5WQW

X-ray structure of catalytic domain of autolysin from Clostridium perfringens

• PDB DOI: https://doi.org/10.2210/pdb5WQW/pdb
• Entry: 5WQW supersedes: 5AZM

• Classification: HYDROLASE
• Organism(s): Clostridium perfringens str. 13
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-11-29 Released: 2016-12-07 
• Deposition Author(s): Tamai, E., Sekiya, H., Goda, E., Makihata, N., Maki, J., Yoshida, H., Kamitori, S.
• Funding Organization(s): JSPS KAKENHI

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.192 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 

Literature

Structural and biochemical characterization of the Clostridium perfringens autolysin catalytic domain

Tamai, E., Sekiya, H., Goda, E., Makihata, N., Maki, J., Yoshida, H., Kamitori, S.

(2017) FEBS Lett 591: 231-239

• PubMed: 27926788 
• DOI: https://doi.org/10.1002/1873-3468.12515
• Primary Citation of Related Structures:  
  5WQW


• PubMed Abstract: 
  

  Bacterial autolysins can partially hydrolyze cell wall peptidoglycans into small sections to regulate cell separation/division and the growth phase. Clostridium perfringens autolysin (Acp) has an N-terminal cell wall-binding domain and a C-terminal catalytic domain with glucosaminidase activity that belongs to the glycoside hydrolase 73 family. Here, we determined the X-ray structure of the Acp catalytic domain (AcpCD) at 1.76 Å resolution. AcpCD has a unique crescent-shaped structure, forming a deep groove for substrate-binding at the center of the protein. The modeling study of the enzyme/substrate complex demonstrated that the length of the substrate-binding groove is closely related to the glucosaminidase activity. Mutagenesis analysis showed that AcpCD likely adopts a neighboring-group mechanism for the catalytic reaction.

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Organizational Affiliation: 

Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Bunkyo-cho, Ehime, Japan.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 30.95 kDa 
• Atom Count: 2,159 
• Modelled Residue Count: 254 
• Deposited Residue Count: 271 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylglucosaminidase	A	271	Clostridium perfringens str. 13	Mutation(s): 0  Gene Names: CPE1231
UniProt
Find proteins for Q8XL11 (Clostridium perfringens (strain 13 / Type A)) Explore Q8XL11  Go to UniProtKB:  Q8XL11

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.192 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.32	α = 90
b = 37.17	β = 100.34
c = 64	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): Tamai, E., Sekiya, H., Goda, E., Makihata, N., Maki, J., Yoshida, H., Kamitori, S.
• This entry supersedes: 5AZM

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Funding Organization	Location	Grant Number
JSPS KAKENHI	Japan	JP15K06973, JP15K08482

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2017-02-01
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references