7O84

Structure of the PL6 family alginate lyase Pedsa0632 from Pseudopedobacter saltans in complex with substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 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-/exo-lyase) ...

    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-/exo-lyase). Thorough exploration of the structures of Pedsa0632 and Patl3640 in complex with their substrates as well as docking experiments confirm that the conserved residues in subsites -1 to +3 of the catalytic site form a common platform which 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, 69367 Lyon, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alginate lyaseA, B426Pseudopedobacter 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
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acidC3N/A Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acidD4N/A Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.182α = 90
b = 47.583β = 98.25
c = 116.2γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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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: Data collection, Database references