5T4A | pdb_00005t4a

Crystal structure of BhGH81 in complex with laminaro-hexaose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.202 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.160 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.1 of the entry. See complete history

Literature

Structural Analysis of a Family 81 Glycoside Hydrolase Implicates Its Recognition of beta-1,3-Glucan Quaternary Structure.

Pluvinage, B.Fillo, A.Massel, P.Boraston, A.B.

(2017) Structure 25: 1348-1359.e3

  • DOI: https://doi.org/10.1016/j.str.2017.06.019
  • Primary Citation Related Structures: 
    5T49, 5T4A, 5T4C, 5T4G

  • PubMed Abstract: 

    Family 81 glycoside hydrolases (GHs), which are known to cleave β-1,3-glucans, are found in archaea, bacteria, eukaryotes, and viruses. Here we examine the structural and functional features of the GH81 catalytic module, BhGH81, from the Bacillus halodurans protein BH0236 to probe the molecular basis of β-1,3-glucan recognition and cleavage. BhGH81 displayed activity on laminarin, curdlan, and pachyman, but not scleroglucan; the enzyme also cleaved β-1,3-glucooligosaccharides as small as β-1,3-glucotriose. The crystal structures of BhGH81 in complex with various β-1,3-glucooligosaccharides revealed distorted sugars in the -1 catalytic subsite and an arrangement consistent with an inverting catalytic mechanism having a proposed conformational itinerary of 2 S 0 2,5 B 5 S 1 . Notably, the architecture of the catalytic site, location of an adjacent ancillary β-1,3-glucan binding site, and the surface properties of the enzyme indicate the likely ability to recognize the double and/or triple-helical quaternary structures adopted by β-1,3-glucans.


  • Organizational Affiliation
    • Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.

Macromolecule Content 

  • Total Structure Weight: 89.79 kDa 
  • Atom Count: 6,699 
  • Modeled Residue Count: 752 
  • Deposited Residue Count: 783 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycoside Hydrolase783Halalkalibacterium halodurans C-125Mutation(s): 0 
Gene Names: BH0236
EC: 3.2.1.39
UniProt
Find proteins for Q9KG76 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Explore Q9KG76 
Go to UniProtKB:  Q9KG76
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KG76
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan: G89266VM
GlyCosmos: G89266VM
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose
C
3N/A
Glycosylation Resources
GlyTouCan: G00024MO
GlyCosmos: G00024MO
GlyGen: G00024MO

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.202 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.91α = 90
b = 96.14β = 90
c = 104.79γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2019-03-27
    Changes: Author supporting evidence, Data collection, Database references
  • Version 1.2: 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
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary