6co6: Difference between revisions
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==Crystal structure of Rhodococcus jostii RHA1 IpdAB== | ==Crystal structure of Rhodococcus jostii RHA1 IpdAB== | ||
<StructureSection load='6co6' size='340' side='right' caption='[[6co6]], [[Resolution|resolution]] 1.70Å' scene=''> | <StructureSection load='6co6' size='340' side='right'caption='[[6co6]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6co6]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[6co6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_jostii_RHA1 Rhodococcus jostii RHA1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CO6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CO6 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.701Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6co6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6co6 OCA], [https://pdbe.org/6co6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6co6 RCSB], [https://www.ebi.ac.uk/pdbsum/6co6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6co6 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/IPDA_RHOJR IPDA_RHOJR] Involved in the final steps of cholesterol and steroid degradation (PubMed:28377529, PubMed:29581275). Opens the last steroid ring of cholesterol by catalyzing the hydrolysis of (3E)-2-(2-carboxylatoethyl)-3-methyl-6-oxocyclohex-1-ene-1-carboxyl-CoA (COCHEA-CoA) to 6-methyl-3,7-dioxodecanedioyl-CoA (MeDODA-CoA) (Probable) (PubMed:29581275).<ref>PMID:28377529</ref> <ref>PMID:29581275</ref> <ref>PMID:28377529</ref> | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Crowe | [[Category: Rhodococcus jostii RHA1]] | ||
[[Category: Eltis | [[Category: Crowe AM]] | ||
[[Category: Strynadka | [[Category: Eltis LD]] | ||
[[Category: Watanabe | [[Category: Strynadka NCJ]] | ||
[[Category: Workman | [[Category: Watanabe N]] | ||
[[Category: Worrall | [[Category: Workman SD]] | ||
[[Category: Worrall LJ]] | |||
Latest revision as of 18:08, 4 October 2023
Crystal structure of Rhodococcus jostii RHA1 IpdABCrystal structure of Rhodococcus jostii RHA1 IpdAB
Structural highlights
FunctionIPDA_RHOJR Involved in the final steps of cholesterol and steroid degradation (PubMed:28377529, PubMed:29581275). Opens the last steroid ring of cholesterol by catalyzing the hydrolysis of (3E)-2-(2-carboxylatoethyl)-3-methyl-6-oxocyclohex-1-ene-1-carboxyl-CoA (COCHEA-CoA) to 6-methyl-3,7-dioxodecanedioyl-CoA (MeDODA-CoA) (Probable) (PubMed:29581275).[1] [2] [3] Publication Abstract from PubMedMycobacterium tuberculosis (Mtb) grows on host-derived cholesterol during infection. IpdAB, found in all steroid-degrading bacteria and a determinant of pathogenicity, has been implicated in the hydrolysis of the last steroid ring. Phylogenetic analyses revealed that IpdAB orthologs form a clade of CoA transferases (CoTs). In a coupled assay with a thiolase, IpdAB transformed the cholesterol catabolite (R)-2-(2-carboxyethyl)-3-methyl-6-oxocyclohex-1-ene-1-carboxyl-CoA (COCHEA-CoA) and CoASH to 4-methyl-5-oxo-octanedioyl-CoA (MOODA-CoA) and acetyl-CoA with high specificity (kcat/Km = 5.8 +/- 0.8 x 10(4) M(-1)s(-1)). The structure of MOODA-CoA was consistent with IpdAB hydrolyzing COCHEA-CoA to a beta-keto-thioester, a thiolase substrate. Contrary to characterized CoTs, IpdAB exhibited no activity toward small CoA thioesters. Further, IpdAB lacks the catalytic glutamate residue that is conserved in the beta-subunit of characterized CoTs and a glutamyl-CoA intermediate was not trapped during turnover. By contrast, Glu105(A), conserved in the alpha-subunit of IpdAB, was essential for catalysis. A crystal structure of the IpdAB.COCHEA-CoA complex, solved to 1.4 A, revealed that Glu105(A) is positioned to act as a catalytic base. Upon titration with COCHEA-CoA, the E105A(A) variant accumulated a yellow-colored species (lambdamax = 310 nm; Kd = 0.4 +/- 0.2 muM) typical of beta-keto enolates. In the presence of D2O, IpdAB catalyzed the deuteration of COCHEA-CoA adjacent to the hydroxylation site at rates consistent with kcat Based on these data and additional IpdAB variants, we propose a retro-Claisen condensation-like mechanism for the IpdAB-mediated hydrolysis of COCHEA-CoA. This study expands the range of known reactions catalyzed by the CoT superfamily and provides mechanistic insight into an important determinant of Mtb pathogenesis. IpdAB, a virulence factor in Mycobacterium tuberculosis, is a cholesterol ring-cleaving hydrolase.,Crowe AM, Workman SD, Watanabe N, Worrall LJ, Strynadka NCJ, Eltis LD Proc Natl Acad Sci U S A. 2018 Mar 26. pii: 1717015115. doi:, 10.1073/pnas.1717015115. PMID:29581275[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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