Pseudoenzyme


Pseudoenzymes are variants of enzymes that are catalytically-deficient, meaning that they perform little or no enzyme catalysis. 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. 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 , the re-purposing of proteins in distinct cellular roles. They are also suggesting new ways to target and interpret cellular signalling mechanisms using small molecules and drugs. 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.

Structures and roles

The difference between enzymatically active and inactive homologues has been noted for some time at the sequence level, and some pseudoenzymes have also been referred to as 'prozymes' when they were analysed in protozoan parasites. The best studied pseudoenzymes reside amongst various key signalling superfamilies of enzymes, such as the proteases, the protein kinases, protein phosphatases and ubiquitin modifying enzymes. The role of pseudoenzymes as "pseudo scaffolds" has also been recognised 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 for drug design in the context of intracellular cellular signalling complexes.

Examples classes

ClassFunctionExamples
PseudokinaseAllosteric regulation of conventional protein kinaseSTRADα 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
PseudokinaseAllosteric regulation of other enzymesVRK3 regulates activity of the phosphatase, VHR
Pseudo-Histidine kinaseProtein interaction domainCaulobacter DivL binds the phosphorylated response regulator, DivK, allowing DivL to negatively regulate the asymmetric cell division regulatory kinase, CckA
PseudophosphataseOcclusion of conventional phosphatase access to substrateEGG-4/EGG-5 binds to the phosphorylated activation loop of the kinase, MBK-2
STYX competes with DUSP4 for binding to ERK1/2
PseudophosphataseAllosteric regulation of conventional phosphatasesMTMR13 binds and promotes lipid phosphatase activity of MTMR2
PseudophosphataseRegulation of protein localisation in a cellSTYX acts as a nuclear anchor for ERK1/2
PseudophosphataseRegulation of signalling complex assemblySTYX binds the F-box protein, FBXW7, to inhibit its recruitment to the SCF Ubiquitin ligase complex
PseudoproteaseAllosteric regulator of conventional proteasecFLIP binds and inhibits the cysteine protease, Caspase-8, to block extrinsic apoptosis
PseudoproteaseRegulation of protein localisation in a cellMammalian iRhom proteins bind and regulate trafficking single pass transmembrane proteins to plasma membrane or ER-associated degradation pathway
Pseudodeubiquitinase Allosteric regulator of conventional DUBKIAA0157 is crucial to assembly of a higher order heterotetramer with DUB, BRCC36, and DUB activity
Pseudoligase Allosteric regulator of conventional E2 ligaseMms2 is a ubiquitin E2 variant that binds active E2, Ubc13, to direct K63 ubiquitin linkages
Pseudoligase Regulation of protein localisation in a cellTsg101 is a component of the ESCRT-I trafficking complex, and plays a key role in HIV-1 Gag binding and HIV budding
Pseudoligase Possible allosteric regulator of conventional RBR family E3 ligaseBRcat regulates interdomain architecture in RBR family E3 Ubiquitin ligases, such as Parkin and Ariadne-1/2
PseudonucleaseAllosteric regulator of conventional nucleaseCPSF-100 is a component of the pre-mRNA 3´ end processing complex containing the active counterpart, CPSF-73
PseudoATPaseAllosteric regulator of conventional ATPaseEccC comprises two pseudoATPase domains that regulate the N-terminal conventional ATPase domain
PseudoGTPaseAllosteric regulator of conventional GTPaseGTP-bound Rnd1 or Rnd3/RhoE bind p190RhoGAP to regulate the catalytic activity of the conventional GTPase, RhoA
PseudoGTPaseScaffold for assembly of signalling complexesMiD51, 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
PseudoGTPaseRegulation of protein localisation in a cellYeast light intermediate domain 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.
PseudochitinaseSubstrate recruitment or sequestrationYKL-39 binds, but does not process, chitooligosaccharides via 5 binding subsites
PseudosialidaseScaffold for assembly of signalling complexesCyRPA nucleates assembly of the P. falciparum PfRh5/PfRipr complex that binds the erythrocyte receptor, basigin, and mediates host cell invasion
PseudolyaseAllosteric activation of conventional enzyme counterpartProzyme heterodimerisation with S-adenosylmethionine decarboxylase activates catalytic activity 1000-fold
PseudotransferaseAllosteric activation of cellular enzyme counterpartViral GAT recruits cellular PFAS to deaminate RIG-I and counter host antiviral defence. T. brucei deoxyhypusine synthase dead paralog, DHSp, binds to and activates DHSc >1000-fold.
Pseudo-histone acetyl transferase Possible scaffold for assembly of signalling complexesHuman O-GlcNAcase lacks catalytic residues and acetyl CoA binding, unlike bacterial counterpart
Pseudo-phospholipasePossible scaffold for assembly of signalling complexesFAM83 family proteins presumed to have acquired new functions in preference to ancestral phospholipase D catalytic activity
Pseudo-phospholipaseAllosteric inactivation of conventional enzyme counterpartViper phospholipase A2 inhibitor structurally resembles the human cellular protein it targets, phospholipase A2.
Pseudo-oxidoreductaseAllosteric inactivation of conventional enzyme counterpartALDH2*2 thwarts assembly of the active counterpart, ALDH2*1, into a tetramer.
Pseudo-dismutaseAllosteric activation of conventional enzyme counterpartCopper chaperone for superoxide dismutase binds and activates catalysis by its enzyme counterpart, SOD1
Pseudo-dihydroorotaseRegulating folding or complex assembly of conventional enzymePseudomonas pDHO is required for either folding of the aspartate transcarbamoylase catalytic subunit, or its assembly into an active oligomer
Pseudo-RNaseFacilitating complex assembly/stability and promoting association of catalytic paralogKREPB4 may act as a pseudoenzyme to form the noncatalytic half of an RNase III heterodimer with the editing endonuclease