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. 2020 Dec 16;44(6):1703-1712.
doi: 10.3906/kim-2006-19. eCollection 2020.

Structural insights of two novel N-acetyl-glucosaminidase enzymes through in silico methods

Arif Sercan ŞahutoĞlu  1 , Hatice Duman  2 , Steven Alex Frese  3   4 , Sercan Karav  2
Affiliations

Structural insights of two novel N-acetyl-glucosaminidase enzymes through in silico methods

Arif Sercan ŞahutoĞlu et al. Turk J Chem. .

Abstract

EndoBI-1 and EndoBI-2 are two endo- β-N- acetylglucosaminidase isoenzymes that cleave N-N'- diacetylchitobiosyl moieties found in various types of native N -glycans. These N -glycans are indigestible by human infants and adults due to the lack of responsible glycosyl hydrolases and they act as selective prebiotics for a probiotic microorganism, Bifidobacterium longum subsp . infantis , in the large intestine. The selectivity and the thermostability of EndoBI-1 and EndoBI-2 suggest that these enzymes may be useful for many scientific and industrial applications. In this study, the growing numbers of homologous sequences in different databases were exploited in a comparative approach to investigate structural properties of EndoBI-1 and EndoBI-2 enzymes. Moreover, the complete and partial homology models of these two enzymes were generated and evaluated. Selected models were used for docking studies of the plus subsite ligand of these enzymes for further understanding on the substrate selectivity of EndoBI enzymes.

Keywords: EndoBI-1; EndoBI-2; N -glycan; endo- β - N -acetylglucosaminidase.

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Conflict of interest statement

CONFLICT OF INTEREST: none declared

Figures

Figure 1
Figure 1
Representation of common N-glycan cores and different types of N-glycan structures. The figure was prepared with GlycoWorkbench software (v2.1, release 146).
Figure 2
Figure 2
Graphical summaries of secondary structures (PDBsum) together with conserved domain information (CDD) of the EndoBI-1 and EndoBI-2 homology models.
Figure 3
Figure 3
Structural alignments of the GH domains of A) EndoBI-1 and EndoBI-2; and B) EndoBI-1, EndoBI-2, and the template (Endo-COM).
Figure 4
Figure 4
Proposed mechanism for EndoBI-1 and EndoBI-2 enzymes. Amino acid residues are numbered for EndoBI-1 and EndoBI-2 respectively.
Figure 5
Figure 5
Loop organization of EndoBI-1 (A) and EndoBI-2 (B) enzymes.
Figure 6
Figure 6
PoseView images of ligand bound template mutant (D154N/E156Q) crystal structure (6KPN) (A) and EndoBI dock result (B).
Figure 7
Figure 7
Sequence logos of the amino acid residues responsible for the +1’ (A) and +1 (B) subsites’ substrate recognition for ENGase enzymes.
See this image and copyright information in PMC

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