View source for 3zhu


==Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, second post-decarboxylation intermediate from 2-oxoadipate==
<StructureSection load='3zhu' size='340' side='right'caption='[[3zhu]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3zhu]] 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=3ZHU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZHU 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]] 2.3&#8491;</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=TD8:(5R)-5-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-5-(2-{[(PHOSPHONATOOXY)PHOSPHINATO]OXY}ETHYL)-1,3-THIAZOL-3-IUM-2-YL}-5-HYDROXYPENTANOATE'>TD8</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=3zhu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhu OCA], [https://pdbe.org/3zhu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zhu RCSB], [https://www.ebi.ac.uk/pdbsum/3zhu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zhu 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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3zhu" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Mycolicibacterium smegmatis]]
[[Category: Alzari PM]]
[[Category: Barilone N]]
[[Category: Bellinzoni M]]
[[Category: Wagner T]]