Abstract
Thermoalkaliphilic GH11 xylanases are largely favored for paper pulp biobleaching process. The present work aimed to comparatively investigate the molecular phylogeny, amino acid sequences, molecular structure, and enzyme–substrate interaction of six thermoalkaliphilic GH11 xylanases from different bacterial species (Oxalobacteraceae bacterium xylanase = ObXyl, Sphingomonas sp. xylanase = SsXyl, Hymenobacter sp. xylanase = HsXyl, Amycolatopsis vastitatis xylanase = AvXyl, Lentzea deserti xylanase = LdXyl, Streptomyces rubellomurinus xylanase = SrXyl). For this purpose, six bacterial thermoalkaliphilic GH11 xylanase sequences derived from unreviewed protein entries of UniProt/TrEMBL database were analyzed for their phylogenetic relationships and sequence similarities. Also, 3D predicted structures of the enzymes were built and computationally validated by different bioinformatics tools. The enzyme–substrate interactions were investigated by molecular docking analysis using various substrates. Phylogenetic analysis showed that six enzymes were grouped into two different clusters: the first cluster included ObXyl, SsXyl, and HsXyl, whereas the second cluster had AvXyl, LdXyl, and SrXyl. Multiple sequence alignment showed that the second cluster xylanases possessed longer N-terminal regions indicating higher thermostability, compared to the first cluster xylanases. The structural analyses showed that six predicted structures were largely conserved. Molecular docking results indicated that binding efficiency to xylotriose, xylotetraose, and xylopentaose was higher in second cluster enzymes than that in first cluster enzymes, exhibiting mostly above -8.0 kCal/mol of binding energy. Arginine in B8 β-strand was commonly involved in substrate interactions in all the second cluster xylanases, different from the first cluster ones. Thus, the present work predicted that the thermoalkaliphilic xylanases in the second cluster might be greater potential candidates for the paper pulp bleaching process.
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Abbreviations
- CAZy:
-
Carbohydrate Active Enzymes
- GH:
-
Glycoside Hydrolase
- WGS:
-
Whole-Genome Shotgun WGS
- pI:
-
Isoelectric Point
- Tm :
-
Melting Temperature
- NCR:
-
Negatively Charged Residues
- PCR:
-
Positively Charged Residues
- ML:
-
Maximum Likelihood
- JTT:
-
Jones-Taylor-Thornton
- LGA:
-
Lamarckian Genetic Algorithm
- SDF:
-
Spatial Data File
- PDB:
-
Protein Data Bank
- ObXyl:
-
Oxalobacteraceae Bacterium xylanase
- SsXyl:
-
Sphingomonas sp. Xylanase
- HsXyl:
-
Hymenobacter sp. Xylanase
- AvXyl:
-
Amycolatopsis vastitatis Xylanase
- LdXyl:
-
Lentzea deserti Xylanase
- SrXyl:
-
Streptomyces rubellomurinus Xylanase
- Tx-xyl:
-
Xylanase from Thermobacillus xylanilyticus
- GMQE:
-
Global Model Quality Estimate
- UniProt:
-
The Universal Protein Knowledgebase
- X2 :
-
Xylobiose
- X3 :
-
Xylotriose
- X4 :
-
Xylotetraose
- X5 :
-
Xylopentaose
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Sürmeli, Y. Comparative investigation of bacterial thermoalkaliphilic GH11 xylanases at molecular phylogeny, sequence and structure level. Biologia 77, 3241–3253 (2022). https://doi.org/10.1007/s11756-022-01169-6
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DOI: https://doi.org/10.1007/s11756-022-01169-6