4CD7

The structure of GH113 beta-mannanase AaManA from Alicyclobacillus acidocaldarius in complex with ManIFG and beta-1,4-mannobiose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Combined Inhibitor Free-Energy Landscape and Structural Analysis Reports on the Mannosidase Conformational Coordinate.

Williams, R.J.Iglesias-Fernandez, J.Stepper, J.Jackson, A.Thompson, A.J.Lowe, E.C.White, J.M.Gilbert, H.J.Rovira, C.Davies, G.J.Williams, S.J.

(2014) Angew.Chem.Int.Ed.Engl. 53: 1087

  • DOI: 10.1002/anie.201308334
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mannosidases catalyze the hydrolysis of a diverse range of polysaccharides and glycoconjugates, and the various sequence-based mannosidase families have evolved ingenious strategies to overcome the stereoelectronic challenges of mannoside chemistry. ...

    Mannosidases catalyze the hydrolysis of a diverse range of polysaccharides and glycoconjugates, and the various sequence-based mannosidase families have evolved ingenious strategies to overcome the stereoelectronic challenges of mannoside chemistry. Using a combination of computational chemistry, inhibitor design and synthesis, and X-ray crystallography of inhibitor/enzyme complexes, it is demonstrated that mannoimidazole-type inhibitors are energetically poised to report faithfully on mannosidase transition-state conformation, and provide direct evidence for the conformational itinerary used by diverse mannosidases, including β-mannanases from families GH26 and GH113. Isofagomine-type inhibitors are poor mimics of transition-state conformation, owing to the high energy barriers that must be crossed to attain mechanistically relevant conformations, however, these sugar-shaped heterocycles allow the acquisition of ternary complexes that span the active site, thus providing valuable insight into active-site residues involved in substrate recognition.


    Organizational Affiliation

    School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Vic 3010 (Australia).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDO-BETA-1,4-MANNANASE
A, B
320Alicyclobacillus acidocaldariusMutation(s): 0 
Find proteins for A5H1I6 (Alicyclobacillus acidocaldarius)
Go to UniProtKB:  A5H1I6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IFM
Query on IFM

Download SDF File 
Download CCD File 
A, B
5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE
Afegostat, isofagomine, (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL
C6 H13 N O3
QPYJXFZUIJOGNX-HSUXUTPPSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.472α = 90.00
b = 76.586β = 90.00
c = 140.212γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2015-07-15
    Type: Non-polymer description