Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 82.29 kDa 
• Atom Count: 6158 
• Modelled Residue Count: 641 
• Deposited Residue Count: 696 
• Unique protein chains: 1

7DWA

Structure of a novel beta-mannanase BaMan113A with mannotriose, N236Y mutation

• PDB DOI: 10.2210/pdb7DWA/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus sp. N16-5
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-01-15 Released: 2021-06-02 
• Deposition Author(s): Liu, W.T., Liu, W.D., Zheng, Y.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.175 
• R-Value Work: 0.146 
• R-Value Observed: 0.148 

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

• PubMed: 33865894 
• 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. 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.

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Related Citations: 

• Functional and structural investigation of a Novel beta-Mannanase BaMan113B from Bacillus sp. N16-5
  Liu, W.T., Liu, W.D., Zheng, Y.Y.
  () To be published --: --

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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: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-beta-1,4-mannanase	A, B	348	Bacillus sp. N16-5	Mutation(s): 2
UniProt
Find proteins for A0A140EH91 (Bacillus sp. N16-5) Explore A0A140EH91  Go to UniProtKB:  A0A140EH91

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose	C [auth G], D [auth H]	3		N/A
Glycosylation Resources
GlyTouCan:  G98033RN GlyCosmos:  G98033RN GlyGen:  G98033RN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.175 
• R-Value Work: 0.146 
• R-Value Observed: 0.148 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.114	α = 90
b = 109.15	β = 90
c = 150.656	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2021-01-15 
• Released Date: 2021-06-02 
Deposition Author(s): Liu, W.T., Liu, W.D., Zheng, Y.Y.

Revision History  

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