2W63 | pdb_00002w63

SACCHAROMYCES CEREVISIAE GAS2P IN COMPLEX WITH LAMINARITRIOSE AND LAMINARITETRAOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.190 (Depositor), 0.194 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2W63

This is version 2.2 of the entry. See complete history

Literature

Molecular Mechanisms of Yeast Cell Wall Glucan Remodeling.

Hurtado-Guerrero, R.Schuttelkopf, A.W.Mouyna, I.Ibrahim, A.F.M.Shepherd, S.Fontaine, T.Latge, J.Van Aalten, D.M.F.

(2009) J Biological Chem 284: 8461

  • DOI: https://doi.org/10.1074/jbc.M807990200
  • Primary Citation Related Structures: 
    2W61, 2W62, 2W63

  • PubMed Abstract: 

    Yeast cell wall remodeling is controlled by the equilibrium between glycoside hydrolases, glycosyltransferases, and transglycosylases. Family 72 glycoside hydrolases (GH72) are ubiquitous in fungal organisms and are known to possess significant transglycosylase activity, producing elongated beta(1-3) glucan chains. However, the molecular mechanisms that control the balance between hydrolysis and transglycosylation in these enzymes are not understood. Here we present the first crystal structure of a glucan transglycosylase, Saccharomyces cerevisiae Gas2 (ScGas2), revealing a multidomain fold, with a (betaalpha)(8) catalytic core and a separate glucan binding domain with an elongated, conserved glucan binding groove. Structures of ScGas2 complexes with different beta-glucan substrate/product oligosaccharides provide "snapshots" of substrate binding and hydrolysis/transglycosylation giving the first insights into the mechanisms these enzymes employ to drive beta(1-3) glucan elongation. Together with mutagenesis and analysis of reaction products, the structures suggest a "base occlusion" mechanism through which these enzymes protect the covalent protein-enzyme intermediate from a water nucleophile, thus controlling the balance between hydrolysis and transglycosylation and driving the elongation of beta(1-3) glucan chains in the yeast cell wall.


  • Organizational Affiliation
    • Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom. R.Hurtadoguerrero@dundee.ac.uk

Macromolecule Content 

  • Total Structure Weight: 63.6 kDa 
  • Atom Count: 3,833 
  • Modeled Residue Count: 432 
  • Deposited Residue Count: 555 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLYCOLIPID-ANCHORED SURFACE PROTEIN 2555Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.4.1
UniProt
Find proteins for Q06135 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06135 
Go to UniProtKB:  Q06135
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06135
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose
B
4N/A
Glycosylation Resources
GlyTouCan: G87841AX
GlyCosmos: G87841AX
GlyGen: G87841AX
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: 1.90 Å
  • R-Value Free:  0.190 (Depositor), 0.194 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.02α = 90
b = 70.267β = 90
c = 148.913γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2011-09-21
    Changes: Atomic model, Derived calculations, Non-polymer description, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-11-13
    Changes: Structure summary