Prolyl Endopeptidase: Difference between revisions
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<applet load='1yr2' size='300' frame='true' align='right' caption='Prolyl endopeptidase of Sphingomonas capsulata at 1.80Å' /> | <applet load='1yr2' size='300' frame='true' align='right' caption='Prolyl endopeptidase of Sphingomonas capsulata at 1.80Å [1]' /> | ||
Prolyl endopeptidases (PEPs) are a class of serine proteases which cleave peptide bonds on the C-terminal side of internal proline residues. | Prolyl endopeptidases (PEPs) are a class of serine proteases which cleave peptide bonds on the C-terminal side of internal proline residues. | ||
== Structure == | == Structure == | ||
[[Image:1yr2_ribbon2.png|thumb|300x300px|alt=Alt text|Catalytic(bottom) and β-propeller domains(top) with peptide linkages shown in | [[Image:1yr2_ribbon2.png|thumb|300x300px|alt=Alt text|Catalytic(bottom) and β-propeller domains(top) with peptide linkages shown in green and blue]] | ||
Prolyl endopeptidases are relatively large enzymes(75 kDa) and contain two distinct domains: a catalytic domain and a β-propeller domain. | Prolyl endopeptidases are relatively large enzymes(75 kDa) and contain two distinct domains: a catalytic domain and a β-propeller domain[2]. | ||
=== β-Propeller Domain === | === β-Propeller Domain === | ||
The β-propeller domain is made up of repeated antiparallel β-sheets with connecting peptide strands which form a tight lid over the active site located on the catalytic domain. The β-propeller domain is cylindrical in structure and contains a very tight central channel through its core that is roughly 4Å in diameter in the resting state. It has been found that this domain is roughly 2% conserved indicating that it likely doesnt play a major role in substrate binding []. | The β-propeller domain is made up of repeated antiparallel β-sheets with connecting peptide strands which form a tight lid over the active site located on the catalytic domain. The β-propeller domain is cylindrical in structure and contains a very tight central channel through its core that is roughly 4Å in diameter in the resting state. It has been found that this domain is roughly 2% conserved indicating that it likely doesnt play a major role in substrate binding [2]. | ||
=== Catalytic Domain === | === Catalytic Domain === | ||
The catalytic domain mainly consists of an [http://en.wikipedia.org/wiki/Alpha/beta_hydrolase_fold α/β hydrolase fold] which is a series of 8 strands connected by helices in a fold common to many enzymes. The catalytic domain was found to be much more conserved than the β-propeller domain(~50%) []. | The catalytic domain mainly consists of an [http://en.wikipedia.org/wiki/Alpha/beta_hydrolase_fold α/β hydrolase fold] which is a series of 8 strands connected by helices in a fold common to many enzymes. The catalytic domain was found to be much more conserved than the β-propeller domain(~50%) [3]. The catalytic site contains a catalytic triad of Ser-Asp-His and lies in a cavity near the interface to the β-propeller domain. | ||
=== Binding Mechanism === | === Binding Mechanism === | ||
From observed interactions between the β-propeller and catalytic domains several possible substrate binding mechanism have been proposed. | From observed interactions between the β-propeller and catalytic domains several possible substrate binding mechanism have been proposed. | ||
The first theory of substrate binding was that the substrate would be able to travel through the central channel in the β-propeller domain to the active site. This theory was proved less likely as the central channel is only 4Å wide in its relaxed state compared to the medium length peptides catalyzed by PEP which are 6-12Å in diameter. This theory is still possible as a conformational change could allow the much larger substrate to travel through the β-propeller domain. | The first theory of substrate binding was that the substrate would be able to travel through the central channel in the β-propeller domain to the active site. This theory was proved less likely as the central channel is only 4Å wide in its relaxed state compared to the medium length peptides catalyzed by PEP which are 6-12Å in diameter [4]. This theory is still possible as a conformational change could allow the much larger substrate to travel through the β-propeller domain. | ||
A newer proposed mechanism of substrate binding is that the β-propeller domain acts as a gate to the active site and that the whole domain moves during a conformational change. This theory has gathered support as a structure for the PEP of ''Sphingomonas capsulata'' clearly shows the β-propeller in an open configuration connected to the catalytic domain by two peptide strands on the same side of the enzyme forming a hinge [3]. | |||
Both mechanistic binding theories account for the observed activity of PEP as being limited to acting on peptides of less than 30 residues. | |||
=== Inhibition === | === Inhibition === | ||
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== References == | == References == | ||
[] | [1] Shan L, Mathews II, Khosla C. Structural and mechanistic analysis of two prolyl endopeptidases: Role of interdomain dynamics in catalysis and specificity. PNAS. 2005 Mar 8; 102(10)3599-604. | ||
[] | [2] Besedin DV, Rudenskaya GN. Proline-Specific Endopeptidases. Russ. J. Bioorg. Chem. 2002 Feb 28; 29(1)1-17. | ||
[] | [3] Gass J, Khosla C. Biomedicine and Diseases: Review Prolyl Endopeptidases. Cell. Mol. Life Sci. 2007; 64 345-55. | ||
[] Shan L, Marti T, Sollid LM, Gray GM, Khosla C. Comparative biochemical analysis of three bacterial prolyl endopeptidases: implications for coeliac sprue. Biochem. J. 2008; 383 311-18. | [4] Shan L, Marti T, Sollid LM, Gray GM, Khosla C. Comparative biochemical analysis of three bacterial prolyl endopeptidases: implications for coeliac sprue. Biochem. J. 2008; 383 311-18. | ||
[5] Ehren J, Govindarajan S, Morón B, Minshull J, Khosla C. Protein engineering of improved prolyl endopeptidases for celiac sprue therapy. Protein Eng. Des. Sel. 2008 Oct 4; 21(12)699-707. | [5] Ehren J, Govindarajan S, Morón B, Minshull J, Khosla C. Protein engineering of improved prolyl endopeptidases for celiac sprue therapy. Protein Eng. Des. Sel. 2008 Oct 4; 21(12)699-707. | ||