4plf: Difference between revisions
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==Crystal structure of ancestral apicomplexan lactate dehydrogenase with lactate.== | ==Crystal structure of ancestral apicomplexan lactate dehydrogenase with lactate.== | ||
<StructureSection load='4plf' size='340' side='right' caption='[[4plf]], [[Resolution|resolution]] 1.35Å' scene=''> | <StructureSection load='4plf' size='340' side='right'caption='[[4plf]], [[Resolution|resolution]] 1.35Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4plf]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4plf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Apicomplexa Apicomplexa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PLF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PLF FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</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]] 1.35Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</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=4plf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4plf OCA], [https://pdbe.org/4plf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4plf RCSB], [https://www.ebi.ac.uk/pdbsum/4plf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4plf ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A075B5G8_9APIC A0A075B5G8_9APIC] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 17: | Line 19: | ||
</div> | </div> | ||
<div class="pdbe-citations 4plf" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 4plf" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Lactate dehydrogenase 3D structures|Lactate dehydrogenase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Apicomplexa]] | [[Category: Apicomplexa]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Beckett BC]] | ||
[[Category: | [[Category: Boucher JI]] | ||
[[Category: Classen S]] | |||
[[Category: Jacobowitz JR]] | |||
[[Category: Theobald DL]] | |||
Latest revision as of 10:17, 27 September 2023
Crystal structure of ancestral apicomplexan lactate dehydrogenase with lactate.Crystal structure of ancestral apicomplexan lactate dehydrogenase with lactate.
Structural highlights
FunctionPublication Abstract from PubMedMalate and lactate dehydrogenases (MDH and LDH) are homologous, core metabolic enzymes that share a fold and catalytic mechanism yet possess strict specificity for their substrates. In the Apicomplexa, convergent evolution of an unusual LDH from MDH resulted in a difference in substrate preference exceeding 12 orders of magnitude. The molecular and evolutionary mechanisms responsible for this extraordinary functional shift are currently unknown. Using ancestral sequence reconstruction, we find that the evolution of pyruvate specificity in apicomplexan LDHs arose through a classic neofunctionalization mechanism characterized by long-range epistasis, a promiscuous intermediate, and relatively few gain-of-function mutations of large effect. Residues far from the active site determine specificity, as shown by the crystal structures of three ancestral proteins that bracket the key gene duplication event. This work provides an unprecedented atomic-resolution view of evolutionary trajectories resulting in the de novo creation of a nascent enzymatic function. An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases.,Boucher JI, Jacobowitz JR, Beckett BC, Classen S, Theobald DL Elife. 2014 Jun 25:e02304. doi: 10.7554/eLife.02304. PMID:24966208[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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