Abstract
Bioinformatics analysis was focused on unique acetylesterases annotated in the CAZy database within the CE16 family and simultaneously belonging to the SGNH hydrolase superfamily. The CE16 acetylesterases were compared to structurally related SGNH hydrolases: (i) selected members of the CE2, CE3, CE6, CE12 and CE17 family of the CAZy database and (ii) structural representatives of the Lipase_GDSL and Lipase_GDSL_2 families according to the Pfam database. Sequence alignment based on four conserved sequence regions (CSRs) containing active-site residues was used to calculate sequence logos specific for each CE family and to construct a phylogenetic tree. In many members of the CE16 family, aspartic acid from the Ser–His–Asp catalytic triad has been replaced by asparagine, and based on structure–sequence comparison, an alternative catalytic dyad mechanism was predicted for these enzymes. In addition to four conserved regions, CSR-I, CSR-II, CSR-III and CSR-V, containing catalytic and oxyanion-hole residues, CSR-IV was found in the CE16 family as the only CAZy family. Tertiary structures of the characterized CE16 members prepared by homology modeling showed that the α/β/α sandwich fold as well as the topology of their active sites are preserved. The phylogenetic tree and sequence alignment indicate the existence of a subfamily in the CE16 family fully consistent with the known biochemical data. In addition, nonstandard CE16 members that differ from others were analyzed and their active-site residues were predicted. A better understanding of the structure–function relationship of acetylesterases can help in the targeted design of these enzymes for biotechnology.
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source organism (Aspnig, Aspergillus niger; Aspnid, Aspergillus nidulans; Fusven, Fusarium venenatum; Serind, Serendipita indica; Cormil, Cordyceps militaris). The numbers in square brackets indicate the position of the domain and the total length of the sequence. CSRs are in frames, additional amino acid residues are underlined, conserved residues (at least 60% identity) are in black and white inversion. The active-site residues are marked with asterisks
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Abbreviations
- AE:
-
Acetylesterase
- AnAE:
-
CE16 acetylesterase from Aspergillus niger (GenBank accession No.: CAK45102.1)
- AxE:
-
Acetylxylan esterase
- CAZy:
-
Carbohydrate-active enzymes database
- CBM:
-
Carbohydrate-binding module
- CE:
-
Carbohydrate esterase
- CDD:
-
Conserved domain database
- GH:
-
Glycoside hydrolase
- PaAE:
-
CE16 acetylesterase from Podospora anserina (GenBank accession No.: CDP30204.1)
- PDB:
-
Protein Data Bank
- Pfam:
-
Protein family database
- TrAE:
-
CE16 acetylesterase from Trichoderma reesei (GenBank accession No.: ABI34466.1)
- TtAE:
-
CE16 acetylesterase from Thermothelomyces thermophilus (GenBank accession No.: AGW01024.1)
- Xylp:
-
Xylopyranosyl
- 3″-Ac3MeGlcA3Xyl3:
-
4-O-methyl-α-D-glucopyranuronosyl-(1 → 2)-(3-O-acetyl)-β-D-xylopyranosyl-(1 → 4)-β-D-xylopyranosyl-(1 → 4)-D-xylose
- 4″-Ac3MeGlcA3Xyl3:
-
4-O-methyl-α-D-glucopyranuronosyl-(1 → 2)-(4-O-acetyl)-β-D-xylopyranosyl-(1 → 4)-β-D-xylopyranosyl-(1 → 4)-D-xylose
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Acknowledgements
LU thanks to Štefan Janeček for his help with designing the study and to Luboš Vajner for VBA Excel programming. This work was financially supported by the projects Nos. 2/0190/14 and 2/0146/17 from the Slovak Academy of Sciences Grant Agency VEGA.
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Urbániková, Ľ. CE16 acetylesterases: in silico analysis, catalytic machinery prediction and comparison with related SGNH hydrolases. 3 Biotech 11, 84 (2021). https://doi.org/10.1007/s13205-020-02575-w
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DOI: https://doi.org/10.1007/s13205-020-02575-w