Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase

Journal Article · Wed Feb 20 00:00:00 EST 2019 · Biochemistry

DOI:https://doi.org/10.1021/acs.biochem.9b00031· OSTI ID:1512994

Ellis-Guardiola, Ken ^[1]; Rui, Huan ^[1]; Beckner, Ryan L. ^[1]; Srivastava, Poonam ^[1]; Sukumar, Narayanasami ^[2]; Roux, Benoît ^[1]; Lewis, Jared C. ^[3]

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1. Univ. of Chicago, IL (United States)
2. Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS), Northeastern Collaborative Access Team (NE-CAT) and Department of Chemistry and Chemical Biology; Cornell Univ., Ithaca, NY (United States)
3. Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States

Enzymes in the prolyl oligopeptidase family possess unique structures and substrate specificities that are important for their biological activity and for potential biocatalytic applications. In this work, the crystal structures of Pyrococcus furiosus (Pfu) prolyl oligopeptidase (POP) and the corresponding S477C mutant were determined to 1.9 and 2.2 Å resolution, respectively. The wild type enzyme crystallized in an open conformation, indicating that this state is readily accessible, and it contained bound chloride ions and a prolylproline ligand. These structures were used as starting points for molecular dynamics simulations of Pfu POP conformational dynamics. The simulations showed that large-scale domain opening and closing occurred spontaneously, providing facile substrate access to the active site. Movement of the loop containing the catalytically essential histidine into a conformation similar to those found in structures with fully formed catalytic triads also occurred. This movement was modulated by chloride binding, providing a rationale for experimentally observed activation of POP peptidase catalysis by chloride. Thus, the structures and simulations reported in this study, combined with existing biochemical data, provide a number of insights into POP catalysis.

• Research Organization: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
• Sponsoring Organization: Indiana METACyt Initiative; Lilly Endowment, Inc.; National Institute of General Medical Sciences (NIGMS); National Institutes of Health (NIH); National Science Foundation (NSF); The David and Lucile Packard Foundation; US Army Research Laboratory (USARL); US Army Research Office (ARO); USDOE Office of Science (SC)
• Grant/Contract Number: AC02-06CH11357
• OSTI ID: 1512994
• Journal Information: Biochemistry, Journal Name: Biochemistry Journal Issue: 12 Vol. 58; ISSN 0006-2960
• Publisher: American Chemical Society (ACS)
• Country of Publication: United States
• Language: ENGLISH

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
59 BASIC BIOLOGICAL SCIENCES
Chemical structure
Conformation
Crystal structure
Ions
Peptides and proteins