Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 76.47 kDa 
• Atom Count: 6,929 
• Modelled Residue Count: 685 
• Deposited Residue Count: 697 
• Unique protein chains: 1

 6P2L

Crystal structure of Niastella koreensis GH74 (NkGH74) enzyme

• PDB DOI: 10.2210/pdb6P2L/pdb

• Classification: HYDROLASE
• Organism(s): Niastella koreensis GR20-10
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-05-21 Released: 2019-07-31 
• Deposition Author(s): Stogios, P.J., Skarina, T., Arnal, G., Brumer, H., Savchenko, A.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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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 

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

• PubMed: 31324716 
• DOI: 10.1074/jbc.RA119.009861
• Primary Citation of Related Structures:  
  6P2K, 6P2L, 6P2M, 6P2N, 6P2O


• 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. 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.

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Organizational Affiliation: 

Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase BNR repeat-containing protein	A	697	Niastella koreensis GR20-10	Mutation(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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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-glucopyranose	B	8		N/A
Glycosylation Resources
GlyTouCan:  G80923GO GlyCosmos:  G80923GO

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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-glucopyranose	C	7		N/A
Glycosylation Resources
GlyTouCan:  G24181CY GlyCosmos:  G24181CY

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	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

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 = 42.869	α = 90
b = 119.096	β = 90
c = 127.043	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-31 
Deposition Author(s): Stogios, P.J., Skarina, T., Arnal, G., Brumer, H., Savchenko, A.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	Industrial Biocatalysis Network

Revision History  

• 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