3N9K

F229A/E292S Double Mutant of Exo-beta-1,3-glucanase from Candida albicans in Complex with Laminaritriose at 1.7 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Carbohydrate binding sites in Candida albicans exo-beta-1,3-glucanase and the role of the Phe-Phe 'clamp' at the active site entrance

Patrick, W.M.Nakatani, Y.Cutfield, S.M.Sharpe, M.L.Ramsay, R.J.Cutfield, J.F.

(2010) FEBS J 277: 4549-4561

  • DOI: 10.1111/j.1742-4658.2010.07869.x
  • Primary Citation of Related Structures:  
    2PC8, 2PF0, 3O6A, 3N9K

  • PubMed Abstract: 
  • Candida albicans exo-β-1,3-glucanase (Exg; EC 3.2.1.58) is implicated in cell wall β-D-glucan remodelling through its glucosyl hydrolase and/or transglucosylase activities. A pair of antiparallel phenylalanyl residues (F144 and F258) flank the entrance to the active site pocket ...

    Candida albicans exo-β-1,3-glucanase (Exg; EC 3.2.1.58) is implicated in cell wall β-D-glucan remodelling through its glucosyl hydrolase and/or transglucosylase activities. A pair of antiparallel phenylalanyl residues (F144 and F258) flank the entrance to the active site pocket. Various Exg mutants were studied using steady-state kinetics and crystallography aiming to understand the roles played by these residues in positioning the β-1,3-D-glucan substrate. Mutations at the Phe-Phe entranceway demonstrated the requirement for double-sided CH/π interactions at the +1 subsite, and the necessity for phenylalanine rather than tyrosine or tryptophan. The Tyr-Tyr double mutations introduced ordered water molecules into the entranceway. A third Phe residue (F229) nearby was evaluated as a possible +2 subsite. The inactive double mutant E292S/F229A complexed with laminaritriose has provided the first picture of substrate binding to Exg and demonstrated how the Phe-Phe arrangement acts as a clamp at the +1 subsite. The terminal sugar at the -1 site showed displacement from the position of a monosaccharide analogue with interchange of water molecules and sugar hydroxyls. An unexpected additional glucose binding site, well removed from the active site, was revealed. This site may enable Exg to associate with the branched glucan structure of the C. albicans cell wall.


    Organizational Affiliation

    Department of Biochemistry, University of Otago, Dunedin, New Zealand.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucan 1,3-beta-glucosidaseA399Candida albicansMutation(s): 2 
Gene Names: XOG
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
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranoseB3 N/A Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranoseC2 N/A Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900024
Query on PRD_900024
Cbeta-laminaribioseOligosaccharide /  Antimicrobial

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.725α = 90
b = 64.397β = 90
c = 94.866γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary