5A95

Crystal structure of beta-glucanase SdGluc5_26A from Saccharophagus degradans in complex with tetrasaccharide A, form 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.129 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

The Quaternary Structure of a Glycoside Hydrolase Dictates Specificity Towards Beta-Glucans

Lafond, M.Sulzenbacher, G.Freyd, T.Henrissat, B.Berrin, J.G.Garron, M.L.

(2016) J.Biol.Chem. 291: 7183

  • DOI: 10.1074/jbc.M115.695999
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In the Carbohydrate-Active Enzyme (CAZy) database, glycoside hydrolase family 5 (GH5) is a large family with more than 6,000 sequences. Among the 51 described GH5 subfamilies, subfamily GH5_26 contains members that display either endo-β(1,4)-glucanas ...

    In the Carbohydrate-Active Enzyme (CAZy) database, glycoside hydrolase family 5 (GH5) is a large family with more than 6,000 sequences. Among the 51 described GH5 subfamilies, subfamily GH5_26 contains members that display either endo-β(1,4)-glucanase or β(1,3;1,4)-glucanase activities. In this study, we focused on the GH5_26 enzyme fromSaccharophagus degradans(SdGluc5_26A), a marine bacterium known for its capacity to degrade a wide diversity of complex polysaccharides.SdGluc5_26A displays lichenase activity toward β(1,3;1,4)-glucans with a side cellobiohydrolase activity toward β(1,4)-glucans. The three-dimensional structure ofSdGluc5_26A adopts a stable trimeric quaternary structure also observable in solution. The N-terminal region ofSdGluc5_26A protrudes into the active site of an adjacent monomer. To understand whether this occupation of the active site could influence its activity, we conducted a comprehensive enzymatic characterization ofSdGluc5_26A and of a mutant truncated at the N terminus. Ligand complex structures and kinetic analyses reveal that the N terminus governs the substrate specificity ofSdGluc5_26A. Its deletion opens the enzyme cleft at the -3 subsite and turns the enzyme into an endo-β(1,4)-glucanase. This study demonstrates that experimental approaches can reveal structure-function relationships out of reach of current bioinformatic predictions.


    Organizational Affiliation

    the Architecture et Fonction des Macromolécules Biologiques, UMR7257 CNRS, Aix-Marseille University, F-13288 Marseille, France.,From the Institut des Sciences Moléculaires de Marseille-BiosCiences, UMR7313 CNRS, Aix-Marseille University, Pôle de l'Etoile, 13284 Marseille, France, the INRA, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille University, Polytech'Marseille, F-13288 Marseille, France.,the Architecture et Fonction des Macromolécules Biologiques, UMR7257 CNRS, Aix-Marseille University, F-13288 Marseille, France, the INRA, USC1408 Architecture et Fonction des Macromolécules Biologiques, F-13288 Marseille, France, and.,the INRA, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille University, Polytech'Marseille, F-13288 Marseille, France, jean-guy.berrin@univ-amu.fr.,the Architecture et Fonction des Macromolécules Biologiques, UMR7257 CNRS, Aix-Marseille University, F-13288 Marseille, France, the INRA, USC1408 Architecture et Fonction des Macromolécules Biologiques, F-13288 Marseille, France, and the Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE RETAINING B-GLYCOSIDASE
A, B, C
365Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)Mutation(s): 1 
Gene Names: cel5F
Find proteins for Q21KE5 (Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024))
Go to UniProtKB:  Q21KE5
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BGC
Query on BGC

Download SDF File 
Download CCD File 
A, B, C
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
C
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.129 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 72.048α = 90.00
b = 60.384β = 104.75
c = 130.326γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-04-06
    Type: Database references
  • Version 2.0: 2017-06-14
    Type: Advisory, Atomic model, Derived calculations, Structure summary
  • Version 2.1: 2017-09-13
    Type: Data collection, Structure summary