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4qdn

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==Crystal Structure of the endo-beta-N-acetylglucosaminidase from Thermotoga maritima==
==Crystal Structure of the endo-beta-N-acetylglucosaminidase from Thermotoga maritima==
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<StructureSection load='4qdn' size='340' side='right' caption='[[4qdn]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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<StructureSection load='4qdn' size='340' side='right'caption='[[4qdn]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4qdn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QDN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QDN FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4qdn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QDN FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qdn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qdn RCSB], [http://www.ebi.ac.uk/pdbsum/4qdn PDBsum]</span></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4qdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qdn OCA], [https://pdbe.org/4qdn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qdn RCSB], [https://www.ebi.ac.uk/pdbsum/4qdn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qdn ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q9WZA1_THEMA Q9WZA1_THEMA]
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Members of the GH73 glycosidase family cleave the beta-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 alpha/beta 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 alpha/beta fold of the family and displays beta-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 beta-hairpin region above the active site confers ligand binding specificity and modulates the catalytic mechanisms within the GH73 family.
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Structural and biochemical characterization of the beta-N-acetylglucosaminidase from Thermotoga maritima: toward rationalization of mechanistic knowledge in the GH73 family.,Lipski A, Herve M, Lombard V, Nurizzo D, Mengin-Lecreulx D, Bourne Y, Vincent F Glycobiology. 2014 Oct 24. pii: cwu113. PMID:25344445<ref>PMID:25344445</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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==See Also==
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</div>
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*[[Flagellar protein 3D structures|Flagellar protein 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bourne, Y]]
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[[Category: Large Structures]]
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[[Category: Lipski, A]]
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[[Category: Thermotoga maritima MSB8]]
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[[Category: Nurizzo, D]]
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[[Category: Bourne Y]]
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[[Category: Vincent, F]]
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[[Category: Lipski A]]
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[[Category: Bacterial peptidoglycan hydrolysis]]
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[[Category: Nurizzo D]]
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[[Category: Glycoside hydrolase]]
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[[Category: Vincent F]]
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[[Category: Hydrolase]]
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[[Category: Inverting mechanism]]
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[[Category: Typical lysozyme alpha-beta fold with only the alpha-lobe]]
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Current revision

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

PDB ID 4qdn

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