Structural and mechanistic analysis of two prolyl endopeptidases: Role of interdomain dynamics in catalysis and specificity Lu Shan†, Irimpan I. Mathews‡, and Chaitan Khosla†§¶ʈ Departments of †Chemical Engineering, ¶Chemistry, and §Biochemistry, Stanford University, Stanford, CA 94305; and ‡Stanford Synchrotron Radiation Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 Edited by Christopher T. Walsh, Harvard Medical School, Boston, MA, and approved January 16, 2005 (received for review November 7, 2004) Prolyl endopeptidases (PEPs) are a unique class of serine proteases domain forms a tight barrel-shaped lid over the active site and is with considerable therapeutic potential for the treatment of celiac postulated to regulate substrate size. sprue. The crystal structures of two didomain PEPs have been Mechanisms have been proposed to account for the observed solved in alternative configurations, thereby providing insights bias of PEPs for shorter substrates. It had long been speculated that into the mode of action of these enzymes. The structure of the some conformational change might be involved in substrate binding Sphingomonas capsulata PEP, solved and refined to 1.8-Å resolu- (15). One mechanism suggested that the oscillating ␤-propeller tion, revealed an open configuration of the active site. In contrast, blades act as a ‘‘gating filter’’ during catalysis to let only short the inhibitor-bound PEP from Myxococcus xanthus was crystallized peptide substrates into the active site via the central tunnel of the (1.5-Å resolution) in a closed form. Comparative analysis of the two propeller (12, 13, 16, 17). This proposal was supported by experi- structures highlights a critical role for the domain interface in ments that connected the first and seventh blades of the propeller regulating interdomain dynamics and substrate specificity. Struc- domain with disulfide bonds, which resulted in reduced enzymatic ture-based mutagenesis of the M. xanthus PEP confirms an impor- activity. A more recent study suggests that relative movement of the tant role for several interfacial residues. A salt bridge between two domains might be required to allow substrates into the active Arg-572 and Asp-196͞Glu-197 appears to act as a latch for opening site (18). The nature of the substrate-binding mode is pertinent or closing the didomain enzyme, and Arg-572 and Ile-575 may also from both fundamental mechanistic and practical therapeutic help secure the incoming peptide substrate to the open form of the points of view. Control of chain-length specificity is of particular enzyme. Arg-618 and Asp-145 are responsible for anchoring the importance for the therapeutic use of PEPs in celiac sprue, because invariant proline residue in the active site of this postproline- many of the immunotoxic peptides released by the gastrointestinal cleaving enzyme. A model is proposed for the docking of a metabolism of dietary gluten are relatively long (8, 19). representative substrate PQPQLPYPQPQLP in the active site, where Here, we have solved the x-ray crystal structures of two thera- the N-terminal substrate residues interact extensively with the peutically promising bacterial PEPs from Myxococcus xanthus (MX) catalytic domain, and the C-terminal residues stretch into the and Sphingomonas capsulata (SC) (10). Comparison of the archi- propeller domain. Given the promise of the M. xanthus PEP as an tecture of the two enzymes, one crystallizing in an open (i.e., oral therapeutic enzyme for treating celiac sprue, our results unoccupied) configuration and the other in a closed (i.e., inhibitor- provide a strong foundation for further optimization of the PEP’s bound) configuration, provided direct insight into the mechanism clinically useful features. by which substrate access to the active site is controlled. A docking model of MX PEP with peptide PQPQLPYPQPQLP further celiac sprue ͉ gluten ͉ prolyl oligopeptidase ͉ serine protease revealed an extended binding pocket that could accommodate a larger substrate. Supporting the structural analysis, mutagenesis of rolyl endopeptidases (PEPs), also known as prolyl oligopepti- a salt bridge that hinges the two domains yielded enzymes with Pdases or postproline cleaving enzymes, are a family of serine unaffected catalytic capability but altered chain-length specificity. proteases that cleave after proline residues in peptides. These Alteration of residues responsible for anchoring the invariant proline side chain in the substrate led to greatly reduced catalytic endoproteolytic enzymes are widely distributed in bacteria, fungi, activity, illustrating the delicate interplay between specificity and animals, and plants (1–5). The human PEP is a cytosolic enzyme catalysis in this class of enzymes. involved in physiological processes such as the degradation of certain peptide hormones and neuropeptides. It has been impli- Materials and Methods cated in the regulation of blood pressure and in neurological Expression and Purification of SC and MX PEP. Both PEPs were disorders and is, therefore, an attractive pharmacological target (6, expressed as recombinant proteins with C-terminal His -tags in 7). Recently, PEPs have also been evaluated as oral therapeutic 6 Escherichia coli and purified according the protocols described in agents for celiac sprue because of a unique ability to accelerate the ref. 10. Site-directed mutagenesis was performed by using the PCR breakdown of proline-rich gluten in the gut lumen (8, 9). QuikChange method (Stratagene). From a structural and mechanistic standpoint, PEPs are rela- tively unusual serine proteases. As peptidases, their activity is Crystallization and Diffraction Data Collection. Initial crystallization restricted to substrates that are shorter than 30 amino acid residues, conditions for native SC PEP were determined by using Wizard with the possible exception of the Flavobacterium meningosepticum and Pyrococcus furiosus PEPs, which can break down longer pep- tides (10, 11). PEPs are also significantly larger than typical serine This paper was submitted directly (Track II) to the PNAS office. proteases (75 kDa vs. 30 kDa). The x-ray crystal structure of a Abbreviations: MX, Myxococcus xanthus; PEP, prolyl endopeptidase; pNA, p-nitroanilide; prototypical PEP from porcine muscle was solved by Polgar and SC, Sphingomonas capsulata. coworkers (12–14) and revealed a distinctive two-domain structure, Data deposition: The atomic coordinates have been deposited in the Protein Data Bank, a smaller N-terminal catalytic domain, and an unusual ␤-propeller www.pdb.org (PDB ID codes 2BKL and 1YR2). ʈ domain. The catalytic domain resembles canonical serine proteases To whom correspondence should be addressed. E-mail: [email protected]. BIOCHEMISTRY such as trypsin and chymotrypsin, whereas the unique propeller © 2005 by The National Academy of Sciences of the USA www.pnas.org͞cgi͞doi͞10.1073͞pnas.0408286102 PNAS ͉ March 8, 2005 ͉ vol. 102 ͉ no. 10 ͉ 3599–3604 Downloaded by guest on September 26, 2021 Table 1. Data collection and refinement statistics SC MXϩbocNFP Data collection Space group P21 P21 Unit cell, Å 53.34, 91.22, 79.79 65.69, 114.72, 99.28 ␤ ϭ 91.0° ␤ ϭ 103.6° Wavelength, Å 1.00 1.00 Resolution, Å 50.0–1.80 (1.86–1.80) 50.0–1.50 (1.55–1.50) No. of reflections 353,562 918,495 No. of unique reflections 68,648 225,366 Redundancy 5.2 (2.1) 4.1 (4.0) Completeness 98.9 (92.2) 98.9 (97.7) Rsym,% 7.1 (50.2) 6.8 (47.6) I͞␴ 13.0 (1.7) 12.8 (2.8) Refinement Resolution, Å 30.0–1.80 (1.85–1.80) 30.0–1.50 (1.54–1.50) Reflections (working) 62,633 (4,393) 202,805 (15,555) Reflections (test) 3,538 (237) 11,252 (812) Rwork,* % 16.1 (25.0) 16.0 (22.4) † Rfree, % 18.6 (26.3) 18.2 (25.6) No. of protein atoms 5,252 10,717 No. of ligand atoms 0 67 No. of buffer͞glycerol͞ion atoms 12 41 No. of water atoms 660 1,371 rms deviations Bonds, Å 0.017 0.015 Angles, ° 1.56 1.49 Average B factor, Å2 Protein atoms 16.7 11.0 Ligand atoms N͞A 19.6 Buffer͞glycerol͞ions 47.4 28.5 Solvent atoms 34.7 25.0 Values for the outer shell are given in parentheses. *Rwork ϭ͚hkl ʈFo͉ Ϫ ͉Fcʈ͚͞hkl ͉Fo͉, where Fo and Fc are observed and calculated structure factors, respectively. † For Rfree, the above summation is extended over a subset of reflections (5%) that were excluded from all stages of refinement. I and Wizard II crystal screens (Emerald Biostructures, Bain- Systems) with a crystal-to-detector distance of 190 mm. Both data bridge Island, WA) with 19.4 mg/ml protein in 20 mM Hepes (pH sets were processed and scaled by using HKL2000 (HKL Research, 7.0)͞2mMDTT͞5% glycerol. Crystals were grown at 22°C by Charlottesville, VA) (20, 21). Final data-processing statistics are using the hanging-drop vapor-diffusion technique. The opti- shown in Table 1. mized crystallization conditions involved mixing 1.2 ␮l of protein solution with 1.2 ␮l of reservoir solution containing 23% PEG Structure Determination and Refinement. The structure of the SC 8K and 0.1 M Tris (pH 8.6). Diffraction-quality crystals ap- PEP protein was determined by molecular replacement by using the peared in 2–3 days. Crystals were cryoprotected by 2-min program MOLREP from the CCP4 suite (30). Because the initial stepwise soaks in solutions of the well solution plus 2%, 5%, 8%, attempts with reported structures (closed forms) of the PEPs were 12%, and, finally, 17% glycerol and were then flash-frozen in unsuccessful, individual searches for the catalytic domain and the liquid nitrogen. ␤-barrel domain were performed. This procedure enabled the The complex of MX PEP–Z-Ala-prolinal was prepared by mixing structure solution and revealed the open conformation of the SC the protein sample witha5Mexcess of the ligand. Crystals of the PEP structure. complex were grown at 4°C by using the hanging-drop vapor- The MX PEP structure was determined by molecular replace- diffusion technique.