5ej5

From Proteopedia

(Difference between revisions)

Revision as of 07:00, 22 April 2020

EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 1.5 h

Structural highlights

5ej5 is a 8 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	5ej4, 5ej6, 5ej7, 5ej8, 5ej9, 5eja, 5ejm
Gene:	menD, b2264, JW5374 (ECOLI)
Activity:	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase, with EC number 2.2.1.9
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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).^[1] ^[2]

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^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Palaniappan C, Sharma V, Hudspeth ME, Meganathan R. Menaquinone (vitamin K2) biosynthesis: evidence that the Escherichia coli menD gene encodes both 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid synthase and alpha-ketoglutarate decarboxylase activities. J Bacteriol. 1992 Dec;174(24):8111-8. PMID:1459959
↑ Jiang M, Cao Y, Guo ZF, Chen M, Chen X, Guo Z. Menaquinone biosynthesis in Escherichia coli: identification of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate as a novel intermediate and re-evaluation of MenD activity. Biochemistry. 2007 Sep 25;46(38):10979-89. Epub 2007 Aug 31. PMID:17760421 doi:http://dx.doi.org/10.1021/bi700810x
↑ Song H, Dong C, Qin M, Chen Y, Sun Y, Liu J, Chan W, Guo Z. A thiamine-dependent enzyme utilizes an active tetrahedral intermediate in vitamin K biosynthesis. J Am Chem Soc. 2016 May 23. PMID:27213829 doi:http://dx.doi.org/10.1021/jacs.6b03437

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5ej5"

@@ Line 1: / Line 1: @@
 ==EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 1.5 h==
-<StructureSection load='5ej5' size='340' side='right' caption='[[5ej5]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='5ej5' size='340' side='right'caption='[[5ej5]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ej5]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EJ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EJ5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ej5]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EJ5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5EJ5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ej4|5ej4]], [[5ej6|5ej6]], [[5ej7|5ej7]], [[5ej8|5ej8]], [[5ej9|5ej9]], [[5eja|5eja]], [[5ejm|5ejm]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">menD, b2264, JW5374 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ej5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ej5 OCA], [http://pdbe.org/5ej5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ej5 RCSB], [http://www.ebi.ac.uk/pdbsum/5ej5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ej5 ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ej5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ej5 OCA], [http://pdbe.org/5ej5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ej5 RCSB], [http://www.ebi.ac.uk/pdbsum/5ej5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ej5 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 25: / Line 26: @@
 </StructureSection>
 [[Category: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase]]
+[[Category: Ecoli]]
+[[Category: Large Structures]]
 [[Category: Chen, Y Z]]
 [[Category: Dong, C]]

5ej5

From Proteopedia

Revision as of 07:00, 22 April 2020

EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 1.5 h

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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