Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 131.9 kDa 
• Atom Count: 9,903 
• Modelled Residue Count: 1,011 
• Deposited Residue Count: 1,095 
• Unique protein chains: 1

 5A8M

Crystal structure of the selenomethionine derivative of beta-glucanase SdGluc5_26A from Saccharophagus degradans

• PDB DOI:  https://doi.org/10.2210/pdb5A8M/pdb

• Classification: HYDROLASE
• Organism(s): Saccharophagus degradans 2-40
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-16 Released: 2016-01-20 
• Deposition Author(s): Sulzenbacher, G., Lafond, M., Freyd, T., Henrissat, B., Coutinho, R.M., Berrin, J.G., Garron, M.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.165 
• R-Value Work: 0.143 
• R-Value Observed: 0.144 

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

• PubMed: 26755730 
• DOI: https://doi.org/10.1074/jbc.M115.695999
• Primary Citation of Related Structures:  
  5A8M, 5A8N, 5A8O, 5A8P, 5A8Q, 5A94, 5A95


• 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)-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.

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Organizational Affiliation: 

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.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE RETAINING B-GLYCOSIDASE	A, B, C	365	Saccharophagus degradans 2-40	Mutation(s): 0  Gene Names: cel5F, Sde_1572 EC: 3.2.1.73
UniProt
Find proteins for Q21KE5 (Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)) Explore Q21KE5  Go to UniProtKB:  Q21KE5

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], SA [auth C], TA [auth C], UA [auth C], Z [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	H [auth A], MA [auth C], W [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth A], J [auth A], K [auth A], NA [auth C], OA [auth C], X [auth B], Y [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A], IA [auth C], JA [auth C], KA [auth C], S [auth B], T [auth B], U [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	G [auth A], LA [auth C], V [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.165 
• R-Value Work: 0.143 
• R-Value Observed: 0.144 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.605	α = 90
b = 142.605	β = 90
c = 136.277	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Sulzenbacher, G., Lafond, M., Freyd, T., Henrissat, B., Coutinho, R.M., Berrin, J.G., Garron, M.L.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2016-04-06
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Data collection, Structure summary