2oi2: Difference between revisions

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-[[Image:2oi2.jpg|left|200px]]
- {{Structure
+==Streptococcus pneumoniae Mevalonate Kinase in Complex with Diphosphomevalonate==
-|PDB= 2oi2 |SIZE=350|CAPTION= <scene name='initialview01'>2oi2</scene>, resolution 2.50&Aring;
+<StructureSection load='2oi2' size='340' side='right'caption='[[2oi2]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=DP6:(3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC+ACID'>DP6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
+<table><tr><td colspan='2'>[[2oi2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OI2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OI2 FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Mevalonate_kinase Mevalonate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.36 2.7.1.36] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-|GENE= mvk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1313 Streptococcus pneumoniae])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DP6:(3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC+ACID'>DP6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2oi2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oi2 OCA], [https://pdbe.org/2oi2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oi2 RCSB], [https://www.ebi.ac.uk/pdbsum/2oi2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oi2 ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2oi2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oi2 OCA], [http://www.ebi.ac.uk/pdbsum/2oi2 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2oi2 RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/A0A0H2UNK6_STRPN A0A0H2UNK6_STRPN]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oi/2oi2_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2oi2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Streptococcus pneumoniae, a ubiquitous gram-positive pathogen with an alarming, steadily evolving resistance to frontline antimicrobials, poses a severe global health threat both in the community and in the clinic. The recent discovery that diphosphomevalonate (DPM), an essential intermediate in the isoprenoid biosynthetic pathway, potently and allosterically inhibits S. pneumoniae mevalonate kinase (SpMK) without affecting the human isozyme established a new target and lead compound for antimicrobial design. Here we present the crystal structure of the first S. pneumoniae mevalonate kinase, at a resolution of 2.5 A and in complex with DPM.Mg(2+) in the active-site cleft. Structural comparison of SpMK with other members of the GHMP kinase family reveals that DPM functions as a partial bisubstrate analog (mevalonate linked to the pyrophosphoryl moiety of ATP) in that it elicits a ternary-complexlike form of the enzyme, except for localized disordering in a region that would otherwise interact with the missing portion of the nucleotide. Features of the SpMK-binding pockets are discussed in the context of established mechanistic findings and inherited human diseases linked to MK deficiency.
-'''Streptococcus pneumoniae Mevalonate Kinase in Complex with Diphosphomevalonate'''
+Crystal structure of the Streptococcus pneumoniae mevalonate kinase in complex with diphosphomevalonate.,Andreassi JL 2nd, Bilder PW, Vetting MW, Roderick SL, Leyh TS Protein Sci. 2007 May;16(5):983-9. Epub 2007 Mar 30. PMID:17400916<ref>PMID:17400916</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2oi2" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Streptococcus pneumoniae, a ubiquitous gram-positive pathogen with an alarming, steadily evolving resistance to frontline antimicrobials, poses a severe global health threat both in the community and in the clinic. The recent discovery that diphosphomevalonate (DPM), an essential intermediate in the isoprenoid biosynthetic pathway, potently and allosterically inhibits S. pneumoniae mevalonate kinase (SpMK) without affecting the human isozyme established a new target and lead compound for antimicrobial design. Here we present the crystal structure of the first S. pneumoniae mevalonate kinase, at a resolution of 2.5 A and in complex with DPM.Mg(2+) in the active-site cleft. Structural comparison of SpMK with other members of the GHMP kinase family reveals that DPM functions as a partial bisubstrate analog (mevalonate linked to the pyrophosphoryl moiety of ATP) in that it elicits a ternary-complexlike form of the enzyme, except for localized disordering in a region that would otherwise interact with the missing portion of the nucleotide. Features of the SpMK-binding pockets are discussed in the context of established mechanistic findings and inherited human diseases linked to MK deficiency.
+*[[Mevalonate kinase|Mevalonate kinase]]
+== References ==
-==About this Structure==
+<references/>
-OI2 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OI2 OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-Crystal structure of the Streptococcus pneumoniae mevalonate kinase in complex with diphosphomevalonate., Andreassi JL 2nd, Bilder PW, Vetting MW, Roderick SL, Leyh TS, Protein Sci. 2007 May;16(5):983-9. Epub 2007 Mar 30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17400916 17400916]
-[[Category: Mevalonate kinase]]
-[[Category: Single protein]]
 [[Category: Streptococcus pneumoniae]]
-[[Category: Andreassi, J L.]]
+[[Category: Andreassi JL]]
-[[Category: Bilder, P W.]]
+[[Category: Bilder PW]]
-[[Category: Leyh, T S.]]
+[[Category: Leyh TS]]
-[[Category: Roderick, S L.]]
+[[Category: Roderick SL]]
-[[Category: Vetting, M W.]]
+[[Category: Vetting MW]]
-[[Category: enzyme-inhibitor complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:18:09 2008''