2v4c
From Proteopedia
(Difference between revisions)
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==Structure of sialic acid binding protein (SiaP) in the presence of KDN== | ==Structure of sialic acid binding protein (SiaP) in the presence of KDN== | ||
| - | <StructureSection load='2v4c' size='340' side='right' | + | <StructureSection load='2v4c' size='340' side='right'caption='[[2v4c]], [[Resolution|resolution]] 1.70Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[2v4c]] is a 1 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[2v4c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V4C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V4C FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=KDN:3-DEOXY-D-GLYCERO-BETA-D-GALACTO-NON-2-ULOPYRANOSONIC+ACID'>KDN</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KDN:3-DEOXY-D-GLYCERO-BETA-D-GALACTO-NON-2-ULOPYRANOSONIC+ACID'>KDN</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2wyk|2wyk]], [[2cey|2cey]], [[2cex|2cex]], [[2wyp|2wyp]], [[2wx9|2wx9]]</td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2wyk|2wyk]], [[2cey|2cey]], [[2cex|2cex]], [[2wyp|2wyp]], [[2wx9|2wx9]]</div></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2v4c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v4c OCA], [https://pdbe.org/2v4c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v4c RCSB], [https://www.ebi.ac.uk/pdbsum/2v4c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v4c ProSAT]</span></td></tr> |
</table> | </table> | ||
== Function == | == Function == | ||
| - | [[ | + | [[https://www.uniprot.org/uniprot/SIAP_HAEIN SIAP_HAEIN]] Part of the tripartite ATP-independent periplasmic (TRAP) transport system SiaPT involved in the uptake of sialic acid. This protein specifically binds sialic acid with high affinity. |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</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=2v4c 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=2v4c ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Solvent organization is a key but underexploited contributor to the thermodynamics of protein-ligand recognition, with implications for ligand discovery, drug resistance, and protein engineering. Here, we explore the contribution of solvent to ligand binding in the Haemophilus influenzae virulence protein SiaP. By introducing a single mutation without direct ligand contacts, we observed a >1000-fold change in sialic acid binding affinity. Crystallographic and calorimetric data of wild-type and mutant SiaP showed that this change results from an enthalpically unfavorable perturbation of the solvent network. This disruption is reflected by changes in the normalized atomic displacement parameters of crystallographic water molecules. In SiaP's enclosed cavity, relative differences in water-network dynamics serve as a simple predictor of changes in the free energy of binding upon changing protein, ligand, or both. This suggests that solvent structure is an evolutionary constraint on protein sequence that contributes to ligand affinity and selectivity. | ||
| + | |||
| + | Water Networks Can Determine the Affinity of Ligand Binding to Proteins.,Darby JF, Hopkins AP, Shimizu S, Roberts SM, Brannigan JA, Turkenburg JP, Thomas GH, Hubbard RE, Fischer M J Am Chem Soc. 2019 Oct 9;141(40):15818-15826. doi: 10.1021/jacs.9b06275. Epub, 2019 Sep 26. PMID:31518131<ref>PMID:31518131</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 2v4c" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacterium influenzae lehmann and neumann 1896]] | [[Category: Bacterium influenzae lehmann and neumann 1896]] | ||
| + | [[Category: Large Structures]] | ||
[[Category: Fischer, M]] | [[Category: Fischer, M]] | ||
[[Category: Hubbard, R E]] | [[Category: Hubbard, R E]] | ||
Revision as of 10:41, 7 July 2021
Structure of sialic acid binding protein (SiaP) in the presence of KDN
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