9G4N | pdb_00009g4n

Glycoside Hydrolase Family 157 from Labilibaculum antarcticum (LaGH157) E224A mutant in complex with Laminaritriose and Glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 
    0.247 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Family GH157 enzyme exhibits broad linkage tolerance and a dual endo/exo-beta-glucanase activity on beta-glucans.

Caseiro, C.McGregor, N.G.S.Alves, V.D.Carvalho, A.L.Romao, M.J.Davies, G.J.Fontes, C.M.G.A.Bule, P.

(2024) Int J Biol Macromol 282: 137402-137402

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.137402
  • Primary Citation of Related Structures:  
    9FZ9, 9G4N, 9G5G

  • PubMed Abstract: 

    The structural and chemical diversity of β-glucans is reflected on the variety of essential biological roles tackled by these polysaccharides. This natural heterogeneity requires an elaborate assortment of enzymatic mechanisms to assemble, degrade or modify, as well as to extract their full biotechnological potential. Recent metagenomic efforts have provided an unprecedented growth in potential new biocatalysts, most of which remain unconfirmed or uncharacterized. Here we report the first biochemical and structural characterization of two bacterial β-glucanases from the recently created glycoside hydrolase family 157 (LaGH157 and BcGH157) and investigate their molecular basis for substrate hydrolysis. Structural analysis by X-ray crystallography revealed that GH157 enzymes belong to clan GH-A, possessing a (β/α) 8 -barrel fold catalytic domain, two β-sandwich accessory domains and two conserved catalytic glutamates residues, with relative positions compatible with a retaining mechanism of hydrolysis. Specificity screening and enzyme kinetics suggest that the enzymes prefer mixed-linkage glucans over β-1,3-glucans. Activity screening showed that both enzymes exhibit pH optimum at 6.5 and temperature optimum for LaGH157 and BcGH157 at 25 °C and 48 °C, respectively. Product analysis with HPAEC-PAD and LC-MS revealed that both enzymes are endo-1,3(4)-β-glucanases, capable of cleaving β-1,3 and β-1,4-linked glucoses, when preceded by a β-1,3 linkage. Moreover, BcGH157 needs a minimum of 4 subsites occupied for hydrolysis to occur, while LaGH157 only requires 3 subsites. Additionally, LaGH157 possesses exohydrolytic activity on β-1,3 and branching β-1,6 linkages. This unusual bifunctional endo-1,3(4)/exo-1,3-1,6 activity constitutes an expansion on our understanding of β-glucan deconstruction, with the potential to inspire future applications.


  • Organizational Affiliation
    • CIISA-Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal; Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), Lisbon, Portugal.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoside hydrolase family 2 catalytic domain-containing protein
A, B, C, D
537Labilibaculum antarcticumMutation(s): 1 
Gene Names: ALGA_4297
UniProt
Find proteins for A0A1Y1CQ89 (Labilibaculum antarcticum)
Explore A0A1Y1CQ89 
Go to UniProtKB:  A0A1Y1CQ89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Y1CQ89
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose
E, F, G, H
3N/A
Glycosylation Resources
GlyTouCan:  G00024MO
GlyCosmos:  G00024MO
GlyGen:  G00024MO
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BGC (Subject of Investigation/LOI)
Query on BGC

Download Ideal Coordinates CCD File 
J [auth A],
M [auth B],
U [auth D]
beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
S [auth C]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth D]
K [auth A]
N [auth B]
P [auth B]
Q [auth B]
AA [auth D],
K [auth A],
N [auth B],
P [auth B],
Q [auth B],
T [auth C],
V [auth D],
X [auth D],
Y [auth D],
Z [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B],
O [auth B],
R [auth C],
W [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free:  0.247 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.854α = 90
b = 127.548β = 90
c = 171.411γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Foundation for Science and Technology (FCT)PortugalSFRH/BD/147152/2019

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release