PDBsum entry 1vz3

Hydrolase

PDB id: 1vz3

Contents

Protein chain

710 a.a. *

Ligands

GOL ×5

Waters ×1161

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Concerted structural changes in the peptidase and the propeller domains of prolyl oligopeptidase are required for substrate binding.

Authors

Z.Szeltner, D.Rea, T.Juhász, V.Renner, V.Fülöp, L.Polgár.

Ref.

J Mol Biol, 2004, 340, 627-637. [DOI no: 10.1016/j.jmb.2004.05.011]

PubMed id

15210359

Abstract

Prolyl oligopeptidase contains a peptidase domain and its catalytic triad is covered by the central tunnel of a seven-bladed beta-propeller. This domain makes the enzyme an oligopeptidase by excluding large structured peptides from the active site. The apparently rigid crystal structure does not explain how the substrate can approach the catalytic groups. Two possibilities of substrate access were investigated: either blades 1 and 7 of the propeller domain move apart, or the peptidase and/or propeller domains move to create an entry site at the domain interface. Engineering disulfide bridges to the expected oscillating structures prevented such movements, which destroyed the catalytic activity and precluded substrate binding. This indicated that concerted movements of the propeller and the peptidase domains are essential for the enzyme action.

Figure 4.
Figure 4. Oxidation of prolyl oligopeptidase variants by air. The activity of the T597C variant was measured with Z-Gly-Pro-Nap (0m) or Abz-Gly-Phe-Gly-Pro-Phe-Gly-Phe(NO[2])-Ala-NH[2] (+). The C255A variant was used as control ( triangle, open ).

Figure 5.
Figure 5. Reactivation of the oxidized T597C variant of prolyl oligopeptidase. Reduction of the disulfide bond was achieved with 1.5 mM DTE.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 340, 627-637) copyright 2004.

Secondary reference #1

Title

Electrostatic environment at the active site of prolyl oligopeptidase is highly influential during substrate binding.

Authors

Z.Szeltner, D.Rea, V.Renner, L.Juliano, V.Fülop, L.Polgár.

Ref.

J Biol Chem, 2003, 278, 48786-48793. [DOI no: 10.1074/jbc.M309555200]

PubMed id

14514675

Figure 2.
FIG. 2. The pH rate profiles for the reactions of prolyl oligopeptidase ( ) and its R252S variant ( ) with the substrate containing P3 Glu.

Figure 4.
FIG. 4. Arrhenius plots for k[cat]. Shown are Arg at the P2 (x), Glu at the P3 ( ), and Glu at the P5 ( ) positions.

The above figures are reproduced from the cited reference with permission from the ASBMB

Secondary reference #2

Title

Electrostatic effects and binding determinants in the catalysis of prolyl oligopeptidase. Site specific mutagenesis at the oxyanion binding site.

Authors

Z.Szeltner, D.Rea, V.Renner, V.Fulop, L.Polgar.

Ref.

J Biol Chem, 2002, 277, 42613-42622. [DOI no: 10.1074/jbc.M208043200]

PubMed id

12202494

Figure 6.
Fig. 6. Eyring plots for reactions of Z-Gly-Pro-Nap. The k[1] represents the rate constant for the formation of the enzyme-substrate complex. Symbols and reactions are identical with those shown in Fig. 5A.

Figure 7.
Fig. 7. Stereo view of the covalently bound transition state analogue Z-Pro-prolinal (A) to the wild-type enzyme (drawn from PDB entry 1qfs (20)) and (B) to the Y473F variant (drawn as Fig. 4).

The above figures are reproduced from the cited reference with permission from the ASBMB

Secondary reference #3

Title

Substrate-Dependent competency of the catalytic triad of prolyl oligopeptidase.

Authors

Z.Szeltner, D.Rea, T.Juhász, V.Renner, Z.Mucsi, G.Orosz, V.Fülöp, L.Polgár.

Ref.

J Biol Chem, 2002, 277, 44597-44605. [DOI no: 10.1074/jbc.M207386200]

PubMed id

12228249

Figure 5.
Fig. 5. Stereo view of the mutated site of prolyl oligopeptidase. A, D641A variant; the corresponding Asp641 side chain is shown as the thin line. B, D641N variant. Residues 638-643 of the wild-type enzyme are shown as thin lines (from PDB entry 1qfm). The hydrolyzed substrate suc-Gly-Pro-OH is shown darker than the protein residues. The SIGMAA (50) weighted 2mF[o] F[c] electron density using phases from the final model is contoured at 1 level, where represents the r.m.s. electron density for the unit cell. Contours more than 1.4 Å from any of the displayed atoms have been removed for clarity. Dashed lines indicate hydrogen bonds (drawn with MolScript; see Refs. 51 and 52).

Figure 6.
Fig. 6. The catalytic triad and surrounding residues (A) standard catalytic triad (Asp, His, and Ser), (B) D102N trypsin (drawn from Ref. 12), and (C) D641N prolyl oligopeptidase. Hydrogen bonds are shown as dotted lines. Distances are shown using double-headed arrows. The figure was drawn using ISIS Draw (www.mdli.com).

The above figures are reproduced from the cited reference with permission from the ASBMB

Secondary reference #4

Title

Structures of prolyl oligopeptidase substrate/inhibitor complexes. Use of inhibitor binding for titration of the catalytic histidine residue.

Authors

V.Fülöp, Z.Szeltner, V.Renner, L.Polgár.

Ref.

J Biol Chem, 2001, 276, 1262-1266. [DOI no: 10.1074/jbc.M007003200]

PubMed id

11031266

Figure 1.
Fig. 1. Stereo view of the peptide/inhibitor binding site of prolyl oligopeptidase. A, octapeptide binding. B, Z-Gly-Pro-OH binding to the S554A variant. The bound ligands are shown darker than the protein residues. The SIGMAA (28) weighted 2mF[o] F[c] electron density using phases from the final model is contoured at 1 level, where represents the root-mean-square electron density for the unit cell. Contours more than 1.4 Å from any of the displayed atoms have been removed for clarity. C, covalently bound inhibitor Z-Pro-prolinal to Ser554 of the wild type enzyme (drawn from Protein Data Bank code 1qfs (14)). Dashed lines indicate hydrogen bonds (drawn with MolScript (29, 30)).

Figure 2.
Fig. 2. A, the pH rate profiles for the reaction of prolyl oligopeptidase with the octapeptide. The reactions were performed in the presence ( ) and absence ( circle ) of 0.5 M NaCl. The broken lines calculated from Equation 1 stand for the two pH-dependent forms in the presence of 0.5 M NaCl. B, formation of enzyme-inhibitor complex as a function of pH. The association constants (1/K[i]) were calculated from Equation 3 for prolyl oligopeptidase and Z-Gly-Pro-OH in the presence ( ) and absence ( circle ) of 0.5 M NaCl. First-order rate constants were measured with 2-20 nM enzyme and 0.29 µM Z-Gly-Pro-Nap as substrate.

The above figures are reproduced from the cited reference with permission from the ASBMB

Secondary reference #5

Title

Catalysis of serine oligopeptidases is controlled by a gating filter mechanism.

Authors

V.Fülöp, Z.Szeltner, L.Polgár.

Ref.

Embo Rep, 2000, 1, 277-281. [DOI no: 10.1093/embo-reports/kvd048]

PubMed id

11256612

Figure 1.
Figure 1 Oxidation of prolyl oligopeptidase variants. Reaction of the enzymes was carried out with 1.0 mM oxidized glutathione at pH 9.0 and 28�C. Open circles, C78A/C255T variant; filled circles, C255T/Q397C variant. The curves represent single exponential decays.

Figure 2.
Figure 2 Electron density around the disulfide bond of the C255T/Q397C variant of prolyl oligopeptidase. The SIGMAA (Read, 1986) weighted 2mF[o] - DF[c] electron density using phases from the final model is contoured at 1 level, where represents the r.m.s. electron density for the unit cell. Contours >1.4 � from any of the displayed atoms have been removed for clarity. The position of the Glu397 side chain of the wild-type enzyme is also shown in thin lines. The picture was drawn with MolScript (Kraulis, 1991; Esnouf, 1997).

The above figures are reproduced from the cited reference which is an Open Access publication published by Macmillan Publishers Ltd

Secondary reference #6

Title

Prolyl oligopeptidase: an unusual beta-Propeller domain regulates proteolysis.

Authors

V.Fülöp, Z.Böcskei, L.Polgár.

Ref.

Cell, 1998, 94, 161-170. [DOI no: 10.1016/S0092-8674(00)81416-6]

PubMed id

9695945

Figure 4.
Figure 4. Comparison of the Fold of the Noncatalytic Domain of Prolyl Oligopeptidase with a Typical β-Propeller Structure(A) The protein chain of the β-propeller domain of prolyl oligopeptidase is colored as in Figure 2 and viewed perpendicular to that, down the pseudo 7-fold axis. The β sheets of the seven blades are joined in succession (β1/1 to β7/4, cf. Figure 1) around the central axis. The “Velcro” is not closed; there are only hydrophobic interactions between the first (blue) and last (green) blades. Residues (Lys82, Glu134, His180, Asp242, Lys389, and Lys390) narrowing the entrance to the tunnel of the propeller are shown in a ball-and-stick representation.(B) The structure of G-protein β subunit (PDB entry 1tbg). The “Velcro” is closed between the two termini of the polypeptide chain by the main chain hydrogen bonds between the N terminus (blue) and the three antiparallel β strands from the C terminus (green). (Drawn with MolScript and rendered with Raster3D.)

Figure 6.
Figure 6. Surface Representation of Prolyl OligopeptidaseThe molecular surface is superimposed on the polypeptide chain. The picture shows a slab of the molecule, hence the cropping of the chain. The large cavity extends from the central tunnel of the β propeller to the catalytic domain and is accessible through the narrow hole at the bottom of the propeller. The covalently bound inhibitor, Z-Pro-prolinal, is shown in a ball-and-stick representation. The molecular surface was calculated by the method published by [11], and the figure was prepared using XOBJECTS (M. E. M. Noble, Oxford, unpublished program).

The above figures are reproduced from the cited reference with permission from Cell Press