6P2K

Crystal structure of AFV00434, an ancestral GH74 enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74.

Arnal, G.Stogios, P.J.Asohan, J.Attia, M.A.Skarina, T.Viborg, A.H.Henrissat, B.Savchenko, A.Brumer, H.

(2019) J.Biol.Chem. 294: 13233-13247

  • DOI: 10.1074/jbc.RA119.009861
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycoside hydrolase family 74 (GH74) is a historically important family of endo-beta-glucanases. On the basis of early reports of detectable activity on cellulose and soluble cellulose derivatives, GH74 was originally considered to be a "cellulase" f ...

    Glycoside hydrolase family 74 (GH74) is a historically important family of endo-beta-glucanases. On the basis of early reports of detectable activity on cellulose and soluble cellulose derivatives, GH74 was originally considered to be a "cellulase" family, although more recent studies have generally indicated a high specificity toward the ubiquitous plant cell wall matrix glycan xyloglucan. Previous studies have indicated that GH74 xyloglucanases differ in backbone cleavage regiospecificities and can adopt three distinct hydrolytic modes of action: exo, endo-dissociative and endo-processive. To improve functional predictions within GH74, here we coupled in-depth biochemical characterization of 17 recombinant proteins with structural biology-based investigations in the context of a comprehensive molecular phylogeny, including all previously characterized family members. Elucidation of four new GH74 tertiary structures, as well as one distantly related dual seven-bladed β-propeller protein from a marine bacterium, highlighted key structure-function relationships along protein evolutionary trajectories. We could define five phylogenetic groups, which delineated the mode of action and the regiospecificity of GH74 members. At the extremes, a major group of enzymes diverged to hydrolyze the backbone of xyloglucan non specifically with a dissociative mode of action and relaxed backbone regiospecificity. In contrast, a sister group of GH74 enzymes has evolved a large hydrophobic platform comprising 10 subsites, which facilitates processivity. Overall, the findings of our study refine our understanding of catalysis in GH74, providing a framework for future experimentation as well as for bioinformatics predictions of sequences emerging from (meta)genomic studies.


    Organizational Affiliation

    Chemical Engineering and Applied Chemistry, University of Toronto, Canada.,University of Toronto, Canada.,CNRS & Universities of Aix-Marseille, France.,Michael Smith Laboratories & Dept. of Chem., University of British Columbia, Canada.,Banting and Best Department for Medical Science, University of Toronto, Canada.,University of British Columbia, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fibronectin type III domain-containing protein
A, B
779Simiduia agarivorans (strain DSM 21679 / JCM 13881 / BCRC 17597 / SA1)Mutation(s): 0 
Find proteins for K4KQN2 (Simiduia agarivorans (strain DSM 21679 / JCM 13881 / BCRC 17597 / SA1))
Go to UniProtKB:  K4KQN2
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PE3
Query on PE3

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Download CCD File 
A, B
3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
POLYETHYLENE GLYCOL
C28 H58 O15
ILLKMACMBHTSHP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.154 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 173.427α = 90.00
b = 173.427β = 90.00
c = 173.427γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXmodel building
Cootmodel building
PHENIXphasing
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaIndustrial Biocatalysis Network

Revision History 

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-08-07
    Type: Data collection, Database references
  • Version 1.2: 2019-09-18
    Type: Data collection, Database references
  • Version 1.3: 2020-01-08
    Type: Author supporting evidence