5exd: Difference between revisions
New page: '''Unreleased structure''' The entry 5exd is ON HOLD until Paper Publication Authors: Gibson, M.I., Chen, P.Y.-T., Drennan, C.L. Description: Crystal structure of oxalate oxidoreductas... |
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==Crystal structure of oxalate oxidoreductase from Moorella thermoacetica bound with carboxy-di-oxido-methyl-TPP (COOM-TPP) intermediate== | |||
<StructureSection load='5exd' size='340' side='right'caption='[[5exd]], [[Resolution|resolution]] 2.50Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5exd]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Moorella_thermoacetica_ATCC_39073 Moorella thermoacetica ATCC 39073]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EXD FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=O2T:[2-[3-[(4-AZANYL-2-METHYL-PYRIMIDIN-5-YL)METHYL]-4-METHYL-2-[1,1,2-TRIS(OXIDANYL)-2-OXIDANYLIDENE-ETHYL]-1,3-THIAZOL-3-IUM-5-YL]ETHOXY-OXIDANYL-PHOSPHORYL]+HYDROGEN+PHOSPHATE'>O2T</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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=5exd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5exd OCA], [https://pdbe.org/5exd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5exd RCSB], [https://www.ebi.ac.uk/pdbsum/5exd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5exd ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/OORA_MOOTA OORA_MOOTA] Catalyzes the anaerobic oxidation of oxalate using a broad range of electron acceptors, including ferredoxin and the nickel-dependent carbon monoxide dehydrogenase. Does not require coenzyme A as cosubstrate. Enables anaerobic growth on oxalate which is used as energy source by the bacteria.<ref>PMID:20956531</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Thiamine pyrophosphate (TPP)-dependent oxalate oxidoreductase (OOR) metabolizes oxalate, generating two molecules of CO2 and two low-potential electrons, thus providing both the carbon and reducing equivalents for operation of the Wood-Ljungdahl pathway of acetogenesis. Here we present structures of OOR in which two different reaction intermediate bound states have been trapped: the covalent adducts between TPP and oxalate and between TPP and CO2. These structures, along with the previously determined structure of substrate-free OOR, allow us to visualize how active site rearrangements can drive catalysis. Our results suggest that OOR operates via a bait-and-switch mechanism, attracting substrate into the active site through the presence of positively charged and polar residues, and then altering the electrostatic environment through loop and side chain movements to drive catalysis. This simple but elegant mechanism explains how oxalate, a molecule that humans and most animals cannot break down, can be used for growth by acetogenic bacteria. | |||
One-carbon chemistry of oxalate oxidoreductase captured by X-ray crystallography.,Gibson MI, Chen PY, Johnson AC, Pierce E, Can M, Ragsdale SW, Drennan CL Proc Natl Acad Sci U S A. 2015 Dec 28. pii: 201518537. PMID:26712008<ref>PMID:26712008</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5exd" style="background-color:#fffaf0;"></div> | ||
[[Category: Drennan | == References == | ||
[[Category: | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Moorella thermoacetica ATCC 39073]] | |||
[[Category: Chen PY-T]] | |||
[[Category: Drennan CL]] | |||
[[Category: Gibson MI]] | |||
Latest revision as of 11:31, 12 July 2023
Crystal structure of oxalate oxidoreductase from Moorella thermoacetica bound with carboxy-di-oxido-methyl-TPP (COOM-TPP) intermediateCrystal structure of oxalate oxidoreductase from Moorella thermoacetica bound with carboxy-di-oxido-methyl-TPP (COOM-TPP) intermediate
Structural highlights
FunctionOORA_MOOTA Catalyzes the anaerobic oxidation of oxalate using a broad range of electron acceptors, including ferredoxin and the nickel-dependent carbon monoxide dehydrogenase. Does not require coenzyme A as cosubstrate. Enables anaerobic growth on oxalate which is used as energy source by the bacteria.[1] Publication Abstract from PubMedThiamine pyrophosphate (TPP)-dependent oxalate oxidoreductase (OOR) metabolizes oxalate, generating two molecules of CO2 and two low-potential electrons, thus providing both the carbon and reducing equivalents for operation of the Wood-Ljungdahl pathway of acetogenesis. Here we present structures of OOR in which two different reaction intermediate bound states have been trapped: the covalent adducts between TPP and oxalate and between TPP and CO2. These structures, along with the previously determined structure of substrate-free OOR, allow us to visualize how active site rearrangements can drive catalysis. Our results suggest that OOR operates via a bait-and-switch mechanism, attracting substrate into the active site through the presence of positively charged and polar residues, and then altering the electrostatic environment through loop and side chain movements to drive catalysis. This simple but elegant mechanism explains how oxalate, a molecule that humans and most animals cannot break down, can be used for growth by acetogenic bacteria. One-carbon chemistry of oxalate oxidoreductase captured by X-ray crystallography.,Gibson MI, Chen PY, Johnson AC, Pierce E, Can M, Ragsdale SW, Drennan CL Proc Natl Acad Sci U S A. 2015 Dec 28. pii: 201518537. PMID:26712008[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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