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 
  • R-Value Observed: 0.123 

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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:  
    5JTS, 5JU9, 5JUG

  • 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 in a range of families of the CAZy sequence-based glycoside hydrolase (GH) classification scheme including families 5, 26, and 113 ...

    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: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
beta-1,4-mannanaseA168Streptomyces sp. NRRL B-16215Mutation(s): 0 
EC: 3.2.1.78
UniProt
Find proteins for A0A1L1QK16 (Streptomyces sp. NRRL B-16215)
Explore A0A1L1QK16 
Go to UniProtKB:  A0A1L1QK16
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L1QK16
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranoseB 5N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G91924WY
GlyCosmos:  G91924WY
GlyGen:  G91924WY
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN
Download Ideal Coordinates CCD File 
C [auth A]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 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 
  • R-Value Observed: 0.123 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.707α = 90
b = 53.841β = 90
c = 82.636γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
ACORNphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2017-01-18
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary