4dpt - Revision history

OCA at 14:41, 14 March 2024

2024-03-14T14:41:52Z

←Older revision		Revision as of 14:41, 14 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dpt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_epidermidis Staphylococcus epidermidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DPT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DPT FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dpt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_epidermidis Staphylococcus epidermidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DPT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DPT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=FM0:(3R)-3-(FLUOROMETHYL)-3-HYDROXY-5-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PENTANOIC+ACID'>FM0</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.191Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=FM0:(3R)-3-(FLUOROMETHYL)-3-HYDROXY-5-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PENTANOIC+ACID'>FM0</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=4dpt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dpt OCA], [https://pdbe.org/4dpt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dpt RCSB], [https://www.ebi.ac.uk/pdbsum/4dpt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dpt ProSAT]</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=4dpt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dpt OCA], [https://pdbe.org/4dpt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dpt RCSB], [https://www.ebi.ac.uk/pdbsum/4dpt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dpt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/Q9FD73_STAEP Q9FD73_STAEP]]	+	[https://www.uniprot.org/uniprot/Q9FD73_STAEP Q9FD73_STAEP]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Mevalonate diphosphate decarboxylase (MDD) catalyzes the final step of the mevalonate pathway, the Mg(2+)-ATP dependent decarboxylation of mevalonate 5-diphosphate (MVAPP), producing isopentenyl diphosphate (IPP). Synthesis of IPP, an isoprenoid precursor molecule that is a critical intermediate in peptidoglycan and polyisoprenoid biosynthesis, is essential in Gram-positive bacteria (e.g., Staphylococcus, Streptococcus, and Enterococcus spp.), and thus the enzymes of the mevalonate pathway are ideal antimicrobial targets. MDD belongs to the GHMP superfamily of metabolite kinases that have been extensively studied for the past 50 years, yet the crystallization of GHMP kinase ternary complexes has proven to be difficult. To further our understanding of the catalytic mechanism of GHMP kinases with the purpose of developing broad spectrum antimicrobial agents that target the substrate and nucleotide binding sites, we report the crystal structures of wild-type and mutant (S192A and D283A) ternary complexes of Staphylococcus epidermidis MDD. Comparison of apo, MVAPP-bound, and ternary complex wild-type MDD provides structural information about the mode of substrate binding and the catalytic mechanism. Structural characterization of ternary complexes of catalytically deficient MDD S192A and D283A (k(cat) decreased 10(3)- and 10(5)-fold, respectively) provides insight into MDD function. The carboxylate side chain of invariant Asp(283) functions as a catalytic base and is essential for the proper orientation of the MVAPP C3-hydroxyl group within the active site funnel. Several MDD amino acids within the conserved phosphate binding loop ("P-loop") provide key interactions, stabilizing the nucleotide triphosphoryl moiety. The crystal structures presented here provide a useful foundation for structure-based drug design.	+
-		+
-	Structural Basis for Nucleotide Binding and Reaction Catalysis in Mevalonate Diphosphate Decarboxylase.,Barta ML, McWhorter WJ, Miziorko HM, Geisbrecht BV Biochemistry. 2012 Jul 6. PMID:22734632<ref>PMID:22734632</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 4dpt" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:33, 21 September 2022

2022-09-21T08:33:41Z

←Older revision		Revision as of 08:33, 21 September 2022
Line 1:		Line 1:

	==Crystal structure of Staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with inhibitor 6-FMVAPP and ATPgS==		==Crystal structure of Staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with inhibitor 6-FMVAPP and ATPgS==
-	<StructureSection load='4dpt' size='340' side='right' caption='[[4dpt]], [[Resolution\|resolution]] 2.19Å' scene=''>	+	<StructureSection load='4dpt' size='340' side='right'caption='[[4dpt]], [[Resolution\|resolution]] 2.19Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4dpt]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"albococcus_epidermidis"_winslow_and_winslow_1908 "albococcus~~ epidermidis~~" winslow and winslow 1908~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DPT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4DPT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4dpt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_epidermidis Staphylococcus epidermidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DPT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DPT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=FM0:(3R)-3-(FLUOROMETHYL)-3-HYDROXY-5-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PENTANOIC+ACID'>FM0</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=FM0:(3R)-3-(FLUOROMETHYL)-3-HYDROXY-5-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PENTANOIC+ACID'>FM0</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qt5\|3qt5]], [[3qt6\|3qt6]], [[3qt7\|3qt7]], [[3qt8\|3qt8]], [[4dpu\|4dpu]], [[4dpw\|4dpw]], [[4dpx\|4dpx]], [[4dpy\|4dpy]], [[4du7\|4du7]], [[4du8\|4du8]]</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=4dpt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dpt OCA], [https://pdbe.org/4dpt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dpt RCSB], [https://www.ebi.ac.uk/pdbsum/4dpt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dpt ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mvaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1282 "Albococcus epidermidis" Winslow and Winslow 1908])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diphosphomevalonate_decarboxylase Diphosphomevalonate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.33 4.1.1.33] </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=4dpt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dpt OCA], [~~http~~://pdbe.org/4dpt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4dpt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4dpt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4dpt ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/Q9FD73_STAEP Q9FD73_STAEP]]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Albococcus epidermidis winslow and winslow 1908~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Diphosphomevalonate decarboxylase~~]]	+	[[Category: Staphylococcus epidermidis]]
-	[[Category: Barta~~, M L~~]]	+	[[Category: Barta ML]]
-	[[Category: Geisbrecht~~, B V~~]]	+	[[Category: Geisbrecht BV]]
-	[[Category: McWhorter~~, W J]]~~	+	[[Category: McWhorter WJ]]
-	~~[[Category: Ghmp kinase family]]~~	+
-	~~[[Category: Lyase-lyase inhibitor complex~~]]	+

OCA at 15:50, 11 August 2016

2016-08-11T15:50:55Z

←Older revision		Revision as of 15:50, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with inhibitor 6-FMVAPP and ATPgS==		==Crystal structure of Staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with inhibitor 6-FMVAPP and ATPgS==
	<StructureSection load='4dpt' size='340' side='right' caption='[[4dpt]], [[Resolution\|resolution]] 2.19Å' scene=''>		<StructureSection load='4dpt' size='340' side='right' caption='[[4dpt]], [[Resolution\|resolution]] 2.19Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4dpt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Staphylococcus_epidermidis Staphylococcus~~ epidermidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DPT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DPT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4dpt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"albococcus_epidermidis"_winslow_and_winslow_1908 "albococcus epidermidis" winslow and winslow 1908]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DPT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DPT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=FM0:(3R)-3-(FLUOROMETHYL)-3-HYDROXY-5-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PENTANOIC+ACID'>FM0</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=FM0:(3R)-3-(FLUOROMETHYL)-3-HYDROXY-5-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PENTANOIC+ACID'>FM0</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qt5\|3qt5]], [[3qt6\|3qt6]], [[3qt7\|3qt7]], [[3qt8\|3qt8]], [[4dpu\|4dpu]], [[4dpw\|4dpw]], [[4dpx\|4dpx]], [[4dpy\|4dpy]], [[4du7\|4du7]], [[4du8\|4du8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qt5\|3qt5]], [[3qt6\|3qt6]], [[3qt7\|3qt7]], [[3qt8\|3qt8]], [[4dpu\|4dpu]], [[4dpw\|4dpw]], [[4dpx\|4dpx]], [[4dpy\|4dpy]], [[4du7\|4du7]], [[4du8\|4du8]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mvaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1282 ~~Staphylococcus~~ epidermidis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mvaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1282 "Albococcus epidermidis" Winslow and Winslow 1908])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diphosphomevalonate_decarboxylase Diphosphomevalonate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.33 4.1.1.33] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diphosphomevalonate_decarboxylase Diphosphomevalonate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.33 4.1.1.33] </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=4dpt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dpt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dpt RCSB], [http://www.ebi.ac.uk/pdbsum/4dpt PDBsum]</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=4dpt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dpt OCA], [http://pdbe.org/4dpt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dpt RCSB], [http://www.ebi.ac.uk/pdbsum/4dpt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dpt ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4dpt" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Albococcus epidermidis winslow and winslow 1908]]
	[[Category: Diphosphomevalonate decarboxylase]]		[[Category: Diphosphomevalonate decarboxylase]]
-	[[Category: Staphylococcus epidermidis]]
	[[Category: Barta, M L]]		[[Category: Barta, M L]]
	[[Category: Geisbrecht, B V]]		[[Category: Geisbrecht, B V]]

OCA at 13:13, 5 January 2015

2015-01-05T13:13:50Z

OCA at 07:49, 9 July 2014

2014-07-09T07:49:29Z

←Older revision		Revision as of 07:49, 9 July 2014
Line 1:		Line 1:
-	[[~~Image:~~4dpt.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of Staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with inhibitor 6-FMVAPP and ATPgS==
		+	<StructureSection load='4dpt' size='340' side='right' caption='[[4dpt]], [[Resolution\|resolution]] 2.19Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4dpt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_epidermidis Staphylococcus epidermidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DPT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DPT FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=FM0:(3R)-3-(FLUOROMETHYL)-3-HYDROXY-5-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PENTANOIC+ACID'>FM0</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qt5\|3qt5]], [[3qt6\|3qt6]], [[3qt7\|3qt7]], [[3qt8\|3qt8]], [[4dpu\|4dpu]], [[4dpw\|4dpw]], [[4dpx\|4dpx]], [[4dpy\|4dpy]], [[4du7\|4du7]], [[4du8\|4du8]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mvaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1282 Staphylococcus epidermidis])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diphosphomevalonate_decarboxylase Diphosphomevalonate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.33 4.1.1.33] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4dpt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dpt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dpt RCSB], [http://www.ebi.ac.uk/pdbsum/4dpt PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mevalonate diphosphate decarboxylase (MDD) catalyzes the final step of the mevalonate pathway, the Mg(2+)-ATP dependent decarboxylation of mevalonate 5-diphosphate (MVAPP), producing isopentenyl diphosphate (IPP). Synthesis of IPP, an isoprenoid precursor molecule that is a critical intermediate in peptidoglycan and polyisoprenoid biosynthesis, is essential in Gram-positive bacteria (e.g., Staphylococcus, Streptococcus, and Enterococcus spp.), and thus the enzymes of the mevalonate pathway are ideal antimicrobial targets. MDD belongs to the GHMP superfamily of metabolite kinases that have been extensively studied for the past 50 years, yet the crystallization of GHMP kinase ternary complexes has proven to be difficult. To further our understanding of the catalytic mechanism of GHMP kinases with the purpose of developing broad spectrum antimicrobial agents that target the substrate and nucleotide binding sites, we report the crystal structures of wild-type and mutant (S192A and D283A) ternary complexes of Staphylococcus epidermidis MDD. Comparison of apo, MVAPP-bound, and ternary complex wild-type MDD provides structural information about the mode of substrate binding and the catalytic mechanism. Structural characterization of ternary complexes of catalytically deficient MDD S192A and D283A (k(cat) decreased 10(3)- and 10(5)-fold, respectively) provides insight into MDD function. The carboxylate side chain of invariant Asp(283) functions as a catalytic base and is essential for the proper orientation of the MVAPP C3-hydroxyl group within the active site funnel. Several MDD amino acids within the conserved phosphate binding loop ("P-loop") provide key interactions, stabilizing the nucleotide triphosphoryl moiety. The crystal structures presented here provide a useful foundation for structure-based drug design.

-	~~{{STRUCTURE_4dpt\| PDB=4dpt \| SCENE= }}~~	+	Structural Basis for Nucleotide Binding and Reaction Catalysis in Mevalonate Diphosphate Decarboxylase.,Barta ML, McWhorter WJ, Miziorko HM, Geisbrecht BV Biochemistry. 2012 Jul 6. PMID:22734632<ref>PMID:22734632</ref>

-	~~===Crystal structure~~ of ~~Staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with inhibitor 6-FMVAPP and ATPgS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_22734632}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[4dpt]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Staphylococcus_epidermidis Staphylococcus epidermidis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4DPT OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022734632<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Diphosphomevalonate decarboxylase]]		[[Category: Diphosphomevalonate decarboxylase]]
	[[Category: Staphylococcus epidermidis]]		[[Category: Staphylococcus epidermidis]]

OCA at 06:35, 3 October 2012

2012-10-03T06:35:05Z

←Older revision		Revision as of 06:35, 3 October 2012
Line 1:		Line 1:
-	[[Image:4dpt.~~jpg~~\|left\|200px]]	+	[[Image:4dpt.png\|left\|200px]]

	{{STRUCTURE_4dpt\| PDB=4dpt \| SCENE= }}		{{STRUCTURE_4dpt\| PDB=4dpt \| SCENE= }}

OCA at 08:14, 11 July 2012

2012-07-11T08:14:43Z

←Older revision		Revision as of 08:14, 11 July 2012
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-	~~'''Unreleased structure'''~~	+	[[Image:4dpt.jpg\|left\|200px]]

-	~~The entry~~ 4dpt ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4dpt\| PDB=4dpt \| SCENE= }}

-	~~Authors: Barta, M.L., McWhorter, W.J., Geisbrecht, B.V.~~	+	===Crystal structure of Staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with inhibitor 6-FMVAPP and ATPgS===

-	~~Description: Crystal~~ structure of Staphylococcus epidermidis ~~mevalonate diphosphate~~ decarboxylase ~~complexed with inhibitor 6~~-~~FMVAPP and ATPgS~~	+	{{ABSTRACT_PUBMED_22734632}}
		+
		+	==About this Structure==
		+	[[4dpt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_epidermidis Staphylococcus epidermidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DPT OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022734632</ref><references group="xtra"/>
		+	[[Category: Diphosphomevalonate decarboxylase]]
		+	[[Category: Staphylococcus epidermidis]]
		+	[[Category: Barta, M L.]]
		+	[[Category: Geisbrecht, B V.]]
		+	[[Category: McWhorter, W J.]]
		+	[[Category: Ghmp kinase family]]
		+	[[Category: Lyase-lyase inhibitor complex]]

OCA at 08:24, 29 February 2012

2012-02-29T08:24:11Z

←Older revision		Revision as of 08:24, 29 February 2012
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4dpt is ON HOLD	+	The entry 4dpt is ON HOLD until Paper Publication

	Authors: Barta, M.L., McWhorter, W.J., Geisbrecht, B.V.		Authors: Barta, M.L., McWhorter, W.J., Geisbrecht, B.V.

	Description: Crystal structure of Staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with inhibitor 6-FMVAPP and ATPgS		Description: Crystal structure of Staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with inhibitor 6-FMVAPP and ATPgS

OCA: Protected "4dpt" [edit=sysop:move=sysop]

2012-02-22T07:32:27Z

Protected "4dpt" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:32, 22 February 2012

OCA: New page: '''Unreleased structure''' The entry 4dpt is ON HOLD Authors: Barta, M.L., McWhorter, W.J., Geisbrecht, B.V. Description: Crystal structure of Staphylococcus epidermidis mevalonate dip...

2012-02-22T07:32:26Z

New page: '''Unreleased structure''' The entry 4dpt is ON HOLD Authors: Barta, M.L., McWhorter, W.J., Geisbrecht, B.V. Description: Crystal structure of Staphylococcus epidermidis mevalonate dip...

New page

'''Unreleased structure'''

The entry 4dpt is ON HOLD

Authors: Barta, M.L., McWhorter, W.J., Geisbrecht, B.V.

Description: Crystal structure of Staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with inhibitor 6-FMVAPP and ATPgS

←Older revision		Revision as of 13:13, 5 January 2015
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dpt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_epidermidis Staphylococcus epidermidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DPT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DPT FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dpt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_epidermidis Staphylococcus epidermidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DPT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DPT FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=FM0:(3R)-3-(FLUOROMETHYL)-3-HYDROXY-5-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PENTANOIC+ACID'>FM0</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=FM0:(3R)-3-(FLUOROMETHYL)-3-HYDROXY-5-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PENTANOIC+ACID'>FM0</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qt5\|3qt5]], [[3qt6\|3qt6]], [[3qt7\|3qt7]], [[3qt8\|3qt8]], [[4dpu\|4dpu]], [[4dpw\|4dpw]], [[4dpx\|4dpx]], [[4dpy\|4dpy]], [[4du7\|4du7]], [[4du8\|4du8]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qt5\|3qt5]], [[3qt6\|3qt6]], [[3qt7\|3qt7]], [[3qt8\|3qt8]], [[4dpu\|4dpu]], [[4dpw\|4dpw]], [[4dpx\|4dpx]], [[4dpy\|4dpy]], [[4du7\|4du7]], [[4du8\|4du8]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mvaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1282 Staphylococcus epidermidis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mvaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1282 Staphylococcus epidermidis])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diphosphomevalonate_decarboxylase Diphosphomevalonate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.33 4.1.1.33] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diphosphomevalonate_decarboxylase Diphosphomevalonate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.33 4.1.1.33] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4dpt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dpt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dpt RCSB], [http://www.ebi.ac.uk/pdbsum/4dpt PDBsum]</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=4dpt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dpt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dpt RCSB], [http://www.ebi.ac.uk/pdbsum/4dpt PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	[[Category: Diphosphomevalonate decarboxylase]]		[[Category: Diphosphomevalonate decarboxylase]]
	[[Category: Staphylococcus epidermidis]]		[[Category: Staphylococcus epidermidis]]
-	[[Category: Barta, M L.]]	+	[[Category: Barta, M L]]
-	[[Category: Geisbrecht, B V.]]	+	[[Category: Geisbrecht, B V]]
-	[[Category: McWhorter, W J.]]	+	[[Category: McWhorter, W J]]
	[[Category: Ghmp kinase family]]		[[Category: Ghmp kinase family]]
	[[Category: Lyase-lyase inhibitor complex]]		[[Category: Lyase-lyase inhibitor complex]]