Crystal structure of SCLam E144S mutant, a non-specific endo-beta-1,3(4)-glucanase from family GH16, co-crystallized with 1,3-beta-D-cellotriosyl-glucose, presenting a 1,3-beta-D-cellobiosyl-glucose at active site

  • Classification: HYDROLASE
  • Organism(s): uncultured bacterium
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2020-07-09 Released: 2021-02-10 
  • Deposition Author(s): Liberato, M.V., Squina, F.
  • Funding Organization(s): Sao Paulo Research Foundation (FAPESP), Brazilian National Council for Scientific and Technological Development (CNPq)

Experimental Data Snapshot

  • Resolution: 1.58 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Insights into the dual cleavage activity of the GH16 laminarinase enzyme class on beta-1,3 and beta-1,4 glycosidic bonds.

Liberato, M.V.Teixeira Prates, E.Goncalves, T.A.Bernardes, A.Vilela, N.Fattori, J.Ematsu, G.C.Chinaglia, M.Machi Gomes, E.R.Migliorini Figueira, A.C.Damasio, A.Polikarpov, I.Skaf, M.S.Squina, F.M.

(2021) J Biol Chem 296: 100385-100385

  • DOI: https://doi.org/10.1016/j.jbc.2021.100385
  • Primary Citation of Related Structures:  
    6XOF, 6XQF, 6XQG, 6XQH, 6XQL, 6XQM

  • PubMed Abstract: 

    Glycoside hydrolases (GHs) are involved in the degradation of a wide diversity of carbohydrates and present several biotechnological applications. Many GH families are composed of enzymes with a single well-defined specificity. In contrast, enzymes from the GH16 family can act on a range of different polysaccharides, including β-glucans and galactans. SCLam, a GH16 member derived from a soil metagenome, an endo-β-1,3(4)-glucanase (EC, can cleave both β-1,3 and β-1,4 glycosidic bonds in glucans, such as laminarin, barley β-glucan, and cello-oligosaccharides. A similar cleavage pattern was previously reported for other GH16 family members. However, the molecular mechanisms for this dual cleavage activity on (1,3)- and (1,4)-β-D-glycosidic bonds by laminarinases have not been elucidated. In this sense, we determined the X-ray structure of a presumably inactive form of SCLam cocrystallized with different oligosaccharides. The solved structures revealed general bound products that are formed owing to residual activities of hydrolysis and transglycosylation. Biochemical and biophysical analyses and molecular dynamics simulations help to rationalize differences in activity toward different substrates. Our results depicted a bulky aromatic residue near the catalytic site critical to select the preferable configuration of glycosidic bonds in the binding cleft. Altogether, these data contribute to understanding the structural basis of recognition and hydrolysis of β-1,3 and β-1,4 glycosidic linkages of the laminarinase enzyme class, which is valuable for future studies on the GH16 family members and applications related to biomass conversion into feedstocks and bioproducts.

  • Organizational Affiliation

    Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil; Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, São Paulo, Brazil.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GH16 family protein269uncultured bacteriumMutation(s): 1 
Gene Names: sclam
Find proteins for A0A0B5H9B3 (uncultured bacterium)
Explore A0A0B5H9B3 
Go to UniProtKB:  A0A0B5H9B3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B5H9B3
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G89925KE
GlyCosmos:  G89925KE
GlyGen:  G89925KE
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.58 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.692α = 90
b = 49.868β = 90
c = 114.474γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2014/04105-4
Sao Paulo Research Foundation (FAPESP)Brazil2015/50590-4
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil310177/2011-1

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-10
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description