This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5ej6

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5ej6"

@@ Line 1: / Line 1: @@
 ==EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2min then soaked with isochorismate for 2 min==
-<StructureSection load='5ej6' size='340' side='right' caption='[[5ej6]], [[Resolution|resolution]] 2.24&Aring;' scene=''>
+<StructureSection load='5ej6' size='340' side='right'caption='[[5ej6]], [[Resolution|resolution]] 2.24&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ej6]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EJ6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EJ6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ej6]] 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=5EJ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EJ6 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TD6:(4S)-4-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3LAMBDA~5~-THIAZOL-2-YL}-4-HYDROXYBUTANOIC+ACID'>TD6</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.243&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ej4|5ej4]], [[5ej5|5ej5]], [[5ej7|5ej7]], [[5ej8|5ej8]], [[5ej9|5ej9]], [[5eja|5eja]], [[5ejm|5ejm]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TD6:(4S)-4-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3LAMBDA~5~-THIAZOL-2-YL}-4-HYDROXYBUTANOIC+ACID'>TD6</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid_synthase 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.2.1.9 2.2.1.9] </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=5ej6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ej6 OCA], [https://pdbe.org/5ej6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ej6 RCSB], [https://www.ebi.ac.uk/pdbsum/5ej6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ej6 ProSAT]</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=5ej6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ej6 OCA], [http://pdbe.org/5ej6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ej6 RCSB], [http://www.ebi.ac.uk/pdbsum/5ej6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ej6 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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.
-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>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5ej6" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase]]
+[[Category: Escherichia coli K-12]]
-[[Category: Chen, Y Z]]
+[[Category: Large Structures]]
-[[Category: Dong, C]]
+[[Category: Chen YZ]]
-[[Category: Guo, Z H]]
+[[Category: Dong C]]
-[[Category: Song, H G]]
+[[Category: Guo ZH]]
-[[Category: Sun, Y R]]
+[[Category: Song HG]]
-[[Category: Post-decarboxylation intermediate]]
+[[Category: Sun YR]]
-[[Category: Transferase]]

5ej6

From Proteopedia

Current revision

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

Structural highlights

Function

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox