7XKS

Crystal structure of an alkaline pectate lyase from Bacillus clausii

Summary for 7XKS

• Entry DOI: 10.2210/pdb7xks/pdb
• Descriptor: Pectate lyase, DI(HYDROXYETHYL)ETHER, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: alkaline pectate, lyase
• Biological source: Alkalihalobacillus clausii
• Total number of polymer chains: 1
• Total formula weight: 34299.90

Authors

Zhou, C.,Zheng, Y.Y.,Liu, W.D.,Ma, Y. (deposition date: 2022-04-20, release date: 2023-03-29, Last modification date: 2023-11-29)

Primary citation

Zhou, C.,Cao, Y.,Xue, Y.,Liu, W.,Ju, J.,Ma, Y.
Structure of an Alkaline Pectate Lyase and Rational Engineering with Improved Thermo-Alkaline Stability for Efficient Ramie Degumming.
Int J Mol Sci, 24:-, 2022

PubMed Abstract: Alkaline pectate lyases have biotechnological applications in plant fiber processing, such as ramie degumming. Previously, we characterized an alkaline pectate lyase from S10, named BacPelA, which showed potential for enzymatic ramie degumming because of its high cleavage activity toward methylated pectins in alkaline conditions. However, BacPelA displayed poor thermo-alkaline stability. Here, we report the 1.78 Å resolution crystal structure of BacPelA in apo form. The enzyme has the characteristic right-handed β-helix fold of members of the polysaccharide lyase 1 family and shows overall structural similarity to them, but it displays some differences in the details of the secondary structure and Ca-binding site. On the basis of the structure, 10 sites located in flexible regions and showing high B-factor and positive Δ values were selected for mutation, aiming to improve the thermo-alkaline stability of the enzyme. Following site-directed saturation mutagenesis and screening, mutants A238C, R150G, and R216H showed an increase in the value at pH 10.0 of 3.0 °C, 6.5 °C, and 7.0 °C, respectively, compared with the wild-type enzyme, interestingly accompanied by a 24.5%, 46.6%, and 61.9% increase in activity. The combined mutant R150G/R216H/A238C showed an 8.5 °C increase in the value at pH 10.0, and an 86.1% increase in the specific activity at 60 °C, with approximately doubled catalytic efficiency, compared with the wild-type enzyme. Moreover, this mutant retained 86.2% activity after incubation in ramie degumming conditions (4 h, 60 °C, pH 10.0), compared with only 3.4% for wild-type BacPelA. The combined mutant increased the weight loss of ramie fibers in degumming by 30.2% compared with wild-type BacPelA. This work provides a thermo-alkaline stable, highly active pectate lyase with great potential for application in the textile industry, and also illustrates an effective strategy for rational design and improvement of pectate lyases.

PubMed: 36613981
DOI: 10.3390/ijms24010538

Experimental method

X-RAY DIFFRACTION (1.78 Å)