3fyo: Difference between revisions

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-{{Seed}}
-[[Image:3fyo.png|left|200px]]
-<!--
+==Crystal structure of the triple mutant (N23C/D247E/P249A) of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis==
-The line below this paragraph, containing "STRUCTURE_3fyo", creates the "Structure Box" on the page.
+<StructureSection load='3fyo' size='340' side='right'caption='[[3fyo]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3fyo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_meningitidis_serogroup_B Neisseria meningitidis serogroup B]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FYO FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene></td></tr>
-{{STRUCTURE_3fyo|  PDB=3fyo  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3fyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyo OCA], [https://pdbe.org/3fyo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fyo RCSB], [https://www.ebi.ac.uk/pdbsum/3fyo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fyo ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/KDSA_NEIMB KDSA_NEIMB]
+== 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/fy/3fyo_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3fyo ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Two distinct groups of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS), a key enzyme of cell-wall biosynthesis, differ by their requirement for a divalent metal ion for enzymatic activity. The unique difference between these groups is the replacement of the metal-binding Cys by Asn. Substitution of just this Asn for a Cys in metal-independent KDO8PS does not create the obligate metal-ion dependency of natural metal-dependent enzymes. We describe how three or four mutations of the metal-independent KDO8PS from Neisseria meningitidis produce a fully functional, obligately metal-dependent KDO8PS. For the substitutions Asn23Cys, Asp247Glu (this Asp binds to the metal ion in all metal-dependent KDO8PS) and Pro249Ala, and for double and triple combinations, mutant enzymes that contained Cys in place of Asn showed an increase in activity in the presence of divalent metal ions. However, combining these mutations with substitution by Ser of the Cys residue in the conserved (246)CysAspGlyPro(249) motif of metal-independent KDO8PS created enzymes with obligate metal dependency. The quadruple mutant (Asn23Cys/Cys246Ser/Asp247Glu/Pro249Ala) showed comparable activity to wild-type enzymes only in the presence of metal ions, with maximum activity with Cd(2+), the metal ion that is strongly inhibitory at micromolar concentrations for the wild-type enzyme. In the absence of metal ions, activity was barely detectable for this quadruple mutant or for triple mutants bearing both Cys246Ser and Asn23Cys mutations. The structures of NmeKDO8PS and its Asn23Cys/Asp247Glu/Pro249Ala and quadruple mutants at pH 4.6 were characterized at resolutions better than 1.85 A. Aged crystals of the Asn23Cys/Asp247Glu/Pro249Ala mutant featured a Cys23-Cys246 disulfide linkage, explaining the spectral bleaching observed when this mutant was incubated with Cu(2+). Such bleaching was not observed for the quadruple mutant. Reverse evolution to a fully functional obligately metal-dependent KDO8PS has been achieved with just three directed mutations for enzymes that have, at best, 47% identity between metal-dependent and metal-independent pairs.
-===Crystal structure of the triple mutant (N23C/D247E/P249A) of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis===
+Reversing evolution: re-establishing obligate metal ion dependence in a metal-independent KDO8P synthase.,Cochrane FC, Cookson TV, Jameson GB, Parker EJ J Mol Biol. 2009 Jul 24;390(4):646-61. Epub 2009 May 15. PMID:19447118<ref>PMID:19447118</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3fyo" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-FYO is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Neisseria_meningitidis_serogroup_b Neisseria meningitidis serogroup b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYO OCA].
+*[[Kdo-8-phosphate synthase|Kdo-8-phosphate synthase]]
-[[Category: 3-deoxy-8-phosphooctulonate synthase]]
+== References ==
-[[Category: Neisseria meningitidis serogroup b]]
+<references/>
-[[Category: Cochrane, F P.]]
+__TOC__
-[[Category: Jameson, G B.]]
+</StructureSection>
-[[Category: Parker, E J.]]
+[[Category: Large Structures]]
-[[Category: Patchett, M L.]]
+[[Category: Neisseria meningitidis serogroup B]]
-[[Category: Biosynthesis]]
+[[Category: Cochrane FP]]
-[[Category: Cytoplasm]]
+[[Category: Jameson GB]]
-[[Category: Kdo8 kdop]]
+[[Category: Parker EJ]]
-[[Category: Kdo8p]]
+[[Category: Patchett ML]]
-[[Category: Kdop]]
-[[Category: Lipopolysaccharide]]
-[[Category: Lipopolysaccharide biosynthesis]]
-[[Category: Lyase]]
-[[Category: Manno-octulosonate]]
-[[Category: Synthase]]
-[[Category: Tim barrel]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 22 20:23:02 2009''