4QDN image
Deposition Date 2014-05-14
Release Date 2014-11-12
Last Version Date 2024-02-28
Entry Detail
PDB ID:
4QDN
Keywords:
Title:
Crystal Structure of the endo-beta-N-acetylglucosaminidase from Thermotoga maritima
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.70 Å
R-Value Free:
0.19
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
C 2 2 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Flagellar protein FlgJ [peptidoglycan hydrolase]
Gene (Uniprot):TM_0633
Chain IDs:A
Chain Length:136
Number of Molecules:1
Biological Source:Thermotoga maritima
Primary Citation
Structural and biochemical characterization of the beta-N-acetylglucosaminidase from Thermotoga maritima: Toward rationalization of mechanistic knowledge in the GH73 family.
Glycobiology 25 319 330 (2015)
PMID: 25344445 DOI: 10.1093/glycob/cwu113

Abstact

Members of the GH73 glycosidase family cleave the β-1,4-glycosidic bond between the N-acetylglucosaminyl (GlcNAc) and N-acetylmuramyl (MurNAc) moieties in bacterial peptidoglycan. A catalytic mechanism has been proposed for members FlgJ, Auto, AcmA and Atl(WM) and the structural analysis of FlgJ and Auto revealed a conserved α/β fold reminiscent of the distantly related GH23 lysozyme. Comparison of the active site residues reveals variability in the nature of the catalytic general base suggesting two distinct catalytic mechanisms: an inverting mechanism involving two distant glutamate residues and a substrate-assisted mechanism involving anchimeric assistance by the C2-acetamido group of the GlcNAc moiety. Herein, we present the biochemical characterization and crystal structure of TM0633 from the hyperthermophilic bacterium Thermotoga maritima. TM0633 adopts the α/β fold of the family and displays β-N-acetylglucosaminidase activity on intact peptidoglycan sacculi. Site-directed mutagenesis identifies Glu34, Glu65 and Tyr118 as important residues for catalysis. A thorough bioinformatic analysis of the GH73 sequences identified five phylogenetic clusters. TM0633, FlgJ and Auto belong to a group of three clusters that conserve two carboxylate residues involved in a classical inverting acid-base mechanism. Members of the other two clusters lack a conserved catalytic general base supporting a substrate-assisted mechanism. Molecular modeling of representative members from each cluster suggests that variability in length of the β-hairpin region above the active site confers ligand-binding specificity and modulates the catalytic mechanisms within the GH73 family.

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