3den: Difference between revisions

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-{{Seed}}
-[[Image:3den.png|left|200px]]
-<!--
+==Structure of E. coli DHDPS mutant Y107W==
-The line below this paragraph, containing "STRUCTURE_3den", creates the "Structure Box" on the page.
+<StructureSection load='3den' size='340' side='right'caption='[[3den]], [[Resolution|resolution]] 2.20&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'>[[3den]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DEN 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]] 2.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=KGC:N~6~-[(2R)-2-CARBOXY-5-OXOTETRAHYDROFURAN-2-YL]-L-LYSINE'>KGC</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-{{STRUCTURE_3den|  PDB=3den  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3den FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3den OCA], [https://pdbe.org/3den PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3den RCSB], [https://www.ebi.ac.uk/pdbsum/3den PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3den ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DAPA_ECOLI DAPA_ECOLI] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).<ref>PMID:20503968</ref> <ref>PMID:8993314</ref>
+== 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/de/3den_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=3den ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Dihydrodipicolinate synthase (DHDPS) is a tetrameric enzyme that is the first enzyme unique to the ( S)-lysine biosynthetic pathway in plants and bacteria. Previous studies have looked at the important role of Tyr107, an amino acid residue located at the tight-dimer interface between two monomers, in participating in a catalytic triad of residues during catalysis. In this study, we examine the importance of this residue in determining the quaternary structure of the DHDPS enzyme. The Tyr107 residue was mutated to tryptophan, and structural, biophysical, and kinetic studies were carried out on the mutant enzyme. These revealed that while the solid-state structure of the mutant enzyme was largely unchanged, as judged by X-ray crystallography, it exists as a mixture of primarily monomer and tetramer in solution, as determined by analytical ultracentrifugation, size-exclusion chromatography, and mass spectrometry. The catalytic ability of the DHDPS enzyme was reduced by the mutation, which also allowed the adventitious binding of alpha-ketoglutarate to the active site. A reduction in the apparent melting temperature of the mutant enzyme was observed. Thus, the tetrameric quaternary structure of DHDPS is critical to controlling specificity, heat stability, and intrinsic activity.
-===Structure of E. coli DHDPS mutant Y107W===
+Mutating the tight-dimer interface of dihydrodipicolinate synthase disrupts the enzyme quaternary structure: toward a monomeric enzyme.,Pearce FG, Dobson RC, Weber A, Lane LA, McCammon MG, Squire MA, Perugini MA, Jameson GB, Robinson CV, Gerrard JA Biochemistry. 2008 Nov 18;47(46):12108-17. Epub 2008 Oct 21. PMID:18937497<ref>PMID:18937497</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3den" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18937497}}, adds the Publication Abstract to the page
+*[[Dihydrodipicolinate synthase|Dihydrodipicolinate synthase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18937497 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18937497}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia coli K-12]]
-DEN is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEN OCA].
+[[Category: Large Structures]]
+[[Category: Gerrard JA]]
-==Reference==
+[[Category: Jameson GB]]
-Mutating the tight-dimer interface of dihydrodipicolinate synthase disrupts the enzyme quaternary structure: toward a monomeric enzyme., Pearce FG, Dobson RC, Weber A, Lane LA, McCammon MG, Squire MA, Perugini MA, Jameson GB, Robinson CV, Gerrard JA, Biochemistry. 2008 Nov 18;47(46):12108-17. Epub 2008 Oct 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18937497 18937497]
+[[Category: Pearce FG]]
-[[Category: Dihydrodipicolinate synthase]]
+[[Category: Perugini MA]]
-[[Category: Escherichia coli k-12]]
-[[Category: Gerrard, J A.]]
-[[Category: Jameson, G B.]]
-[[Category: Pearce, F G.]]
-[[Category: Perugini, M A.]]
-[[Category: Amino-acid biosynthesis]]
-[[Category: Cytoplasm]]
-[[Category: Diaminopimelate biosynthesis]]
-[[Category: Dihydrodipicolinate synthase]]
-[[Category: Lyase]]
-[[Category: Lysine biosynthesis]]
-[[Category: Monomer]]
-[[Category: Quaternary structure]]
-[[Category: Schiff base]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Dec  5 09:52:30 2008''