7DVJ

Structure of beta-mannanase BaMan113A with mannobiose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

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Literature

Functional and structural investigation of a novel beta-mannanase BaMan113A from Bacillus sp. N16-5.

Liu, W.Ma, C.Liu, W.Zheng, Y.Chen, C.C.Liang, A.Luo, X.Li, Z.Ma, W.Song, Y.Guo, R.T.Zhang, T.

(2021) Int J Biol Macromol 182: 899-909

  • DOI: 10.1016/j.ijbiomac.2021.04.075
  • Primary Citation of Related Structures:  
    7DV7, 7DVJ, 7DVZ, 7DW8, 7DWA

  • PubMed Abstract: 
  • Mannan is an important renewable resource whose backbone can be hydrolyzed by β-mannanases to generate manno-oligosaccharides of various sizes. Only a few glycoside hydrolase (GH) 113 family β-mannanases have been functionally and structurally characterize ...

    Mannan is an important renewable resource whose backbone can be hydrolyzed by β-mannanases to generate manno-oligosaccharides of various sizes. Only a few glycoside hydrolase (GH) 113 family β-mannanases have been functionally and structurally characterize. Here, we report the function and structure of a novel GH113 β-mannanase from Bacillus sp. N16-5 (BaMan113A). BaMan113A exhibits a substrate preference toward manno-oligosaccharides and releases mannose and mannobiose as main hydrolytic products. The crystal structure of BaMan113A suggest that the enzyme shows a semi-enclosed substrate-binding cleft and the amino acids surrounding the +2 subsite form a steric barrier to terminate the substrate-binding tunnel. Based on these structural features, we conducted mutagenesis to engineer BaMan113A to remove the steric hindrance of the substrate-binding tunnel. We found that F101E and N236Y variants exhibit increased specific activity toward mannans comparing to the wild-type enzyme. Meanwhile, the product profiles of these two variants toward polysaccharides changed from mannose to a series of manno-oligosaccharides. The crystal structure of variant N236Y was also determined to illustrate the molecular basis underlying the mutation. In conclusion, we report the functional and structural features of a novel GH113 β-mannanase, and successfully improved its endo-acting activity by using structure-based engineering.


    Organizational Affiliation

    Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China. Electronic address: tony@tust.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endo-beta-1,4-mannanaseA, B348Bacillus sp. N16-5Mutation(s): 1 
UniProt
Find proteins for A0A140EH91 (Bacillus sp. N16-5)
Explore A0A140EH91 
Go to UniProtKB:  A0A140EH91
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140EH91
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-mannopyranoseC [auth G],
D [auth H]
2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G78317QO
GlyCosmos:  G78317QO
GlyGen:  G78317QO
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900115
Query on PRD_900115
C [auth G], D [auth H]4beta-beta-mannobioseOligosaccharide / Metabolism Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.493α = 90
b = 110.284β = 90
c = 150.438γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release