4M81

The structure of E292S glycosynthase variant of exo-1,3-beta-glucanase from Candida albicans complexed with 1-fluoro-alpha-D-glucopyranoside (donor) and p-nitrophenyl beta-D-glucopyranoside (acceptor) at 1.86A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Major Change in Regiospecificity for the Exo-1,3-beta-glucanase from Candida albicans following Its Conversion to a Glycosynthase.

Nakatani, Y.Larsen, D.S.Cutfield, S.M.Cutfield, J.F.

(2014) Biochemistry 53: 3318-3326

  • DOI: 10.1021/bi500239m
  • Primary Citation of Related Structures:  
    4M80, 4M81, 4M82

  • PubMed Abstract: 
  • The exo-1,3-β-glucanase (Exg) from Candida albicans is involved in cell wall β-d-glucan metabolism and morphogenesis through its hydrolase and transglycosidase activities. Previous work has shown that both these activities strongly favor β-1,3-linkag ...

    The exo-1,3-β-glucanase (Exg) from Candida albicans is involved in cell wall β-d-glucan metabolism and morphogenesis through its hydrolase and transglycosidase activities. Previous work has shown that both these activities strongly favor β-1,3-linkages. The E292S Exg variant displayed modest glycosynthase activity using α-d-glucopyranosyl fluoride (α-GlcF) as the donor and pNP-β-d-glucopyranoside (pNPGlc) as the acceptor but surprisingly showed a marked preference for synthesizing β-1,6-linked over β-1,3- and β-1,4-linked disaccharide products. With pNPXyl as the acceptor, the preference became β-1,4 over β-1,3. The crystal structure of the glycosynthase bound to both of its substrates, α-GlcF and pNPGlc, is the first such ternary complex structure to be determined. The results revealed that the donor bound in the -1 subsite, as expected, while the acceptor was oriented in the +1 subsite to facilitate β-1,6-linkage, thereby supporting the results from solution studies. A second crystal structure containing the major product of glycosynthesis, pNP-gentiobiose, showed that the -1 subsite allows another docking position for the terminal sugar; i.e., one position is set up for catalysis, whereas the other is an intermediate stage prior to the displacement of water from the active site by the incoming sugar hydroxyls. The +1 subsite, an aromatic "clamp", permits several different sugar positions and orientations, including a 180° flip that explains the observed variable regiospecificity. The p-nitrophenyl group on the acceptor most likely influences the unexpectedly observed β-1,6-specificity through its interaction with F229. These results demonstrate that tailoring the specificity of a particular glycosynthase depends not only on the chemical structure of the acceptor but also on understanding the structural basis of the promiscuity of the native enzyme.


    Organizational Affiliation

    Biochemistry Department, University of Otago , P.O. Box 56, Dunedin 9054, New Zealand.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EXO-1,3-BETA-GLUCANASEA399Candida albicans SC5314Mutation(s): 1 
Gene Names: CaO19.10507XOGXOG1EXGEXG1CAALFM_C102990CACa49C10.05CaO19.2990
EC: 3.2.1.58 (PDB Primary Data), 2.4.1 (UniProt)
Find proteins for P29717 (Candida albicans (strain SC5314 / ATCC MYA-2876))
Explore P29717 
Go to UniProtKB:  P29717
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PNW
Query on PNW

Download CCD File 
A
4-nitrophenyl beta-D-glucopyranoside
C12 H15 N O8
IFBHRQDFSNCLOZ-RMPHRYRLSA-N
 Ligand Interaction
GLF
Query on GLF

Download CCD File 
A
alpha-D-glucopyranosyl fluoride
C6 H11 F O5
ATMYEINZLWEOQU-DVKNGEFBSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.006α = 90
b = 64.202β = 90
c = 95.037γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary