5ej9

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "5ej9" [edit=sysop:move=sysop])
Current revision (06:30, 5 July 2023) (edit) (undo)
 
(4 intermediate revisions not shown.)
Line 1: Line 1:
-
'''Unreleased structure'''
 
-
The entry 5ej9 is ON HOLD
+
==EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2 min and isochorismate for 13 min==
 +
<StructureSection load='5ej9' size='340' side='right'caption='[[5ej9]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[5ej9]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EJ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EJ9 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]] 1.72&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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=5ej9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ej9 OCA], [https://pdbe.org/5ej9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ej9 RCSB], [https://www.ebi.ac.uk/pdbsum/5ej9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ej9 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/MEND_ECOLI MEND_ECOLI] Catalyzes the thiamine diphosphate-dependent decarboxylation of 2-oxoglutarate and the subsequent addition of the resulting succinic semialdehyde-thiamine pyrophosphate anion to isochorismate to yield 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC).<ref>PMID:1459959</ref> <ref>PMID:17760421</ref>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Enamine is a well-known reactive intermediate mediating essential thiamine-dependent catalysis in central metabolic pathways. How-ever, this intermediate is not found in the thiamine-dependent catal-ysis of the vitamin K biosynthetic enzyme MenD. Instead, an active tetrahedral post-decarboxylation intermediate is stably formed in the enzyme and structurally determined at 1.34 A resolution in crystal. This intermediate takes a unique conformation that allows only one proton between its tetrahedral reaction center and the exo-ring ni-trogen atom of the aminopyrimidine moiety in the cofactor with a short distance of 3.0 A. It is readily convertible to the final product of the enzymic reaction with a solvent-exchangeable proton at its reaction center. These results show that the thiamine-dependent enzyme utilizes a tetrahedral intermediate in a mechanism distinct from the enamine catalytic chemistry.
-
Authors: Song, H.G., Dong, C., Chen, Y.Z., Sun, Y.R., Guo, Z.H.
+
A thiamine-dependent enzyme utilizes an active tetrahedral intermediate in vitamin K biosynthesis.,Song H, Dong C, Qin M, Chen Y, Sun Y, Liu J, Chan W, Guo Z J Am Chem Soc. 2016 May 23. PMID:27213829<ref>PMID:27213829</ref>
-
Description: EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2 min and isochorismate for 13 min
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
[[Category: Unreleased Structures]]
+
</div>
-
[[Category: Sun, Y.R]]
+
<div class="pdbe-citations 5ej9" style="background-color:#fffaf0;"></div>
-
[[Category: Guo, Z.H]]
+
== References ==
-
[[Category: Dong, C]]
+
<references/>
-
[[Category: Chen, Y.Z]]
+
__TOC__
-
[[Category: Song, H.G]]
+
</StructureSection>
 +
[[Category: Escherichia coli K-12]]
 +
[[Category: Large Structures]]
 +
[[Category: Chen YZ]]
 +
[[Category: Dong C]]
 +
[[Category: Guo ZH]]
 +
[[Category: Song HG]]
 +
[[Category: Sun YR]]

Current revision

EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2 min and isochorismate for 13 min

PDB ID 5ej9

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/5ej9"
Personal tools