8H2C

Crystal structure of the pseudaminic acid synthase PseI from Campylobacter jejuni


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural analysis of the pseudaminic acid synthase PseI from Campylobacter jejuni.

Song, W.S.Park, M.A.Ki, D.U.Yoon, S.I.

(2022) Biochem Biophys Res Commun 635: 252-258

  • DOI: https://doi.org/10.1016/j.bbrc.2022.10.050
  • Primary Citation of Related Structures:  
    8H2C

  • PubMed Abstract: 

    Campylobacter jejuni PseI is a pseudaminic acid synthase that condenses the 2,4-diacetamido-2,4,6-trideoxy-l-altrose sugar (6-deoxy AltdiNAc) and phosphoenolpyruvate to generate pseudaminic acid, a sialic acid-like 9-carbon backbone α-keto sugar. Pseudaminic acid is conjugated to cell surface proteins and lipids and plays a key role in the mobility and virulence of C. jejuni and other pathogenic bacteria. To provide insights into the catalytic mechanism of PseI, we performed a structural study on PseI. PseI forms a two-domain structure and assembles into a domain-swapped homodimer. The PseI dimer has two cavities, each of which accommodates a metal ion using conserved histidine residues. A comparative analysis of structures and sequences suggests that the cavity of PseI functions as an active site that binds the 6-deoxy AltdiNAc and phosphoenolpyruvate substrates and mediates their condensation. Furthermore, we propose the substrate binding-induced structural rearrangement of PseI and predict 6-deoxy AltdiNAc recognition residues that are specific to PseI.


  • Organizational Affiliation

    Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, 24341, Republic of Korea. Electronic address: bioticsong@gmail.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pseudaminic acid synthase
A, B, C, D
349Campylobacter jejuniMutation(s): 0 
Gene Names: pseIFRQ26_09070
EC: 2.5.1.97
UniProt
Find proteins for Q0P8U0 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168))
Explore Q0P8U0 
Go to UniProtKB:  Q0P8U0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0P8U0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.805α = 90
b = 176.805β = 90
c = 99.824γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2019R1A2C1002100
National Research Foundation (NRF, Korea)Korea, Republic Of2019R1I1A1A01047141

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Data collection, Refinement description