9FZ9 | pdb_00009fz9

Glycoside Hydrolase Family 157 from Labilibaculum antarcticum, wild type SeMet derivative (LaGH157)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 
    0.262 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.249 (Depositor), 0.250 (DCC) 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MLA
Query on MLA

Download Ideal Coordinates CCD File 
H [auth A]MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A],
G [auth A],
I [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free:  0.262 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.249 (Depositor), 0.250 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.154α = 90
b = 112.582β = 90
c = 251.464γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
AutoSolphasing
xia2data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugalUIDB/00276/2020, LA/P/0059/2020
Fundacao para a Ciencia e a TecnologiaPortugalUIDP/04378/2020, UIDB/04378/2020, LA/P/0140/2020

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release