaling". Science Signaling. 12 (594): eaat9797. doi:10.1126/scisignal.aat9797. PMID 31409758.
  2. ^ Kwon A, Scott S, Taujale R, Yeung W, Kochut KJ, Eyers PA, Kannan N (April 2019). "Tracing the origin and evolution of pseudokinases across the tree of life". Science Signaling. 12 (578): eaav3810. doi:10.1126/scisignal.aav3810. PMC 6997932. PMID 31015289.
  3. ^ Jeffery CJ (Feb 2019). "The demise of catalysis, but new functions arise: pseudoenzymes as the phoenixes of the protein world". Biochemical Society Transactions. 47 (1): 371–379. doi:10.1042/BST20180473. PMID 30710059. S2CID 73437705.
  4. ^ Jeffery CJ (Dec 2019). "Multitalented actors inside and outside the cell: recent discoveries add to the number of moonlighting proteins". Biochemical Society Transactions. 47 (6): 1941–1948. doi:10.1042/BST20190798. PMID 31803903. S2CID 208643133.
  5. ^ Eyers PA, Murphy JM (November 2016). "The evolving world of pseudoenzymes: proteins, prejudice and zombies". BMC Biology. 14 (1): 98. doi:10.1186/s12915-016-0322-x. PMC 5106787. PMID 27835992.
  6. ^ Walden M, Masandi SK, Pawlowski K, Zeqiraj E (Feb 2018). "Pseudo-DUBs as allosteric activators and molecular scaffolds of protein complexes" (PDF). Biochem Soc Trans. 46 (2): 453–466. doi:10.1042/BST20160268. PMID 29472364. S2CID 3477709.
  7. ^ Walden M, Tian L, Ross RL, Sykora UM, Byrne DP, Hesketh EL, Masandi SK, Cassel J, George R, Ault JR, El Oualid F, Pawłowski K, Salvino JM, Eyers PA, Ranson NA, Del Galdo F, Greenberg RA, Zeqiraj E (May 2019). "Metabolic control of BRISC–SHMT2 assembly regulates immune signalling" (PDF). Nature. 570 (7760): 194–199. Bibcode:2019Natur.570..194W. doi:10.1038/s41586-019-1232-1. PMC 6914362. PMID 31142841.
  8. ^ Todd AE, Orengo CA, Thornton JM (October 2002). "Sequence and structural differences between enzyme and nonenzyme homologs". Structure. 10 (10): 1435–51. doi:10.1016/s0969-2126(02)00861-4. PMID 12377129.
  9. ^ Willert EK, Fitzpatrick R, Phillips MA (May 2007). "Allosteric regulation of an essential trypanosome polyamine biosynthetic enzyme by a catalytically dead homolog". Proceedings of the National Academy of Sciences of the United States of America. 104 (20): 8275–80. Bibcode:2007PNAS..104.8275W. doi:10.1073/pnas.0701111104. PMC 1895940. PMID 17485680.
  10. ^ Adrain C, Freeman M (July 2012). "New lives for old: evolution of pseudoenzyme function illustrated by iRhoms". Nature Reviews. Molecular Cell Biology. 13 (8): 489–98. doi:10.1038/nrm3392. PMID 22781900. S2CID 806199.
  11. ^ Kwon A, Scott S, Taujale R, Yeung W, Kochut KJ, Eyers PA, Kannan N (April 2019). "Tracing the origin and evolution of pseudokinases across the tree of life". Science Signaling. 12 (578): eaav3810. doi:10.1126/scisignal.aav3810. PMC 6997932. PMID 31015289.
  12. ^ Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S (December 2002). "The protein kinase complement of the human genome". Science. 298 (5600): 1912–34. Bibcode:2002Sci...298.1912M. doi:10.1126/science.1075762. PMID 12471243. S2CID 26554314.
  13. ^ Boudeau J, Miranda-Saavedra D, Barton GJ, Alessi DR (September 2006). "Emerging roles of pseudokinases". Trends in Cell Biology. 16 (9): 443–52. doi:10.1016/j.tcb.2006.07.003. PMID 16879967.
  14. ^ Eyers PA, Keeshan K, Kannan N (April 2017). "Tribbles in the 21st Century: The Evolving Roles of Tribbles Pseudokinases in Biology and Disease". Trends in Cell Biology. 27 (4): 284–298. doi:10.1016/j.tcb.2016.11.002. PMC 5382568. PMID 27908682.
  15. ^ Reiterer V, Eyers PA, Farhan H (September 2014). "Day of the dead: pseudokinases and pseudophosphatases in physiology and disease". Trends in Cell Biology. 24 (9): 489–505. doi:10.1016/j.tcb.2014.03.008. PMID 24818526.
  16. ^ Murphy JM, Czabotar PE, Hildebrand JM, Lucet IS, Zhang JG, Alvarez-Diaz S, Lewis R, Lalaoui N, Metcalf D, Webb AI, Young SN, Varghese LN, Tannahill GM, Hatchell EC, Majewski IJ, Okamoto T, Dobson RC, Hilton DJ, Babon JJ, Nicola NA, Strasser A, Silke J, Alexander WS (September 2013). "The pseudokinase MLKL mediates necroptosis via a molecular switch mechanism". Immunity. 39 (3): 443–53. doi:10.1016/j.immuni.2013.06.018. PMID 24012422.
  17. ^ Wishart MJ, Dixon JE (August 1998). "Gathering STYX: phosphatase-like form predicts functions for unique protein-interaction domains". Trends in Biochemical Sciences. 23 (8): 301–6. doi:10.1016/s0968-0004(98)01241-9. PMID 9757831.
  18. ^ Reiterer V, Eyers PA, Farhan H (September 2014). "Day of the dead: pseudokinases and pseudophosphatases in physiology and disease". Trends in Cell Biology. 24 (9): 489–505. doi:10.1016/j.tcb.2014.03.008. PMID 24818526.
  19. ^ Chen MJ, Dixon JE, Manning G (April 2017). "Genomics and evolution of protein phosphatases". Science Signaling. 10 (474): eaag1796. doi:10.1126/scisignal.aag1796. PMID 28400531. S2CID 41041971.
  20. ^ Zeqiraj E, Tian L, Piggott CA, Pillon MC, Duffy NM, Ceccarelli DF, Keszei AF, Lorenzen K, Kurinov I, Orlicky S, Gish GD, Heck AJ, Guarné A, Greenberg RA, Sicheri F (September 2015). "Higher-Order Assembly of BRCC36-KIAA0157 Is Required for DUB Activity and Biological Function". Molecular Cell. 59 (6): 970–83. doi:10.1016/j.molcel.2015.07.028. PMC 4579573. PMID 26344097.
  21. ^ Strickson S, Emmerich CH, Goh ET, Zhang J, Kelsall IR, Macartney T, Hastie CJ, Knebel A, Peggie M, Marchesi F, Arthur JS, Cohen P (April 2017). "Roles of the TRAF6 and Pellino E3 ligases in MyD88 and RANKL signaling". Proceedings of the National Academy of Sciences of the United States of America. 114 (17): E3481–E3489. Bibcode:2017PNAS..114E3481S. doi:10.1073/pnas.1702367114. PMC 5410814. PMID 28404732.
  22. ^ Aggarwal-Howarth S, Scott JD (April 2017). "Pseudoscaffolds and anchoring proteins: the difference is in the details". Biochemical Society Transactions. 45 (2): 371–379. doi:10.1042/bst20160329. PMC 5497583. PMID 28408477.
  23. ^ Foulkes DM, Byrne DP, Bailey FP, Eyers PA (October 2015). "Tribbles pseudokinases: novel targets for chemical biology and drug discovery?". Biochemical Society Transactions. 43 (5): 1095–103. doi:10.1042/bst20150109. PMID 26517930.
  24. ^ Byrne DP, Foulkes DM, Eyers PA (January 2017). "Pseudokinases: update on their functions and evaluation as new drug targets". Future Medicinal Chemistry. 9 (2): 245–265. doi:10.4155/fmc-2016-0207. PMID 28097887.
  25. ^ Murphy JM, Farhan H, Eyers PA (April 2017). "Bio-Zombie: the rise of pseudoenzymes in biology". Biochemical Society Transactions. 45 (2): 537–544. doi:10.1042/bst20160400. PMID 28408493.
  26. ^ McDermott SM, Stuart K (November 2017). "The essential functions of KREPB4 are developmentally distinct and required for endonuclease association with editosomes". RNA. 23 (11): 1672–1684. doi:10.1261/rna.062786.117. PMC 5648035. PMID 28802260.
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