7O7A

Structure of the PL6 family alginate lyase Pedsa0632 from Pseudopedobacter saltans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Exploring molecular determinants of polysaccharide lyase family 6-1 enzyme activity.

Violot, S.Galisson, F.Carrique, L.Jugnarain, V.Conchou, L.Robert, X.Thureau, A.Helbert, W.Aghajari, N.Ballut, L.

(2021) Glycobiology 31: 1557-1570

  • DOI: https://doi.org/10.1093/glycob/cwab073
  • Primary Citation of Related Structures:  
    7O77, 7O78, 7O79, 7O7A, 7O7T, 7O84

  • PubMed Abstract: 

    The polysaccharide lyase family 6 (PL6) represents one of the 41 polysaccharide lyase families classified in the CAZy database with the vast majority of its members being alginate lyases grouped into three subfamilies, PL6_1-3. To decipher the mode of recognition and action of the enzymes belonging to subfamily PL6_1, we solved the crystal structures of Pedsa0632, Patl3640, Pedsa3628 and Pedsa3807, which all show different substrate specificities and mode of action (endo-/exolyase). Thorough exploration of the structures of Pedsa0632 and Patl3640 in complex with their substrates as well as docking experiments confirms that the conserved residues in subsites -1 to +3 of the catalytic site form a common platform that can accommodate various types of alginate in a very similar manner but with a series of original adaptations bringing them their specificities of action. From comparative studies with existing structures of PL6_1 alginate lyases, we observe that in the right-handed parallel β-helix fold shared by all these enzymes, the substrate-binding site harbors the same overall conserved structures and organization. Despite this apparent similarity, it appears that members of the PL6_1 subfamily specifically accommodate and catalyze the degradation of different alginates suggesting that this common platform is actually a highly adaptable and specific tool.


  • Organizational Affiliation

    Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, Lyon 69367, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aliginate lyase
A, B
427Pseudopedobacter saltans DSM 12145Mutation(s): 0 
Gene Names: Pedsa_0632
UniProt
Find proteins for F0S7Y7 (Pseudopedobacter saltans (strain ATCC 51119 / DSM 12145 / JCM 21818 / CCUG 39354 / LMG 10337 / NBRC 100064 / NCIMB 13643))
Explore F0S7Y7 
Go to UniProtKB:  F0S7Y7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF0S7Y7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.29α = 90
b = 47.29β = 98.03
c = 116.73γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2021-12-29
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description