5JUG

Structure of an inactive (E45Q) variant of a beta-1,4-mannanase, SsGH134, in complex with Man5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.96 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.122 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A beta-Mannanase with a Lysozyme-like Fold and a Novel Molecular Catalytic Mechanism.

Jin, Y.Petricevic, M.John, A.Raich, L.Jenkins, H.Portela De Souza, L.Cuskin, F.Gilbert, H.J.Rovira, C.Goddard-Borger, E.D.Williams, S.J.Davies, G.J.

(2016) ACS Cent Sci 2: 896-903

  • DOI: 10.1021/acscentsci.6b00232
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The enzymatic cleavage of β-1,4-mannans is achieved by endo-β-1,4-mannanases, enzymes involved in germination of seeds and microbial hemicellulose degradation, and which have increasing industrial and consumer product applications. β-Mannanases occur ...

    The enzymatic cleavage of β-1,4-mannans is achieved by endo-β-1,4-mannanases, enzymes involved in germination of seeds and microbial hemicellulose degradation, and which have increasing industrial and consumer product applications. β-Mannanases occur in a range of families of the CAZy sequence-based glycoside hydrolase (GH) classification scheme including families 5, 26, and 113. In this work we reveal that β-mannanases of the newly described GH family 134 differ from other mannanase families in both their mechanism and tertiary structure. A representative GH family 134 endo-β-1,4-mannanase from a Streptomyces sp. displays a fold closely related to that of hen egg white lysozyme but acts with inversion of stereochemistry. A Michaelis complex with mannopentaose, and a product complex with mannotriose, reveal ligands with pyranose rings distorted in an unusual inverted chair conformation. Ab initio quantum mechanics/molecular mechanics metadynamics quantified the energetically accessible ring conformations and provided evidence in support of a 1C4 → 3H4‡ → 3S1 conformational itinerary along the reaction coordinate. This work, in concert with that on GH family 124 cellulases, reveals how the lysozyme fold can be co-opted to catalyze the hydrolysis of different polysaccharides in a mechanistically distinct manner.


    Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York , Heslington, YO10 5DD, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
beta-1,4-mannanase
A
168N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.96 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.122 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.707α = 90.00
b = 53.841β = 90.00
c = 82.636γ = 90.00
Software Package:
Software NamePurpose
xia2data scaling
REFMACrefinement
xia2data reduction
ACORNphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited KingdomAdG-322942
Australian Research CouncilAustralia--

Revision History 

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2017-01-18
    Type: Database references