5ej9: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 5ej9 is ~~ON HOLD until Paper~~ Publication

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

== 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]] 1.72Å</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>

== 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®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased Structures~~]]

</div>

[[Category: ~~Sun, Y.R~~]]

[[Category: ~~Guo, Z.H~~]]

== References ==

[[Category: Dong, C]]

[[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]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5ej9 is ON HOLD  until Paper Publication
+==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]]