Structural Insight into and Mutational Analysis of Family 11 Xylanases: Implications for Mechanisms of Higher pH Catalytic Adaptation

• Published in: PloS one Vol. 10; no. 7; p. e0132834
• Main Authors: Bai, Wenqin, Zhou, Cheng, Zhao, Yueju, Wang, Qinhong, Ma, Yanhe
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 10-07-2015; Public Library of Science (PLoS)
• Subjects: Adaptation; Adaptation, Physiological; Amino Acid Sequence; Amino acids; Amino Acids - metabolism; Bacillus; Bacillus - enzymology; Biocatalysis; Biochemistry; Biotechnology; Catalysis; Catalytic Domain; Cellulase; Chemical bonds; DNA Mutational Analysis; Endo-1,4-beta Xylanases - chemistry; Endo-1,4-beta Xylanases - genetics; Endo-1,4-beta Xylanases - metabolism; Engineering; Enzymes; Genetic aspects; Hydrogen Bonding; Hydrogen ions; Hydrogen-Ion Concentration; Industrial applications; Laboratories; Models, Molecular; Molecular biology; Molecular modelling; Molecular Sequence Data; Multigene Family; Mutagenesis; Mutant Proteins - chemistry; Mutants; Nucleotide sequence; pH effects; Phylogenetics; Phylogeny; Protein Structure, Secondary; Proteins; Residues; Science; Sequence Alignment; Solvents; Trichoderma reesei; Xylanase
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0132834

To understand the molecular basis of higher pH catalytic adaptation of family 11 xylanases, we compared the structures of alkaline, neutral, and acidic active xylanases and analyzed mutants of xylanase Xyn11A-LC from alkalophilic Bacillus sp. SN5. It was revealed that alkaline active xylanases have increased charged residue content, an increased ratio of negatively to positively charged residues, and decreased Ser, Thr, and Tyr residue content relative to non-alkaline active counterparts. Between strands β6 and β7, alkaline xylanases substitute an α-helix for a coil or turn found in their non-alkaline counterparts. Compared with non-alkaline xylanases, alkaline active enzymes have an inserted stretch of seven amino acids rich in charged residues, which may be beneficial for xylanase function in alkaline conditions. Positively charged residues on the molecular surface and ionic bonds may play important roles in higher pH catalytic adaptation of family 11 xylanases. By structure comparison, sequence alignment and mutational analysis, six amino acids (Glu16, Trp18, Asn44, Leu46, Arg48, and Ser187, numbering based on Xyn11A-LC) adjacent to the acid/base catalyst were found to be responsible for xylanase function in higher pH conditions. Our results will contribute to understanding the molecular mechanisms of higher pH catalytic adaptation in family 11 xylanases and engineering xylanases to suit industrial applications.