4QP0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.,Sect.D 70: 2970-2982

  • DOI: 10.1107/S1399004714019762
  • Primary Citation of Related Structures:  

  • 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 al ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endo-beta-mannanase
A
359Rhizomucor mieheiMutation(s): 0 
Gene Names: Man5A
EC: 3.2.1.78
Find proteins for L7SVX1 (Rhizomucor miehei)
Go to UniProtKB:  L7SVX1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.226 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 86.380α = 90.00
b = 89.719β = 90.00
c = 111.293γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXphasing
PHENIXmodel building
HKL-2000data reduction
HKL-2000data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2014-11-26
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description