3lt8: Difference between revisions
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==A non-biological ATP binding protein with a single point mutation (D65V), that contributes to optimized folding and ligand binding, crystallized in the presence of 100 mM ATP.== | ==A non-biological ATP binding protein with a single point mutation (D65V), that contributes to optimized folding and ligand binding, crystallized in the presence of 100 mM ATP.== | ||
<StructureSection load='3lt8' size='340' side='right' caption='[[3lt8]], [[Resolution|resolution]] 2.55Å' scene=''> | <StructureSection load='3lt8' size='340' side='right'caption='[[3lt8]], [[Resolution|resolution]] 2.55Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3lt8]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3lt8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LT8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LT8 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.55Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=3lt8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lt8 OCA], [https://pdbe.org/3lt8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lt8 RCSB], [https://www.ebi.ac.uk/pdbsum/3lt8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lt8 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 3lt8" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Synthetic construct]] | [[Category: Synthetic construct]] | ||
[[Category: Allen | [[Category: Allen JP]] | ||
[[Category: Chaput | [[Category: Chaput JC]] | ||
[[Category: Magee | [[Category: Magee CL]] | ||
[[Category: Simmons | [[Category: Simmons CR]] | ||
Latest revision as of 11:43, 6 September 2023
A non-biological ATP binding protein with a single point mutation (D65V), that contributes to optimized folding and ligand binding, crystallized in the presence of 100 mM ATP.A non-biological ATP binding protein with a single point mutation (D65V), that contributes to optimized folding and ligand binding, crystallized in the presence of 100 mM ATP.
Structural highlights
Publication Abstract from PubMedThe creation of synthetic enzymes with predefined functions represents a major challenge in future synthetic biology applications. Here, we describe six structures of de novo proteins that have been determined using protein crystallography to address how simple enzymes perform catalysis. Three structures are of a protein, DX, selected for its stability and ability to tightly bind ATP. Despite the addition of ATP to the crystallization conditions, the presence of a bound but distorted ATP was found only under excess ATP conditions, with ADP being present under equimolar conditions or when crystallized for a prolonged period of time. A bound ADP cofactor was evident when Asp was substituted for Val at residue 65, but ATP in a linear configuration is present when Phe was substituted for Tyr at residue 43. These new structures complement previously determined structures of DX and the protein with the Phe 43 to Tyr substitution [Simmons, C. R., et al. (2009) ACS Chem. Biol. 4, 649-658] and together demonstrate the multiple ADP/ATP binding modes from which a model emerges in which the DX protein binds ATP in a configuration that represents a transitional state for the catalysis of ATP to ADP through a slow, metal-free reaction capable of multiple turnovers. This unusual observation suggests that design-free methods can be used to generate novel protein scaffolds that are tailor-made for catalysis. Three-Dimensional Structures Reveal Multiple ADP/ATP Binding Modes for a Synthetic Class of Artificial Proteins .,Simmons CR, Magee CL, Smith DA, Lauman L, Chaput JC, Allen JP Biochemistry. 2010 Sep 16. PMID:20822107[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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