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5erx

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Revision as of 08:19, 12 July 2023

Crystal Structure of APO MenD from M. tuberculosis - I222

Structural highlights

5erx is a 1 chain structure with sequence from Mycobacterium tuberculosis H37Rv. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.729Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MEND_MYCTU 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).

Publication Abstract from PubMed

Menaquinone (MQ) is an essential component of the respiratory chains of many pathogenic organisms, including Mycobacterium tuberculosis (Mtb). The first committed step in MQ biosynthesis is catalyzed by 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase (MenD), a thiamin diphosphate (ThDP)-dependent enzyme. Catalysis proceeds through two covalent intermediates as the substrates 2-oxoglutarate and isochorismate are successively added to the cofactor before final cleavage of the product. We have determined a series of crystal structures of Mtb-MenD that map the binding of both substrates, visualizing each step in the MenD catalytic cycle, including both intermediates. ThDP binding induces a marked asymmetry between the coupled active sites of each dimer, and possible mechanisms of communication can be identified. The crystal structures also reveal conformational features of the two intermediates that facilitate reaction but prevent premature product release. These data fully map chemical space to inform early-stage drug discovery targeting MenD.

Structural Views along the Mycobacterium tuberculosis MenD Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms.,Jirgis EN, Bashiri G, Bulloch EM, Johnston JM, Baker EN Structure. 2016 Jul 6;24(7):1167-77. doi: 10.1016/j.str.2016.04.018. Epub 2016, Jun 9. PMID:27291649^[1]

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

References

↑ Jirgis EN, Bashiri G, Bulloch EM, Johnston JM, Baker EN. Structural Views along the Mycobacterium tuberculosis MenD Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms. Structure. 2016 Jul 6;24(7):1167-77. doi: 10.1016/j.str.2016.04.018. Epub 2016, Jun 9. PMID:27291649 doi:http://dx.doi.org/10.1016/j.str.2016.04.018

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/5erx"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of APO MenD from M. tuberculosis - I222==
-<StructureSection load='5erx' size='340' side='right' caption='[[5erx]], [[Resolution|resolution]] 1.73&Aring;' scene=''>
+<StructureSection load='5erx' size='340' side='right'caption='[[5erx]], [[Resolution|resolution]] 1.73&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5erx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ERX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ERX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5erx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ERX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ERX FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ery|5ery]], [[5ess|5ess]], [[5esd|5esd]], [[5eso|5eso]], [[5esu|5esu]]</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]] 1.729&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">menD, Rv0555 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</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=5erx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5erx OCA], [https://pdbe.org/5erx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5erx RCSB], [https://www.ebi.ac.uk/pdbsum/5erx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5erx ProSAT]</span></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=5erx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5erx OCA], [http://pdbe.org/5erx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5erx RCSB], [http://www.ebi.ac.uk/pdbsum/5erx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5erx ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MEND_MYCTU MEND_MYCTU]] 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).
+[https://www.uniprot.org/uniprot/MEND_MYCTU MEND_MYCTU] 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).
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase]]
+[[Category: Large Structures]]
-[[Category: Myctu]]
+[[Category: Mycobacterium tuberculosis H37Rv]]
-[[Category: Baker, E N]]
+[[Category: Baker EN]]
-[[Category: Bashiri, G]]
+[[Category: Bashiri G]]
-[[Category: Bulloch, E M.M]]
+[[Category: Bulloch EMM]]
-[[Category: Jirgis, E N.M]]
+[[Category: Jirgis ENM]]
-[[Category: Johnston, J M]]
+[[Category: Johnston JM]]
-[[Category: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase]]
-[[Category: Menaquinone biosynthesis]]
-[[Category: Mend]]
-[[Category: Pyruvate oxidase family]]
-[[Category: Thiamin-diphosphate dependent enzyme]]
-[[Category: Transferase]]

5erx

From Proteopedia

Revision as of 08:19, 12 July 2023

Crystal Structure of APO MenD from M. tuberculosis - I222

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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