6R2M | pdb_00006r2m

Crystal structure of PssZ from Listeria monocytogenes

• PDB DOI: https://doi.org/10.2210/pdb6R2M/pdb

• Classification: HYDROLASE
• Organism(s): Listeria monocytogenes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-03-18 Released: 2019-07-24 
• Deposition Author(s): Wu, H., Cheng, J., Qiao, S., Li, D., Ma, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.200 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Crystal structure of the glycoside hydrolase PssZ from Listeria monocytogenes.

Wu, H., Qiao, S., Li, D., Guo, L., Zhu, M., Ma, L.Z.

(2019) Acta Crystallogr F Struct Biol Commun 75: 501-506

• PubMed: 31282870 
• DOI: https://doi.org/10.1107/S2053230X19008100
• Primary Citation Related Structures: 
  6R2M


• PubMed Abstract: 
  

  Biofilms are microbial communities that are embedded in the extracellular matrix. The exopolysaccharide (EPS) is a key component of the biofilm matrix that maintains the structure of the biofilm and protects the bacteria from antimicrobials. Microbial glycoside hydrolases have been exploited to disrupt biofilms by breaking down EPSs. PssZ has recently been identified as a glycoside hydrolase that can disperse aggregates of Listeria monocytogenes. In this study, the crystal structure of PssZ has been determined at 1.6 Å resolution. PssZ belongs to glycoside hydrolase family 8 and adopts a classical (α/α) ₆ -barrel fold. This architecture forms a deep groove which may serve as the substrate-binding pocket. The conserved catalytic residues (Glu72, Trp110, Asn119, Phe167, Tyr183 and Asp232) are localized at the centre of the groove. This crystal structure will help to improve the understanding of the hydrolytic mechanism of PssZ and its application as a biofilm disrupter.

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Organizational Affiliation: 
• State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.
Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.
School of Food Science, Washington State University, Pullman, WA 99164, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 75.68 kDa 
• Atom Count: 6,116 
• Modeled Residue Count: 621 
• Deposited Residue Count: 652 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside transferase	A, B	326	Listeria monocytogenes	Mutation(s): 0  Gene Names: RK57_03105
UniProt
Find proteins for A0A3D7VE02 (Listeria monocytogenes) Explore A0A3D7VE02  Go to UniProtKB:  A0A3D7VE02

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.200 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.08	α = 90
b = 71.56	β = 95.8
c = 131.3	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-24 
Deposition Author(s): Wu, H., Cheng, J., Qiao, S., Li, D., Ma, L.

Revision History  

• Version 1.0: 2019-07-24
  Type: Initial release
  
• Version 1.1: 2019-09-25
  Changes: Data collection, Database references, Source and taxonomy
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references