3zhs
From Proteopedia
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| - | {{STRUCTURE_3zhs| PDB=3zhs | SCENE= }} | ||
| - | ===Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, first post-decarboxylation intermediate from alpha-ketoglutarate=== | ||
| - | {{ABSTRACT_PUBMED_24171907}} | ||
| - | == | + | ==Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, first post-decarboxylation intermediate from alpha-ketoglutarate== |
| - | [[http://www.uniprot.org/uniprot/KGD_MYCS2 KGD_MYCS2 | + | <StructureSection load='3zhs' size='340' side='right'caption='[[3zhs]], [[Resolution|resolution]] 2.10Å' scene=''> |
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3zhs]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZHS 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]] 2.1Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TD6:(4S)-4-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3LAMBDA~5~-THIAZOL-2-YL}-4-HYDROXYBUTANOIC+ACID'>TD6</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=3zhs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhs OCA], [https://pdbe.org/3zhs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zhs RCSB], [https://www.ebi.ac.uk/pdbsum/3zhs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zhs ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/KGD_MYCS2 KGD_MYCS2] Shows three enzymatic activities that share a first common step, the attack of thiamine-PP on 2-oxoglutarate (alpha-ketoglutarate, KG), leading to the formation of an enamine-thiamine-PP intermediate upon decarboxylation. Thus, displays KGD activity, catalyzing the decarboxylation from five-carbon 2-oxoglutarate to four-carbon succinate semialdehyde (SSA). Also catalyzes C-C bond formation between the activated aldehyde formed after decarboxylation of alpha-ketoglutarate and the carbonyl of glyoxylate (GLX), to yield 2-hydroxy-3-oxoadipate (HOA), which spontaneously decarboxylates to form 5-hydroxylevulinate (HLA). And is also a component of the 2-oxoglutarate dehydrogenase (ODH) complex, that catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). The KG decarboxylase and KG dehydrogenase reactions provide two alternative, tightly regulated, pathways connecting the oxidative and reductive branches of the TCA cycle.<ref>PMID:19019160</ref> <ref>PMID:21867916</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | alpha-ketoacid dehydrogenases are large multi-enzyme machineries that orchestrate the oxidative decarboxylation of alpha-ketoacids with the concomitant production of acyl-CoA and NADH. The first reaction, catalysed by alpha-ketoacid decarboxylases (E1 enzymes), needs a thiamine diphosphate cofactor and represents the overall rate-limiting step. Although the catalytic cycles of E1 from the pyruvate dehydrogenase (E1p) and branched chain alpha-ketoacid dehydrogenase (E1b) complexes have been elucidated, little structural information is available on E1o, the first component of the alpha-ketoglutarate dehydrogenase complex, despite the central role of this complex at the branching point between the TCA cycle and glutamate metabolism. Here, we provide structural evidence that MsKGD, the E1o from Mycobacterium smegmatis, shows two conformations of the post-decarboxylation intermediate, each one associated with a distinct enzyme state. We also report an overall picture of the catalytic cycle, reconstructed by either crystallographic snapshots or modelling. Our results show that the conformational change leading the enzyme from the initial (early) to the late state, although not required for decarboxylation, plays an essential role in catalysis, and possibly in the regulation of mycobacterial E1o. | ||
| - | + | A dual conformation of the post-decarboxylation intermediate is associated with distinct enzyme states in mycobacterial alpha-ketoglutarate decarboxylase (KGD).,Wagner T, Barilone N, Alzari PM, Bellinzoni M Biochem J. 2013 Oct 31. PMID:24171907<ref>PMID:24171907</ref> | |
| - | + | ||
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | < | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 3zhs" style="background-color:#fffaf0;"></div> |
| - | [[Category: Alzari | + | == References == |
| - | [[Category: Barilone | + | <references/> |
| - | [[Category: Bellinzoni | + | __TOC__ |
| - | [[Category: Wagner | + | </StructureSection> |
| - | + | [[Category: Large Structures]] | |
| - | + | [[Category: Mycolicibacterium smegmatis]] | |
| - | + | [[Category: Alzari PM]] | |
| + | [[Category: Barilone N]] | ||
| + | [[Category: Bellinzoni M]] | ||
| + | [[Category: Wagner T]] | ||
Current revision
Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, first post-decarboxylation intermediate from alpha-ketoglutarate
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