2yic

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:53, 20 December 2023) (edit) (undo)
 
(5 intermediate revisions not shown.)
Line 1: Line 1:
-
==CRYSTAL STRUCTURE OF THE SUCA DOMAIN OF MYCOBACTERIUM SMEGMATIS ALPHA-KETOGLUTARATE DECARBOXYLASE (TRICLINIC FORM)==
+
 
-
<StructureSection load='2yic' size='340' side='right' caption='[[2yic]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
+
==Crystal structure of the SucA domain of Mycobacterium smegmatis alpha- ketoglutarate decarboxylase (triclinic form)==
 +
<StructureSection load='2yic' size='340' side='right'caption='[[2yic]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[2yic]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis Mycobacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YIC OCA]. <br>
+
<table><tr><td colspan='2'>[[2yic]] 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=2YIC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YIC FirstGlance]. <br>
-
</td></tr><tr><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=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene><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]] 1.96&#8491;</td></tr>
-
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2xt8|2xt8]], [[2y0p|2y0p]], [[2xta|2xta]], [[2xt9|2xt9]], [[2xt6|2xt6]], [[2yid|2yid]]</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=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=2yic FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yic OCA], [https://pdbe.org/2yic PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yic RCSB], [https://www.ebi.ac.uk/pdbsum/2yic PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yic ProSAT]</span></td></tr>
-
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2yic FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yic OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yic RCSB], [http://www.ebi.ac.uk/pdbsum/2yic PDBsum]</span></td></tr>
+
</table>
-
<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;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
Line 14: Line 16:
Functional plasticity and allosteric regulation of alpha-ketoglutarate decarboxylase in central mycobacterial metabolism.,Wagner T, Bellinzoni M, Wehenkel A, O'Hare HM, Alzari PM Chem Biol. 2011 Aug 26;18(8):1011-20. PMID:21867916<ref>PMID:21867916</ref>
Functional plasticity and allosteric regulation of alpha-ketoglutarate decarboxylase in central mycobacterial metabolism.,Wagner T, Bellinzoni M, Wehenkel A, O'Hare HM, Alzari PM Chem Biol. 2011 Aug 26;18(8):1011-20. PMID:21867916<ref>PMID:21867916</ref>
-
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
 +
<div class="pdbe-citations 2yic" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: 2-oxoglutarate decarboxylase]]
+
[[Category: Large Structures]]
-
[[Category: Mycobacterium smegmatis]]
+
[[Category: Mycolicibacterium smegmatis]]
-
[[Category: Alzari, P M.]]
+
[[Category: Alzari PM]]
-
[[Category: Bellinzoni, M.]]
+
[[Category: Bellinzoni M]]
-
[[Category: Hare, H M.O.]]
+
[[Category: O'Hare HM]]
-
[[Category: Wagner, T.]]
+
[[Category: Wagner T]]
-
[[Category: Wehenkel, A M.]]
+
[[Category: Wehenkel AM]]
-
[[Category: Lyase]]
+

Current revision

Crystal structure of the SucA domain of Mycobacterium smegmatis alpha- ketoglutarate decarboxylase (triclinic form)

PDB ID 2yic

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2yic"
Personal tools