7DVJ

Structure of beta-mannanase BaMan113A with mannobiose

Summary for 7DVJ

• Entry DOI: 10.2210/pdb7dvj/pdb
• Related PRD ID: PRD_900115
• Descriptor: Endo-beta-1,4-mannanase, beta-D-mannopyranose-(1-4)-beta-D-mannopyranose (3 entities in total)
• Functional Keywords: complex, hydrolase
• Biological source: Bacillus sp. N16-5
• Total number of polymer chains: 2
• Total formula weight: 81863.98

Authors

Liu, W.T.,Liu, W.D.,Zheng, Y.Y. (deposition date: 2021-01-13, release date: 2021-06-02, Last modification date: 2023-11-29)

Primary citation

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.
Functional and structural investigation of a novel beta-mannanase BaMan113A from Bacillus sp. N16-5.
Int.J.Biol.Macromol., 182:899-909, 2021

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.

PubMed: 33865894
DOI: 10.1016/j.ijbiomac.2021.04.075

Experimental method

X-RAY DIFFRACTION (1.65 Å)