4QDN

Crystal Structure of the endo-beta-N-acetylglucosaminidase from Thermotoga maritima

Summary for 4QDN

• Entry DOI: 10.2210/pdb4qdn/pdb
• Descriptor: Flagellar protein FlgJ [peptidoglycan hydrolase], PHOSPHATE ION, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (4 entities in total)
• Functional Keywords: gh73 family (cazy database), inverting mechanism, bacterial peptidoglycan hydrolysis, typical lysozyme alpha-beta fold with only the alpha-lobe, glycoside hydrolase, hydrolase
• Biological source: Thermotoga maritima
• Total number of polymer chains: 1
• Total formula weight: 16059.31

Authors

Lipski, A.,Nurizzo, D.,Bourne, Y.,Vincent, F. (deposition date: 2014-05-14, release date: 2014-11-12, Last modification date: 2024-02-28)

Primary citation

Lipski, A.,Herve, M.,Lombard, V.,Nurizzo, D.,Mengin-Lecreulx, D.,Bourne, Y.,Vincent, F.
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

PubMed Abstract: 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.

PubMed: 25344445
DOI: 10.1093/glycob/cwu113

Experimental method

X-RAY DIFFRACTION (1.7 Å)