Crystal Structure Analysis of the Endo-1,4-beta-mannanase from Rhizomucor miehei

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

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Structural insights into the substrate specificity and transglycosylation activity of a fungal glycoside hydrolase family 5 beta-mannosidase.

Zhou, P.Liu, Y.Yan, Q.Chen, Z.Qin, Z.Jiang, Z.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2970-2982

  • DOI: https://doi.org/10.1107/S1399004714019762
  • Primary Citation of Related Structures:  
    4LYP, 4LYQ, 4LYR, 4NRR, 4NRS, 4QP0

  • PubMed Abstract: 

    β-Mannosidases are exo-acting glycoside hydrolases (GHs) that catalyse the removal of the nonreducing end β-D-mannose from manno-oligosaccharides or mannoside-substituted molecules. They play important roles in fundamental biological processes and also have potential applications in various industries. In this study, the first fungal GH family 5 β-mannosidase (RmMan5B) from Rhizomucor miehei was functionally and structurally characterized. RmMan5B exhibited a much higher activity against manno-oligosaccharides than against p-nitrophenyl β-D-mannopyranoside (pNPM) and had a transglycosylation activity which transferred mannosyl residues to sugars such as fructose. To investigate its substrate specificity and transglycosylation activity, crystal structures of RmMan5B and of its inactive E202A mutant in complex with mannobiose, mannotriose and mannosyl-fructose were determined at resolutions of 1.3, 2.6, 2.0 and 2.4 Å, respectively. In addition, the crystal structure of R. miehei β-mannanase (RmMan5A) was determined at a resolution of 2.3 Å. Both RmMan5A and RmMan5B adopt the (β/α)8-barrel architecture, which is globally similar to the other members of GH family 5. However, RmMan5B shows several differences in the loop around the active site. The extended loop between strand β8 and helix α8 (residues 354-392) forms a `double' steric barrier to `block' the substrate-binding cleft at the end of the -1 subsite. Trp119, Asn260 and Glu380 in the β-mannosidase, which are involved in hydrogen-bond contacts with the -1 mannose, might be essential for exo catalytic activity. Moreover, the structure of RmMan5B in complex with mannosyl-fructose has provided evidence for the interactions between the β-mannosidase and D-fructofuranose. Overall, the present study not only helps in understanding the catalytic mechanism of GH family 5 β-mannosidases, but also provides a basis for further enzymatic engineering of β-mannosidases and β-mannanases.

  • Organizational Affiliation

    Department of Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endo-beta-mannanase359Rhizomucor mieheiMutation(s): 0 
Gene Names: Man5A
Find proteins for L7SVX1 (Rhizomucor miehei)
Explore L7SVX1 
Go to UniProtKB:  L7SVX1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL7SVX1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.38α = 90
b = 89.719β = 90
c = 111.293γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2014-11-26
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description