The prolyl oligopeptidase family

Polgár, László

doi:10.1007/s00018-002-8427-5

Cited by 289 publications

(243 citation statements)

References 138 publications

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“…The structure of PCY1 consists of an α/β hydrolase domain composed of residues Met1-Val77 and Asp437-Asp724 and a β-propeller domain consisting of residues Cys82-Glu432. A hinge region encompassing residues Asn78-Arg81 and Ser433-Pro436 links the two domains and presumably facilitates movement between an open form competent for binding substrate and a closed form where chemistry is carried out (41,42). The PCY1-presegetalin A1 complex was crystallized in the closed form with a large internal cavity (10,317 Å 3 as calculated by CASTp), which can accommodate the binding of large peptides (41,43).…”

Section: Resultsmentioning

confidence: 99%

Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants

Chekan

Estrada

Covello

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Enzymes that can catalyze the macrocyclization of linear peptide substrates have long been sought for the production of libraries of structurally diverse scaffolds via combinatorial gene assembly as well as to afford rapid in vivo screening methods. Orbitides are plant ribosomally synthesized and posttranslationally modified peptides (RiPPs) of various sizes and topologies, several of which are shown to be biologically active. The diversity in size and sequence of orbitides suggests that the corresponding macrocyclases may be ideal catalysts for production of cyclic peptides. Here we present the biochemical characterization and crystal structures of the plant enzyme PCY1 involved in orbitide macrocyclization. These studies demonstrate how the PCY1 S9A protease fold has been adapted for transamidation, rather than hydrolysis, of acyl-enzyme intermediates to yield cyclic products. Notably, PCY1 uses an unusual strategy in which the cleaved C-terminal follower peptide from the substrate stabilizes the enzyme in a productive conformation to facilitate macrocyclization of the N-terminal fragment. The broad substrate tolerance of PCY1 can be exploited as a biotechnological tool to generate structurally diverse arrays of macrocycles, including those with nonproteinogenic elements.RiPP | biosynthesis | peptide | plant | orbitide

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Section: Resultsmentioning

confidence: 99%

Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants

Chekan

Estrada

Covello

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…DPP-IV belongs to the prolyl oligopeptidase (POP) family, a subfamily of serine proteases (12,13). This class of prolyl peptidases includes DPP-IV, prolyl oligopeptidase (POP), DPP-II, DPP8, DPP9, and fibroblast activation protein (FAP) (12,13).…”

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confidence: 99%

“…This class of prolyl peptidases includes DPP-IV, prolyl oligopeptidase (POP), DPP-II, DPP8, DPP9, and fibroblast activation protein (FAP) (12,13). Unlike classic serine proteases, the POP family of enzymes is highly selective toward peptides that have a proline residue at the penultimate position (18).…”

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confidence: 99%

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One Site Mutation Disrupts Dimer Formation in Human DPP-IV Proteins

Chien

Huang

Chou

et al. 2004

Journal of Biological Chemistry

103

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DPP-IV is a prolyl dipeptidase, cleaving the peptide bond after the penultimate proline residue. It is an important drug target for the treatment of type II diabetes. DPP-IV is active as a dimer, and monomeric DPP-IV has been speculated to be inactive. In this study, we have identified the C-terminal loop of DPP-IV, highly conserved among prolyl dipeptidases, as essential for dimer formation and optimal catalysis. The conserved residue His 750 on the loop contributes significantly for dimer stability. We have determined the quaternary structures of the wild type, H750A, and H750E mutant enzymes by several independent methods including chemical crosslinking, gel electrophoresis, size exclusion chromatography, and analytical ultracentrifugation. Wild-type DPP-IV exists as dimers both in the intact cell and in vitro after purification from human semen or insect cells. The H750A mutation results in a mixture of DPP-IV dimer and monomer. H750A dimer has the same kinetic constants as those of the wild type, whereas the H750A monomer has a 60-fold decrease in k cat . Replacement of His 750 with a negatively charged Glu (H750E) results in nearly exclusive monomers with a 300-fold decrease in catalytic activity. Interestingly, there is no dynamic equilibrium between the dimer and the monomer for all forms of DPP-IVs studied here. This is the first study of the function of the C-terminal loop as well as monomeric mutant DPP-IVs with respect to their enzymatic activities. The study has important implications for the discovery of drugs targeted to the dimer interface.

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“…The new family includes enzymes of different specificities like the prolyl oligopeptidase itself, dipeptidyl-peptidase IV, acylaminoacyl-peptidase, and oligopeptidase B (5). These enzymes selectively cleave substrates that are no longer than ϳ30 amino acid residues in total.…”

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confidence: 99%

Electrostatic Environment at the Active Site of Prolyl Oligopeptidase Is Highly Influential during Substrate Binding

Szeltner

Rea

Renner

et al. 2003

Journal of Biological Chemistry

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The positive electrostatic environment of the active site of prolyl oligopeptidase was investigated by using substrates with glutamic acid at positions P2, P3, P4, and P5, respectively. The different substrates gave various pH rate profiles. The pK a values extracted from the curves are apparent parameters, presumably affected by the nearby charged residues, and do not reflect the ionization of a simple catalytic histidine as found in the classic serine peptidases like chymotrypsin and subtilisin. The temperature dependence of k cat /K m did not produce linear Arrhenius plots, indicating different changes in the individual rate constants with the increase in temperature. This rendered it possible to calculate these constants, i.e. the formation (k 1 ) and decomposition (k ؊1 ) of the enzyme-substrate complex and the acylation constant (k 2 ), as well as the corresponding activation energies. The results have revealed the relationship between the complex Michaelis parameters and the individual rate constants. Structure determination of the enzyme-substrate complexes has shown that the different substrates display a uniform binding mode. None of the glutamic acids interacts with a charged group. We conclude that the specific rate constant is controlled by k 1 rather than k 2 and that the charged residues from the substrate and the enzyme can markedly affect the formation but not the structure of the enzyme-substrate complexes.Prolyl oligopeptidase is a member of a relatively new group of serine peptidases unrelated to the well known trypsin and subtilisin families (1-4). The new family includes enzymes of different specificities like the prolyl oligopeptidase itself, dipeptidyl-peptidase IV, acylaminoacyl-peptidase, and oligopeptidase B (5). These enzymes selectively cleave substrates that are no longer than ϳ30 amino acid residues in total. Prolyl oligopeptidase (EC 3.4.21.26) is implicated in the metabolism of peptide hormones and neuropeptides (6 -8). Because specific inhibitors relieve scopolamine-induced amnesia (9 -12), the enzyme is of pharmaceutical interest. The activity of prolyl oligopeptidase has also been associated with depression (13,14) and blood pressure regulation (15).The crystal structure determination of prolyl oligopeptidase has revealed that the carboxyl-terminal peptidase domain of the enzyme displays an ␣/␤ hydrolase fold and that its catalytic triad (Ser-554, His-680, and Asp-641) is covered by the central tunnel of an unusual ␤-propeller (16). Recent engineering of the enzyme provided evidence for a novel strategy of regulation in which oscillating propeller blades act as a gating filter during catalysis, letting small peptide substrates into the active site while excluding large proteins, thereby preventing accidental proteolysis in the cytosol (17).The active site region of prolyl oligopeptidase exhibits several charged residues such as Arg-643, Asp-642, Arg-252, Asp-149, and Arg-128. The complex electrostatic environment created by these residues may considerably influence the binding...

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The prolyl oligopeptidase family

Cited by 289 publications

References 138 publications

Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants

Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants

One Site Mutation Disrupts Dimer Formation in Human DPP-IV Proteins

Electrostatic Environment at the Active Site of Prolyl Oligopeptidase Is Highly Influential during Substrate Binding

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