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4dpw

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==Crystal structure of Staphylococcus epidermidis D283A mevalonate diphosphate decarboxylase complexed with mevalonate diphosphate and ATPgS==
==Crystal structure of Staphylococcus epidermidis D283A mevalonate diphosphate decarboxylase complexed with mevalonate diphosphate and ATPgS==
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<StructureSection load='4dpw' size='340' side='right' caption='[[4dpw]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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<StructureSection load='4dpw' size='340' side='right'caption='[[4dpw]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4dpw]] is a 8 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=4DPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DPW FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4dpw]] is a 8 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=4DPW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DPW FirstGlance]. <br>
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</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=DP6:(3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC+ACID'>DP6</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.605&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3qt5|3qt5]], [[3qt6|3qt6]], [[3qt7|3qt7]], [[3qt8|3qt8]], [[4dpt|4dpt]], [[4dpu|4dpu]], [[4dpx|4dpx]], [[4dpy|4dpy]], [[4du7|4du7]], [[4du8|4du8]]</td></tr>
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<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=DP6:(3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC+ACID'>DP6</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4dpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dpw OCA], [https://pdbe.org/4dpw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dpw RCSB], [https://www.ebi.ac.uk/pdbsum/4dpw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dpw ProSAT]</span></td></tr>
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<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>
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<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=4dpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dpw OCA], [http://pdbe.org/4dpw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dpw RCSB], [http://www.ebi.ac.uk/pdbsum/4dpw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dpw ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q9FD73_STAEP Q9FD73_STAEP]
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 4dpw" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Albococcus epidermidis winslow and winslow 1908]]
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[[Category: Large Structures]]
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[[Category: Diphosphomevalonate decarboxylase]]
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[[Category: Staphylococcus epidermidis]]
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[[Category: Barta, M L]]
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[[Category: Barta ML]]
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[[Category: Geisbrecht, B V]]
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[[Category: Geisbrecht BV]]
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[[Category: McWhorter, W J]]
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[[Category: McWhorter WJ]]
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[[Category: Ghmp kinase family]]
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[[Category: Lyase]]
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Current revision

Crystal structure of Staphylococcus epidermidis D283A mevalonate diphosphate decarboxylase complexed with mevalonate diphosphate and ATPgS

PDB ID 4dpw

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