6JFW

Crystal structure of PA0833 periplasmic domain from Pseudomonas aeruginosa reveals an unexpected enlarged peptidoglycan binding pocket


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of PA0833 periplasmic domain from Pseudomonas aeruginosa reveals an unexpected enlarged peptidoglycan binding pocket.

Lin, X.Ye, F.Lin, S.Yang, F.Chen, Z.Cao, Y.Chen, Z.Gu, J.Lu, G.

(2019) Biochem Biophys Res Commun 511: 875-881

  • DOI: https://doi.org/10.1016/j.bbrc.2019.02.104
  • Primary Citation of Related Structures:  
    6JFW

  • PubMed Abstract: 

    PA0833 of Pseudomonas aeruginosa is recently identified as an OmpA C-like protein that is able to interact with bacterial peptidoglycan (PGN). In this study, we reported the biochemical and structural characterization of the PGN-binding periplasmic-domain of PA0833 (PA0833-PD). Via mutagenesis, key residues responsible for engaging PGN were identified, which also enables us to localize the PGN-binding pocket in a 2.0 Å crystal structure solved in this study. In contrast to its homologous proteins (as represented by AbOmpA-PD of Acinetobacter baumannii) that interact with PGN by directly engaging the DAP (diaminopimelate) moiety, PA0833-PD exhibits an enlarged PGN-binding pocket due to residue insertions and the formation of an extra α-helix in one lateral side of the pocket. Accordingly, single DAP molecule does not show detectable interactions with PA0833-PD in solution, highlighting that other PGN-components, in addition to DAP, are also required to restore the full binding capacity observed between PA0833 and PGN.


  • Organizational Affiliation

    West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PA0833-PD protein
A, B, C, D
160Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: PA0833
UniProt
Find proteins for Q9I5A7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I5A7 
Go to UniProtKB:  Q9I5A7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I5A7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.436α = 89.98
b = 47.727β = 90.03
c = 99.691γ = 90.04
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description