Family GH5 endo-beta-mannanase from Lycopersicon esculentum (tomato)

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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This is version 1.3 of the entry. See complete history


Three-dimensional structure of (1,4)-beta-D-mannan mannanohydrolase from tomato fruit.

Bourgault, R.Oakley, A.J.Bewley, J.D.Wilce, M.C.

(2005) Protein Sci 14: 1233-1241

  • DOI: https://doi.org/10.1110/ps.041260905
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The three-dimensional crystal structure of tomato (Lycopersicon esculentum) beta-mannanase 4a (LeMAN4a) has been determined to 1.5 A resolution. The enzyme adopts the (beta/alpha)(8) fold common to the members of glycohydrolase family GH5. The structure is comparable with those of the homologous Trichoderma reesei and Thermomonospora fusca beta-mannanases: There is a conserved three-stranded beta-sheet located near the N terminus that stacks against the central beta-barrel at the end opposite the active site. Three noncanonical beta-helices surround the active site. Similar helices are found in T. reesei but not T. fusca beta-mannanase. By analogy with other beta-mannanases, the catalytic acid/base residue is E204 and the nucleophile residue is E318. The active site cleft of L. esculentum beta-mannanase most closely resembles that of the T. reesei isozyme. A model of substrate binding in LeMAN4a is proposed in which the mannosyl residue occupying the -1 subsite of the enzyme adopts the (1)S(5) skew-boat conformation.

  • Organizational Affiliation

    Department of Botany, University of Guelph, Ontario, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
endo-beta-mannanase373Solanum lycopersicumMutation(s): 0 
Gene Names: LeMAN4a
Find proteins for Q8L5J1 (Solanum lycopersicum)
Explore Q8L5J1 
Go to UniProtKB:  Q8L5J1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8L5J1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.54α = 90
b = 74.521β = 90
c = 79.006γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-19
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Refinement description