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2yid
From Proteopedia
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==CRYSTAL STRUCTURE OF THE SUCA DOMAIN OF MYCOBACTERIUM SMEGMATIS ALPHA-KETOGLUTARATE DECARBOXYLASE IN COMPLEX WITH THE ENAMINE-THDP INTERMEDIATE== | ==CRYSTAL STRUCTURE OF THE SUCA DOMAIN OF MYCOBACTERIUM SMEGMATIS ALPHA-KETOGLUTARATE DECARBOXYLASE IN COMPLEX WITH THE ENAMINE-THDP INTERMEDIATE== | ||
<StructureSection load='2yid' size='340' side='right' caption='[[2yid]], [[Resolution|resolution]] 2.25Å' scene=''> | <StructureSection load='2yid' size='340' side='right' caption='[[2yid]], [[Resolution|resolution]] 2.25Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[2yid]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/ | + | <table><tr><td colspan='2'>[[2yid]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YID OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YID FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TD7:(4E)-4-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-2(3H)-YLIDENE}-4-HYDROXYBUTANOIC+ACID'>TD7</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TD7:(4E)-4-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-2(3H)-YLIDENE}-4-HYDROXYBUTANOIC+ACID'>TD7</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2xt8|2xt8]], [[2y0p|2y0p]], [[2xta|2xta]], [[2xt9|2xt9]], [[2xt6|2xt6]], [[2yic|2yic]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2xt8|2xt8]], [[2y0p|2y0p]], [[2xta|2xta]], [[2xt9|2xt9]], [[2xt6|2xt6]], [[2yic|2yic]]</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-oxoglutarate_decarboxylase 2-oxoglutarate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.71 4.1.1.71] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-oxoglutarate_decarboxylase 2-oxoglutarate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.71 4.1.1.71] </span></td></tr> | ||
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2yid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yid OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yid RCSB], [http://www.ebi.ac.uk/pdbsum/2yid PDBsum]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2yid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yid OCA], [http://pdbe.org/2yid PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yid RCSB], [http://www.ebi.ac.uk/pdbsum/2yid PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yid ProSAT]</span></td></tr> |
</table> | </table> | ||
| + | == Function == | ||
| + | [[http://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;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
| + | <div class="pdbe-citations 2yid" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Bacillus smegmatis trevisan 1889]] | ||
[[Category: 2-oxoglutarate decarboxylase]] | [[Category: 2-oxoglutarate decarboxylase]] | ||
| - | [[Category: Mycobacterium smegmatis]] | ||
[[Category: Alzari, P M]] | [[Category: Alzari, P M]] | ||
[[Category: Bellinzoni, M]] | [[Category: Bellinzoni, M]] | ||
Revision as of 07:46, 5 August 2016
CRYSTAL STRUCTURE OF THE SUCA DOMAIN OF MYCOBACTERIUM SMEGMATIS ALPHA-KETOGLUTARATE DECARBOXYLASE IN COMPLEX WITH THE ENAMINE-THDP INTERMEDIATE
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