6ZB8

Exo-beta-1,3-glucanase from moose rumen microbiome, active site mutant E167Q/E295Q


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


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Literature

A homodimeric bacterial exo-beta-1,3-glucanase derived from moose rumen microbiome shows a structural framework similar to yeast exo-beta-1,3-glucanases.

Kalyani, D.C.Reichenbach, T.Aspeborg, H.Divne, C.

(2021) Enzyme Microb Technol 143: 109723-109723

  • DOI: 10.1016/j.enzmictec.2020.109723
  • Primary Citation of Related Structures:  
    6ZB8, 6ZB9

  • PubMed Abstract: 
  • The impact of various β-glucans on the gut microbiome and immune system of vertebrates is becoming increasingly recognized. Besides the fundamental interest in understanding how β-glucans support human and animal health, enzymes that metabolize β-glucans are of interest for hemicellulose bioprocessing ...

    The impact of various β-glucans on the gut microbiome and immune system of vertebrates is becoming increasingly recognized. Besides the fundamental interest in understanding how β-glucans support human and animal health, enzymes that metabolize β-glucans are of interest for hemicellulose bioprocessing. Our earlier metagenomic analysis of the moose rumen microbiome identified a gene coding for a bacterial enzyme with a possible role in β-glucan metabolization. Here, we report that the enzyme, mrbExg5, has exo-β-1,3-glucanase activity on β-1,3-linked glucooligosaccharides and laminarin, but not on β-1,6- or β-1,4-glycosidic bonds. Longer oligosaccharides are good substrates, while shorter substrates are readily transglycosylated into longer products. The enzyme belongs to glycoside hydrolase subfamily GH5_44, which is a close phylogenetic neighbor of the subfamily GH5_9 exo-β-1,3-glucanases of the yeasts Saccharomyces cerevisiae and Candida albicans. The crystal structure shows that unlike the eukaryotic relatives, mrbExg5 is a functional homodimer with a binding region characterized by: (i) subsite +1 can accommodate a branched sugar on the β-1,3-glucan backbone; (ii) subsite +2 is restricted to exclude backbone substituents; and (iii) a fourth subsite (+3) formed by a unique loop. mrbExg5 is the first GH5_44 enzyme to be structurally characterized, and the first bacterial GH5 with exo-β-1,3-glucanase activity.


    Organizational Affiliation

    Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, SE-11421 Stockholm, Sweden. Electronic address: divne@kth.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exo-beta-1,3-glucanase variant E167Q/E295QA, B391uncultured bacteriumMutation(s): 0 
EC: 3.2.1.58
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
15P
Query on 15P

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
POLYETHYLENE GLYCOL (N=34)
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.63α = 90
b = 87.79β = 100.96
c = 70.86γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2017-03877

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release