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| | <StructureSection load='2yim' size='340' side='right'caption='[[2yim]], [[Resolution|resolution]] 1.41Å' scene=''> | | <StructureSection load='2yim' size='340' side='right'caption='[[2yim]], [[Resolution|resolution]] 1.41Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2yim]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YIM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2yim]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YIM FirstGlance]. <br> |
| - | </td></tr><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=MC4:2-METHYLACETOACETYL+COA'>MC4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.41Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1x74|1x74]]</div></td></tr> | + | <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=MC4:2-METHYLACETOACETYL+COA'>MC4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alpha-methylacyl-CoA_racemase Alpha-methylacyl-CoA racemase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.4 5.1.99.4] </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=2yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yim OCA], [https://pdbe.org/2yim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yim RCSB], [https://www.ebi.ac.uk/pdbsum/2yim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yim ProSAT]</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=2yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yim OCA], [https://pdbe.org/2yim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yim RCSB], [https://www.ebi.ac.uk/pdbsum/2yim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yim ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/AMACR_MYCTU AMACR_MYCTU] Catalyzes the epimerization of (2R)- and (2S)-methylacyl-coenzyme A (CoA) thioesters (PubMed:15632186, PubMed:19854148, PubMed:26348625). Accepts as substrates a wide range of alpha-methylacyl-CoAs, including (2R)-2-methylmyristoyl-CoA and (2S)-2-methylmyristoyl-CoA, (2R)-pristanoyl-CoA and (2S)-pristanoyl-CoA, and the cholesterol esters (25R)-3-oxo-cholest-4-en-26-oyl-CoA and (25S)-3-oxo-cholest-4-en-26-oyl-CoA (PubMed:15632186, PubMed:26348625). Can also catalyze the interconversion of the non-physiologic substrates (2R)-ibuprofenoyl-CoA and (2S)-ibuprofenoyl-CoA, which are potential competitive inhibitors of the enzyme (PubMed:19854148).<ref>PMID:15632186</ref> <ref>PMID:19854148</ref> <ref>PMID:26348625</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: Alpha-methylacyl-CoA racemase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Myctu]] | + | [[Category: Mycobacterium tuberculosis H37Rv]] |
| - | [[Category: Bhaumik, P]] | + | [[Category: Bhaumik P]] |
| - | [[Category: Conzelmann, E]] | + | [[Category: Conzelmann E]] |
| - | [[Category: Hiltunen, J K]] | + | [[Category: Hiltunen JK]] |
| - | [[Category: Juffer, A H]] | + | [[Category: Juffer AH]] |
| - | [[Category: Sharma, S]] | + | [[Category: Sharma S]] |
| - | [[Category: Venkatesan, R]] | + | [[Category: Venkatesan R]] |
| - | [[Category: Wierenga, R K]] | + | [[Category: Wierenga RK]] |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Methyl-coa racemase]]
| + | |
| - | [[Category: Molecular dynamic]]
| + | |
| - | [[Category: Oxyanion hole]]
| + | |
| - | [[Category: Qm/mm]]
| + | |
| - | [[Category: Transition state]]
| + | |
| Structural highlights
Function
AMACR_MYCTU Catalyzes the epimerization of (2R)- and (2S)-methylacyl-coenzyme A (CoA) thioesters (PubMed:15632186, PubMed:19854148, PubMed:26348625). Accepts as substrates a wide range of alpha-methylacyl-CoAs, including (2R)-2-methylmyristoyl-CoA and (2S)-2-methylmyristoyl-CoA, (2R)-pristanoyl-CoA and (2S)-pristanoyl-CoA, and the cholesterol esters (25R)-3-oxo-cholest-4-en-26-oyl-CoA and (25S)-3-oxo-cholest-4-en-26-oyl-CoA (PubMed:15632186, PubMed:26348625). Can also catalyze the interconversion of the non-physiologic substrates (2R)-ibuprofenoyl-CoA and (2S)-ibuprofenoyl-CoA, which are potential competitive inhibitors of the enzyme (PubMed:19854148).[1] [2] [3]
Publication Abstract from PubMed
In the active site of the bacterial alpha-methylacyl-CoA racemase of Mycobacterium tuberculosis (MCR), the chirality of the 2-methyl branched C2-atom is interconverted between (S) and (R) isomers. Protein crystallographic data and quantum mechanics/molecular mechanics (QM/MM) computational approaches show that this interconversion is achieved via a planar enolate intermediate. The crystal structure, at 1.4 A, visualizes the mode of binding of a reaction intermediate analogue, 2-methylacetoacetyl-CoA, in a well-defined planar enolate form. The computational studies confirm that in the conversion from (S) to (R), first a proton is abstracted by Ndelta1 (His126), and subsequently the planar enolate form is reprotonated by Odelta2 (Asp156). The calculations also show that the negatively charged thioester oxygen of the enolate intermediate is stabilized by an oxyanion hole formed by N (Asp127), as well as by the side chain atoms of the catalytic residues, Asp156 and His126, both being protonated simultaneously, at the intermediate stage of the catalytic cycle. The computational analysis also reveals that the conversion of the (S)- to (R)- chirality is achieved by a movement of 1.7 A of the chiral C2-carbon, with smaller shifts (approximately 1 A) of the carbon atom of the 2-methyl group, the C3-atom of the fatty acid tail, and the C1-carbon and O1-oxygen atoms of the thioester moiety.
The Enolization Chemistry of a Thioester-Dependent Racemase: The 1.4 A Crystal Structure of a Reaction Intermediate Complex Characterized by Detailed QM/MM Calculations.,Sharma S, Bhaumik P, Schmitz W, Venkatesan R, Hiltunen JK, Conzelmann E, Juffer AH, Wierenga RK J Phys Chem B. 2012 Mar 22;116(11):3619-29. Epub 2012 Mar 7. PMID:22360758[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Savolainen K, Bhaumik P, Schmitz W, Kotti TJ, Conzelmann E, Wierenga RK, Hiltunen JK. Alpha-methylacyl-CoA racemase from Mycobacterium tuberculosis. Mutational and structural characterization of the active site and the fold. J Biol Chem. 2005 Apr 1;280(13):12611-20. Epub 2005 Jan 4. PMID:15632186 doi:10.1074/jbc.M409704200
- ↑ Ouazia D, Bearne SL. A continuous assay for alpha-methylacyl-coenzyme A racemase using circular dichroism. Anal Biochem. 2010 Mar 1;398(1):45-51. PMID:19854148 doi:10.1016/j.ab.2009.10.039
- ↑ Lu R, Schmitz W, Sampson NS. α-Methyl Acyl CoA Racemase Provides Mycobacterium tuberculosis Catabolic Access to Cholesterol Esters. Biochemistry. 2015 Sep 22;54(37):5669-72. PMID:26348625 doi:10.1021/acs.biochem.5b00911
- ↑ Sharma S, Bhaumik P, Schmitz W, Venkatesan R, Hiltunen JK, Conzelmann E, Juffer AH, Wierenga RK. The Enolization Chemistry of a Thioester-Dependent Racemase: The 1.4 A Crystal Structure of a Reaction Intermediate Complex Characterized by Detailed QM/MM Calculations. J Phys Chem B. 2012 Mar 22;116(11):3619-29. Epub 2012 Mar 7. PMID:22360758 doi:10.1021/jp210185m
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