6CAN

Prolyl oligopeptidase mutant S477C from Pyrococcus furiosus

• PDB DOI:  https://doi.org/10.2210/pdb6CAN/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-01-31 Released: 2019-02-06 
• Deposition Author(s): Ellis-Guardiola, K., Lewis, J.C., Sukumar, N.
• Funding Organization(s): National Science Foundation (NSF, United States), Army Research Office, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 

Literature

Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase.

Ellis-Guardiola, K., Rui, H., Beckner, R.L., Srivastava, P., Sukumar, N., Roux, B., Lewis, J.C.

(2019) Biochemistry 58: 1616-1626

• PubMed: 30786206 
• DOI: https://doi.org/10.1021/acs.biochem.9b00031
• Primary Citation of Related Structures:  
  5T88, 6CAN


• PubMed Abstract: 
  

Enzymes in the prolyl oligopeptidase family possess unique structures and substrate specificities that are important for their biological activity and for potential biocatalytic applications. 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.

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Organizational Affiliation: 

Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 142.09 kDa 
• Atom Count: 10,866 
• Modelled Residue Count: 1,232 
• Deposited Residue Count: 1,232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prolyl endopeptidase	A, B	616	Pyrococcus furiosus	Mutation(s): 2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.292	α = 90
b = 178.764	β = 104.35
c = 59.293	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
Coot	model building
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Ellis-Guardiola, K., Lewis, J.C., Sukumar, N.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE 1351991
Army Research Office	United States	62247-LS
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM008720
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41 GM103403
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2019-08-21
  Changes: Data collection, Database references
• Version 1.3: 2019-11-27
  Changes: Author supporting evidence