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 <i>endo </i>-β-1,4-mannanases, enzymes involved in germination of seeds and microbial hemicellulose degradation, and which have increasing industrial and consumer product applications. β-Mannana ...

    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 1 C 4 3 H 4 3 S 1 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

    Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University , Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.,Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & IQTCUB, Universitat de Barcelona , 08028 Barcelona, Spain.,Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & IQTCUB, Universitat de Barcelona, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain.,York Structural Biology Laboratory, Department of Chemistry, University of York , Heslington, YO10 5DD, U.K.,ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia; School of Chemistry and Bio21 Molecular Science and Biotechnology Institute and Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia.,School of Chemistry and Bio21 Molecular Science and Biotechnology Institute and Department of Medical Biology, University of Melbourne , Parkville, Victoria 3010, Australia.




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

Download SDF File 
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