5exd: Difference between revisions

Revision as of 08:31, 12 July 2023

Crystal structure of oxalate oxidoreductase from Moorella thermoacetica bound with carboxy-di-oxido-methyl-TPP (COOM-TPP) intermediate

Structural highlights

5exd is a 12 chain structure with sequence from Moorella thermoacetica ATCC 39073. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	MG, O2T, SF4, TPP
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1]

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Pierce E, Becker DF, Ragsdale SW. Identification and characterization of oxalate oxidoreductase, a novel thiamine pyrophosphate-dependent 2-oxoacid oxidoreductase that enables anaerobic growth on oxalate. J Biol Chem. 2010 Dec 24;285(52):40515-24. doi: 10.1074/jbc.M110.155739. Epub, 2010 Oct 18. PMID:20956531 doi:https://dx.doi.org/10.1074/jbc.M110.155739
↑ Gibson MI, Chen PY, Johnson AC, Pierce E, Can M, Ragsdale SW, Drennan CL. One-carbon chemistry of oxalate oxidoreductase captured by X-ray crystallography. Proc Natl Acad Sci U S A. 2015 Dec 28. pii: 201518537. PMID:26712008 doi:https://dx.doi.org/10.1073/pnas.1518537113

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OCA

[1] Pierce E, Becker DF, Ragsdale SW. Identification and characterization of oxalate oxidoreductase, a novel thiamine pyrophosphate-dependent 2-oxoacid oxidoreductase that enables anaerobic growth on oxalate. J Biol Chem. 2010 Dec 24;285(52):40515-24. doi: 10.1074/jbc.M110.155739. Epub, 2010 Oct 18. PMID:20956531 doi:https://dx.doi.org/10.1074/jbc.M110.155739

[2] Gibson MI, Chen PY, Johnson AC, Pierce E, Can M, Ragsdale SW, Drennan CL. One-carbon chemistry of oxalate oxidoreductase captured by X-ray crystallography. Proc Natl Acad Sci U S A. 2015 Dec 28. pii: 201518537. PMID:26712008 doi:https://dx.doi.org/10.1073/pnas.1518537113

[1]

[2]

@@ Line 3: / Line 3: @@
 <StructureSection load='5exd' size='340' side='right'caption='[[5exd]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5exd]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Moorella_thermoacetica_(strain_atcc_39073) Moorella thermoacetica (strain 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 [http://proteopedia.org/fgij/fg.htm?mol=5EXD FirstGlance]. <br>
+<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='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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5exe|5exe]]</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxalate_oxidoreductase Oxalate oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.7.10 1.2.7.10] </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=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>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5exd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5exd OCA], [http://pdbe.org/5exd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5exd RCSB], [http://www.ebi.ac.uk/pdbsum/5exd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5exd ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>  [[http://www.uniprot.org/uniprot/OORB_MOOTA OORB_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>  [[http://www.uniprot.org/uniprot/OORD_MOOTA OORD_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>
+[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 ==
@@ Line 25: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Oxalate oxidoreductase]]
+[[Category: Moorella thermoacetica ATCC 39073]]
-[[Category: Chen, P Y.T]]
+[[Category: Chen PY-T]]
-[[Category: Drennan, C L]]
+[[Category: Drennan CL]]
-[[Category: Gibson, M I]]
+[[Category: Gibson MI]]
-[[Category: Ofor]]
-[[Category: Oxalate]]
-[[Category: Oxidoreductase]]
-[[Category: Thiamine]]

5exd: Difference between revisions

Revision as of 08:31, 12 July 2023

Crystal structure of oxalate oxidoreductase from Moorella thermoacetica bound with carboxy-di-oxido-methyl-TPP (COOM-TPP) intermediate

Structural highlights

Function

Publication Abstract from PubMed

References

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