3ud6: Difference between revisions

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<StructureSection load='3ud6' size='340' side='right'caption='[[3ud6]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
<StructureSection load='3ud6' size='340' side='right'caption='[[3ud6]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ud6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3nl8 3nl8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UD6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UD6 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ud6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3nl8 3nl8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UD6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UD6 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3NK:1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE'>3NK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.091&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3nxf|3nxf]], [[3o6y|3o6y]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3NK:1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE'>3NK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=3ud6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ud6 OCA], [https://pdbe.org/3ud6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ud6 RCSB], [https://www.ebi.ac.uk/pdbsum/3ud6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ud6 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=3ud6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ud6 OCA], [https://pdbe.org/3ud6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ud6 RCSB], [https://www.ebi.ac.uk/pdbsum/3ud6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ud6 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We report the cocrystal structures of a computationally designed and experimentally optimized retro-aldol enzyme with covalently bound substrate analogs. The structure with covalently bound substrate analogs is similar to, but not identical with, the design model, with an RMSD of 1.4 A over active-site residues and equivalent substrate atoms . As in the design model, the binding pocket orients the substrate through hydrophobic interactions with the naphthyl moiety such that the oxygen atoms analogous to the carbinolamine and beta-hydroxyl oxygens are positioned near a network of bound waters. However, there are differences between the design model and the structure: the orientation of the naphthyl group and the conformation of the catalytic lysine are slightly different; the bound water network appears to be more extensive; and the bound substrate analog exhibits more conformational heterogeneity than typical native enzyme-inhibitor complexes. Alanine scanning of the active-site residues shows that both the catalytic lysine and the residues around the binding pocket for the substrate naphthyl group make critical contributions to catalysis. Mutating the set of water-coordinating residues also significantly reduces catalytic activity. The crystal structure of the enzyme with a smaller substrate analog that lacks naphthyl rings shows the catalytic lysine to be more flexible than in the naphthyl-substrate complex; increased preorganization of the active site would likely improve catalysis. The covalently bound complex structures and mutagenesis data highlight the strengths and weaknesses of the de novo enzyme design strategy.
Structural Analyses of Covalent Enzyme-Substrate Analog Complexes Reveal the Strengths and Limitations of De Novo Enzyme Design.,Wang L, Althoff EA, Bolduc J, Jiang L, Moody J, Lassila JK, Giger L, Hilvert D, Stoddard B, Baker D J Mol Biol. 2011 Nov 3. PMID:22075445<ref>PMID:22075445</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ud6" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Aldolase 3D structures|Aldolase 3D structures]]
*[[Aldolase 3D structures|Aldolase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Synthetic construct sequences]]
[[Category: Synthetic construct]]
[[Category: Althoff, E A]]
[[Category: Althoff EA]]
[[Category: Baker, D]]
[[Category: Baker D]]
[[Category: Bolduc, J]]
[[Category: Bolduc J]]
[[Category: Hilvert, D]]
[[Category: Hilvert D]]
[[Category: Jiang, L]]
[[Category: Jiang L]]
[[Category: Lassila, J]]
[[Category: Lassila J]]
[[Category: Moody, J]]
[[Category: Moody J]]
[[Category: Stoddard, B L]]
[[Category: Stoddard BL]]
[[Category: Wang, L]]
[[Category: Wang L]]
[[Category: Computationally designed]]
[[Category: Lyase-lyase inhibitor complex]]
[[Category: Retroaldolase]]
[[Category: Tim barrel]]

Latest revision as of 13:55, 14 March 2024

Structural analyses of covalent enzyme-substrate analogue complexes reveal strengths and limitations of de novo enzyme design

3ud6, resolution 2.09Å

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