|
|
| Line 3: |
Line 3: |
| | <StructureSection load='3zw1' size='340' side='right'caption='[[3zw1]], [[Resolution|resolution]] 1.60Å' scene=''> | | <StructureSection load='3zw1' size='340' side='right'caption='[[3zw1]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3zw1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_baa-244 Atcc baa-244]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZW1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3zw1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_ambifaria Burkholderia ambifaria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZW1 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MHO:S-OXYMETHIONINE'>MHO</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=MHO:S-OXYMETHIONINE'>MHO</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3zw2|3zw2]], [[3zw0|3zw0]]</div></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=3zw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zw1 OCA], [https://pdbe.org/3zw1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zw1 RCSB], [https://www.ebi.ac.uk/pdbsum/3zw1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zw1 ProSAT]</span></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=3zw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zw1 OCA], [https://pdbe.org/3zw1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zw1 RCSB], [https://www.ebi.ac.uk/pdbsum/3zw1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zw1 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q0B4G1_BURCM Q0B4G1_BURCM] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 22: |
Line 23: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc baa-244]] | + | [[Category: Burkholderia ambifaria]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Abounit, S]] | + | [[Category: Abounit S]] |
| - | [[Category: Audfray, A]] | + | [[Category: Audfray A]] |
| - | [[Category: Claudinon, J]] | + | [[Category: Claudinon J]] |
| - | [[Category: Imberty, A]] | + | [[Category: Imberty A]] |
| - | [[Category: Larson, G]] | + | [[Category: Larson G]] |
| - | [[Category: Lependu, J]] | + | [[Category: Lependu J]] |
| - | [[Category: Romer, W]] | + | [[Category: Romer W]] |
| - | [[Category: Ruvoen-Clouet, N]] | + | [[Category: Ruvoen-Clouet N]] |
| - | [[Category: Varrot, A]] | + | [[Category: Varrot A]] |
| - | [[Category: Wimmerova, M]] | + | [[Category: Wimmerova M]] |
| - | [[Category: Fucose binding lectin]]
| + | |
| - | [[Category: Sugar binding protein]]
| + | |
| Structural highlights
3zw1 is a 2 chain structure with sequence from Burkholderia ambifaria. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.6Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
Q0B4G1_BURCM
Publication Abstract from PubMed
Recent advances in glycobiology revealed the essential role of lectins for deciphering the glycocode by specific recognition of carbohydrates. Integrated multiscale approaches are needed for characterizing lectin specificity: combining on one hand high-throughput analysis by glycan array experiments and systematic molecular docking of oligosaccharide libraries and on the other hand detailed analysis of the lectin/oligosaccharide interaction by x-ray crystallography, microcalorimetry and free energy calculations. The lectins LecB from Pseudomonas aeruginosa and BambL from Burkholderia ambifaria are part of the virulence factors used by the pathogenic bacteria to invade the targeted host. These two lectins are not related but both recognize fucosylated oligosaccharides such as the histo-blood group oligosaccharides of the ABH(O) and Lewis epitopes. The specificities were characterized using semi-quantitative data from glycan array and analyzed by molecular docking with the Glide software. Reliable prediction of protein/oligosaccharide structures could be obtained as validated by existing crystal structures of complexes. Additionally, the crystal structure of BambL/Lewis x was determined at 1.6 A resolution, which confirms that Lewis x has to adopt a high-energy conformation so as to bind to this lectin. Free energies of binding were calculated using a procedure combining the Glide docking protocol followed by free energy rescoring with the Prime/Molecular Mechanics Generalized Born Surface Area (MM-GBSA) method. The calculated data were in reasonable agreement with experimental free energies of binding obtained by titration microcalorimetry. The established predictive protocol is proposed to rationalize large sets of data such as glycan arrays and to help in lead discovery projects based on such high throughput technology.
Deciphering the glycan preference of bacterial lectins by glycan array and molecular docking with validation by microcalorimetry and crystallography.,Topin J, Arnaud J, Sarkar A, Audfray A, Gillon E, Perez S, Jamet H, Varrot A, Imberty A, Thomas A PLoS One. 2013 Aug 19;8(8):e71149. doi: 10.1371/journal.pone.0071149. PMID:23976992[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Topin J, Arnaud J, Sarkar A, Audfray A, Gillon E, Perez S, Jamet H, Varrot A, Imberty A, Thomas A. Deciphering the glycan preference of bacterial lectins by glycan array and molecular docking with validation by microcalorimetry and crystallography. PLoS One. 2013 Aug 19;8(8):e71149. doi: 10.1371/journal.pone.0071149. PMID:23976992 doi:http://dx.doi.org/10.1371/journal.pone.0071149
|
