6hm1: Difference between revisions
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<StructureSection load='6hm1' size='340' side='right'caption='[[6hm1]], [[Resolution|resolution]] 1.54Å' scene=''> | <StructureSection load='6hm1' size='340' side='right'caption='[[6hm1]], [[Resolution|resolution]] 1.54Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6hm1]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[6hm1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Serratia_proteamaculans_568 Serratia proteamaculans 568]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HM1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6HM1 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.54Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AO3:ALLOSAMIDIN'>AO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></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=6hm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hm1 OCA], [https://pdbe.org/6hm1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6hm1 RCSB], [https://www.ebi.ac.uk/pdbsum/6hm1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6hm1 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/A8GFD6_SERP5 A8GFD6_SERP5] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</div> | </div> | ||
<div class="pdbe-citations 6hm1" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 6hm1" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Chitinase 3D structures|Chitinase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Serratia proteamaculans 568]] | ||
[[Category: Dalhus | [[Category: Dalhus B]] | ||
[[Category: Eijsink | [[Category: Eijsink VGH]] | ||
[[Category: Madhuprakash | [[Category: Madhuprakash J]] | ||
[[Category: Sorlie | [[Category: Sorlie M]] | ||
[[Category: Vaaje-Kolstad | [[Category: Vaaje-Kolstad G]] | ||
Latest revision as of 14:32, 24 January 2024
Structural and thermodynamic signatures of ligand binding to an enigmatic chitinase-D from Serratia proteamaculansStructural and thermodynamic signatures of ligand binding to an enigmatic chitinase-D from Serratia proteamaculans
Structural highlights
FunctionPublication Abstract from PubMedThe Gram-negative bacteria Serratia marcescens and Serratia proteamaculans have efficient chitinolytic machineries that degrade chitin into N-acetylglucosamine (GlcNAc), which is used as a carbon and energy source. The enzymatic degradation of chitin in these bacteria occurs through the synergistic action of glycoside hydrolases (GHs) that have complementary activities; an endo-acting GH (ChiC) making random scissions on the polysaccharide chains and two exo-acting GHs mainly targeting single reducing (ChiA) and nonreducing (ChiB) chain ends. Both bacteria produce low amounts of a fourth GH18 (ChiD) with an unclear role in chitin degradation. Here, we have determined the thermodynamic signatures for binding of (GlcNAc)6 and the inhibitor allosamidin to SpChiD as well as the crystal structure of SpChiD in complex with allosamidin. The binding free energies for the two ligands are similar (Delta Gr degrees = -8.9 +/- 0.1 and -8.4 +/- 0.1 kcal/mol, respectively) with clear enthalpic penalties (Delta Hr degrees = 3.2 +/- 0.1 and 1.8 +/- 0.1 kcal/mol, respectively). Binding of (GlcNAc)6 is dominated by solvation entropy change (- TDelta Ssolv degrees = -17.4 +/- 0.4 kcal/mol) and the conformational entropy change dominates for allosamidin binding (- TDelta Sconf degrees = -9.0 +/- 0.2 kcal/mol). These signatures as well as the interactions with allosamidin are very similar to those of SmChiB suggesting that both enzymes are nonreducing end-specific. Structural and Thermodynamic Signatures of Ligand Binding to the Enigmatic Chitinase D of Serratia proteamaculans.,Madhuprakash J, Dalhus B, Vaaje-Kolstad G, Sakuda S, Podile AR, Eijsink VGH, Sorlie M J Phys Chem B. 2019 Mar 4. doi: 10.1021/acs.jpcb.8b11448. PMID:30789732[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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