6P2L

Crystal structure of Niastella koreensis GH74 (NkGH74) enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.119 

wwPDB Validation   3D Report Full Report


This is version 2.0 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:  
    6P2K, 6P2M, 6P2L, 6P2O, 6P2N

  • PubMed Abstract: 
  • Glycoside hydrolase family 74 (GH74) is a historically important family of endo -β-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 ...

    Glycoside hydrolase family 74 (GH74) is a historically important family of endo -β-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 nonspecifically 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

    Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycosyl hydrolase BNR repeat-containing proteinA697Niastella koreensis GR20-10Mutation(s): 0 
Gene Names: Niako_1751
UniProt
Find proteins for G8TAF2 (Niastella koreensis (strain DSM 17620 / KACC 11465 / NBRC 106392 / GR20-10))
Explore G8TAF2 
Go to UniProtKB:  G8TAF2
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-alpha-D-glucopyranoseB8N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G80923GO
GlyCosmos:  G80923GO
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranoseC7N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G24181CY
GlyCosmos:  G24181CY
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth A] , BA [auth A] , CA [auth A] , D [auth A] , DA [auth A] , E [auth A] , F [auth A] , G [auth A] , 
AA [auth A],  BA [auth A],  CA [auth A],  D [auth A],  DA [auth A],  E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  O [auth A],  P [auth A],  Q [auth A],  R [auth A],  S [auth A],  T [auth A],  U [auth A],  V [auth A],  W [auth A],  X [auth A],  Y [auth A],  Z [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.119 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.869α = 90
b = 119.096β = 90
c = 127.043γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence, Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary