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4qdn

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Revision as of 11:24, 15 February 2023

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

Structural highlights

4qdn is a 1 chain structure with sequence from Thermotoga maritima MSB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q9WZA1_THEMA

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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. 2014 Oct 24. pii: cwu113. PMID:25344445 doi:http://dx.doi.org/10.1093/glycob/cwu113

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4qdn"

@@ Line 3: / Line 3: @@
 <StructureSection load='4qdn' size='340' side='right'caption='[[4qdn]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4qdn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thema Thema]. 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>
+<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>
-</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>
+</td></tr><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>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">THEMA_01495, TM0633, Tmari_0634, TM_0633 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</td></tr>
+<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>
-<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://pdbe.org/4qdn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qdn RCSB], [http://www.ebi.ac.uk/pdbsum/4qdn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qdn ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9WZA1_THEMA Q9WZA1_THEMA]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 17: / Line 18: @@
 </div>
 <div class="pdbe-citations 4qdn" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Flagellar protein 3D structures|Flagellar protein 3D structures]]
 == References ==
 <references/>
@@ Line 22: / Line 26: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Thema]]
+[[Category: Thermotoga maritima MSB8]]
-[[Category: Bourne, Y]]
+[[Category: Bourne Y]]
-[[Category: Lipski, A]]
+[[Category: Lipski A]]
-[[Category: Nurizzo, D]]
+[[Category: Nurizzo D]]
-[[Category: Vincent, F]]
+[[Category: Vincent F]]
-[[Category: Bacterial peptidoglycan hydrolysis]]
-[[Category: Glycoside hydrolase]]
-[[Category: Hydrolase]]
-[[Category: Inverting mechanism]]
-[[Category: Typical lysozyme alpha-beta fold with only the alpha-lobe]]

4qdn

From Proteopedia

Revision as of 11:24, 15 February 2023

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

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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