5z2p - Revision history

OCA at 08:44, 22 November 2023

2023-11-22T08:44:19Z

←Older revision		Revision as of 08:44, 22 November 2023
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	==ThDP-Mn2+ complex of R413K variant of EcMenD soaked with 2-ketoglutarate for 5 min==		==ThDP-Mn2+ complex of R413K variant of EcMenD soaked with 2-ketoglutarate for 5 min==
-	<StructureSection load='5z2p' size='340' side='right' caption='[[5z2p]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5z2p' size='340' side='right'caption='[[5z2p]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z2p]] 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=5Z2P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Z2P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z2p]] 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=5Z2P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z2P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=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]] 2.3Å</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='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=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=5z2p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z2p OCA], [https://pdbe.org/5z2p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z2p RCSB], [https://www.ebi.ac.uk/pdbsum/5z2p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z2p 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=5z2p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z2p OCA], [~~http~~://pdbe.org/5z2p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5z2p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5z2p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5z2p ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== 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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 2-~~succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase~~]]	+	[[Category: Escherichia coli K-12]]
-	[[Category: ~~Ecoli~~]]	+	[[Category: Large Structures]]
-	[[Category: Guo~~, Z H~~]]	+	[[Category: Guo ZH]]
-	[[Category: Qin~~, M M]]~~	+	[[Category: Qin MM]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 20:22, 2 December 2018

2018-12-02T20:22:54Z

←Older revision		Revision as of 20:22, 2 December 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5z2p is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==ThDP-Mn2+ complex of R413K variant of EcMenD soaked with 2-ketoglutarate for 5 min==
		+	<StructureSection load='5z2p' size='340' side='right' caption='[[5z2p]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5z2p]] 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=5Z2P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z2P FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=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='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=5z2p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z2p OCA], [http://pdbe.org/5z2p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z2p RCSB], [http://www.ebi.ac.uk/pdbsum/5z2p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z2p 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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The bacterial enzyme MenD, or 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) synthase, catalyzes an essential Stetter reaction in menaquinone (vitamin K2) biosynthesis via thiamine diphosphate (ThDP)-bound tetrahedral post-decarboxylation intermediates. The detailed mechanism of this intermediate chemistry, however, is still poorly understood, but of significant interest given that menaquinone is an essential electron transporter in many pathogenic bacteria. Here, we used site-directed mutagenesis, enzyme kinetic assays, and protein crystallography to reveal an active-inactive intermediate equilibrium in MenD catalysis and its modulation by two conserved active-site arginine residues. We observed that these conserved residues play a key role in shifting the equilibrium to the active intermediate by orienting the C2-succinyl group of the intermediates through strong ionic hydrogen bonding. We found that when this interaction is moderately weakened by amino acid substitutions, the resulting proteins are catalytically competent, with the C2-succinyl group taking either the active or the inactive orientation in the post-decarboxylation intermediate. When this hydrogen-bonding interaction was strongly weakened, the succinyl group was re-oriented by 180 degrees relative to the native intermediate, resulting in reversal of the stereochemistry at the reaction center that disabled catalysis. Interestingly, this inactive intermediate was formed with a distinct kinetic behavior, likely as a result of a nonnative mode of enzyme-substrate interaction. The mechanistic insights gained from these findings improve our understanding of the new ThDP-dependent catalysis. More importantly, the nonnative binding site of the inactive MenD intermediate uncovered here provides a new target for development of antibiotics.

-	~~Authors: Qin~~, M.M., ~~Guo~~, Z.H.	+	Two active site arginines are critical determinants of substrate binding and catalysis in MenD, a thiamine-dependent enzyme in menaquinone biosynthesis.,Qin M, Song H, Dai X, Chen Y, Guo Z Biochem J. 2018 Oct 19. pii: BCJ20180548. doi: 10.1042/BCJ20180548. PMID:30341164<ref>PMID:30341164</ref>

-	~~Description: ThDP-Mn2+ complex~~ of ~~R413K variant~~ of ~~EcMenD soaked with~~ 2-~~ketoglutarate for~~ 5 ~~min~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Qin, M.M]]	+	<div class="pdbe-citations 5z2p" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Guo, Z.H~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase]]
		+	[[Category: Ecoli]]
		+	[[Category: Guo, Z H]]
		+	[[Category: Qin, M M]]
		+	[[Category: Complex]]
		+	[[Category: Transferase]]

OCA at 04:57, 7 February 2018

2018-02-07T04:57:40Z

←Older revision		Revision as of 04:57, 7 February 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5z2p is ON HOLD	+	The entry 5z2p is ON HOLD until Paper Publication

	Authors: Qin, M.M., Guo, Z.H.		Authors: Qin, M.M., Guo, Z.H.

OCA: Protected "5z2p" [edit=sysop:move=sysop]

2018-01-10T07:06:23Z

Protected "5z2p" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:06, 10 January 2018

OCA: New page: '''Unreleased structure''' The entry 5z2p is ON HOLD Authors: Qin, M.M., Guo, Z.H. Description: ThDP-Mn2+ complex of R413K variant of EcMenD soaked with 2-ketoglutarate for 5 min [[Cat...

2018-01-10T07:06:22Z

New page: '''Unreleased structure''' The entry 5z2p is ON HOLD Authors: Qin, M.M., Guo, Z.H. Description: ThDP-Mn2+ complex of R413K variant of EcMenD soaked with 2-ketoglutarate for 5 min [[Cat...

New page

'''Unreleased structure'''

The entry 5z2p is ON HOLD

Authors: Qin, M.M., Guo, Z.H.

Description: ThDP-Mn2+ complex of R413K variant of EcMenD soaked with 2-ketoglutarate for 5 min
[[Category: Unreleased Structures]]
[[Category: Qin, M.M]]
[[Category: Guo, Z.H]]