2wyf

From Proteopedia

(Difference between revisions)

Revision as of 00:57, 5 August 2016

CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH AGAL12BGAL-O-MET AT 2.4 A RESOLUTION

Structural highlights

2wyf is a 8 chain structure with sequence from Pseae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	2vxj, 1oko, 1uoj, 1l7l
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PA1L_PSEAE] D-galactose specific lectin. Binds in decreasing order of affinity: melibiose, methyl-alpha-D-galactoside, D-galactose, methyl-beta-D-galactoside, N-acetyl-D-galactosamine. Similar to plant lectins in its selective (carbohydrate-specific) hemagglutinating activity.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Calcium-dependent lectin I from Pseudomonas aeruginosa (PA-IL) binds specifically to oligosaccharides presenting an alpha-galactose residue at their nonreducing end, such as the disaccharides alphaGal1-2betaGalOMe, alphaGal1-3betaGalOMe, and alphaGal1-4betaGalOMe. This provides a unique model for studying the effect of the glycosidic linkage of the ligands on structure and thermodynamics of the complexes by means of experimental and theoretical tools. The structural features of PA-IL in complex with the three disaccharides were established by docking and molecular dynamics simulations and compared with those observed in available crystal structures, including PA-IL.alphaGal1-2betaGalOMe complex, which was solved at 2.4 A resolution and reported herein. The role of a structural bridge water molecule in the binding site of PA-IL was also elucidated through molecular dynamics simulations and free energy calculations. This water molecule establishes three very stable hydrogen bonds with O6 of nonreducing galactose, oxygen from Pro-51 main chain, and nitrogen from Gln-53 main chain of the lectin binding site. Binding free energies for PA-IL in complex with the three disaccharides were investigated, and the results were compared with the experimental data determined by titration microcalorimetry. When the bridge water molecule was included in the free energy calculations, the simulations predicted the correct binding affinity trends with the 1-2-linked disaccharide presenting three times stronger affinity ligand than the other two. These results highlight the role of the water molecule in the binding site of PA-IL and indicate that it should be taken into account when designing glycoderivatives active against P. aeruginosa adhesion.

Role of water molecules in structure and energetics of Pseudomonas aeruginosa lectin I interacting with disaccharides.,Nurisso A, Blanchard B, Audfray A, Rydner L, Oscarson S, Varrot A, Imberty A J Biol Chem. 2010 Jun 25;285(26):20316-27. Epub 2010 Apr 21. PMID:20410292^[1]

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

References

↑ Nurisso A, Blanchard B, Audfray A, Rydner L, Oscarson S, Varrot A, Imberty A. Role of water molecules in structure and energetics of Pseudomonas aeruginosa lectin I interacting with disaccharides. J Biol Chem. 2010 Jun 25;285(26):20316-27. Epub 2010 Apr 21. PMID:20410292 doi:10.1074/jbc.M110.108340

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2wyf"

@@ Line 1: / Line 1: @@
 ==CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH AGAL12BGAL-O-MET AT 2.4 A RESOLUTION==
 <StructureSection load='2wyf' size='340' side='right' caption='[[2wyf]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2wyf]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2WYF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2wyf]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2WYF FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=MBG:METHYL-BETA-GALACTOSE'>MBG</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2vxj|2vxj]], [[1oko|1oko]], [[1uoj|1uoj]], [[1l7l|1l7l]]</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=2wyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wyf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2wyf RCSB], [http://www.ebi.ac.uk/pdbsum/2wyf PDBsum]</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=2wyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wyf OCA], [http://pdbe.org/2wyf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2wyf RCSB], [http://www.ebi.ac.uk/pdbsum/2wyf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2wyf ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 18: @@
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2wyf ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2wyf" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 34: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Pseudomonas aeruginosa]]
+[[Category: Pseae]]
 [[Category: Blanchard, B]]
 [[Category: Imberty, A]]

2wyf

From Proteopedia

Revision as of 00:57, 5 August 2016

CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH AGAL12BGAL-O-MET AT 2.4 A RESOLUTION

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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