5WKA image
Deposition Date 2017-07-24
Release Date 2018-03-07
Last Version Date 2023-10-04
Entry Detail
PDB ID:
5WKA
Keywords:
Title:
Crystal structure of a GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake
Biological Source:
Source Organism:
metagenome (Taxon ID: 256318)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.75 Å
R-Value Free:
0.27
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Beta-glucosidase
Chain IDs:A, B, C, D
Chain Length:473
Number of Molecules:4
Biological Source:metagenome
Primary Citation
A novel beta-glucosidase isolated from the microbial metagenome of Lake Poraque (Amazon, Brazil).
Biochim. Biophys. Acta 1866 569 579 (2018)
PMID: 29454992 DOI: 10.1016/j.bbapap.2018.02.001

Abstact

The Amazon region holds most of the biological richness of Brazil. Despite their ecological and biotechnological importance, studies related to microorganisms from this region are limited. Metagenomics leads to exciting discoveries, mainly regarding non-cultivable microorganisms. Herein, we report the discovery of a novel beta-glucosidase (glycoside hydrolase family 1) gene from a metagenome from Lake Poraque in the Amazon region. The gene encodes a protein of 52.9 kDa, named AmBgl-LP, which was recombinantly expressed in Escherichia coli and biochemically and structurally characterized. Although AmBgl-LP hydrolyzed the synthetic substrate p-nitrophenyl-beta-d-glucopyranoside (pNPbetaG) and the natural substrate cellobiose, it showed higher specificity for pNPbetaG (k(cat)/K(m) = 6 s(-1).mM(-1)) than cellobiose (k(cat)/K(m) = 0.6 s(-1).mM(-1)). AmBgl-LP showed maximum activity at 40  degrees C and pH 6.0 when pNPbetaG was used as the substrate. Glucose is a competitive inhibitor of AmBgl-LP, presenting a K(i) of 14 mM. X-ray crystallography and Small Angle X-ray Scattering were used to determine the AmBgl-LP three-dimensional structure and its oligomeric state. Interestingly, despite sharing similar active site architecture with other structurally characterized GH1 family members which are monomeric, AmBgl-LP forms stable dimers in solution. The identification of new GH1 members by metagenomics might extend our understanding of the molecular mechanisms and diversity of these enzymes, besides enabling us to survey their industrial applications.

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