3gon: Difference between revisions

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-[[Image:3gon.png|left|200px]]
-{{STRUCTURE_3gon|  PDB=3gon  |  SCENE=  }}
+==Streptococcus pneumoniae Phosphomevalonate Kinase in Complex with Phosphomevalonate and AMPPNP==
+<StructureSection load='3gon' size='340' side='right'caption='[[3gon]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3gon]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_R6 Streptococcus pneumoniae R6]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pg9 2pg9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GON OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GON FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PMV:(3R)-3-HYDROXY-3-METHYL-5-(PHOSPHONOOXY)PENTANOIC+ACID'>PMV</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=3gon FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gon OCA], [https://pdbe.org/3gon PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gon RCSB], [https://www.ebi.ac.uk/pdbsum/3gon PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gon ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8DR49_STRR6 Q8DR49_STRR6]
+== 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/go/3gon_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=3gon ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The galacto-, homoserine-, mevalonate-, phosphomevalonate-kinase (GHMP) superfamily encompases a wide-range of protein function. Three members of the family (mevalonate kinase, phosphomevalonate kinase, and diphosphomevalonate decarboxylase) comprise the mevalonate pathway found in S. pneumoniae and other organisms. We have determined the 1.9 A crystal structure of phosphomevalonate kinase (PMK) from S. pneumoniae in complex with phosphomevalonate and AMPPNP.Mg(2+). Comparison of the apo and ternary PMK structures suggests that ligand binding reverses the side-chain orientations of two antiparallel lysines residues (100 and 101) with the result that Lys101 is switched into a position in which its ammonium ion is in direct contact with the beta,gamma-bridging atom of the nucleotide, where it is expected to stabilize both the ground and transition states of the reaction. Analysis of all available GHMP kinase ternary complex structures reveals that while their C(alpha)-scaffolds are highly conserved, their substrates bind in one of two conformations, which appear to be either reactive or nonreactive. The active site of PMK seems spacious enough to accommodate interconversion of the reactive and nonreactive conformers. A substantial fraction of the PMK active site is occupied by ordered water, which clusters near the charged regions of the substrate. Notably, a water pentamer that interacts extensively with the reactive groups of both substrates was discovered at the active site.
-===Streptococcus pneumoniae Phosphomevalonate Kinase in Complex with Phosphomevalonate and AMPPNP===
+Structure of the ternary complex of phosphomevalonate kinase: the enzyme and its family.,Andreassi JL 2nd, Vetting MW, Bilder PW, Roderick SL, Leyh TS Biochemistry. 2009 Jul 14;48(27):6461-8. PMID:19485344<ref>PMID:19485344</ref>
-{{ABSTRACT_PUBMED_19485344}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3gon" style="background-color:#fffaf0;"></div>
-[[3gon]] is a 1 chain structure with 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=3GON OCA].
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:019485344</ref><references group="xtra"/>
+</StructureSection>
-[[Category: Phosphomevalonate kinase]]
+[[Category: Large Structures]]
-[[Category: Streptococcus pneumoniae]]
+[[Category: Streptococcus pneumoniae R6]]
-[[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: Atp-binding]]
-[[Category: Ghmp kinase superfamily]]
-[[Category: Kinase]]
-[[Category: Nucleotide-binding]]
-[[Category: Transferase]]