3du0: Difference between revisions

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-{{Seed}}
-[[Image:3du0.jpg|left|200px]]
-<!--
+==E. coli dihydrodipicolinate synthase with first substrate, pyruvate, bound in active site==
-The line below this paragraph, containing "STRUCTURE_3du0", creates the "Structure Box" on the page.
+<StructureSection load='3du0' size='340' side='right'caption='[[3du0]], [[Resolution|resolution]] 2.00&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'>[[3du0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DU0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DU0 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
--->
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KPI:(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC+ACID'>KPI</scene></td></tr>
-{{STRUCTURE_3du0|  PDB=3du0  |  SCENE=  }}
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1yxc|1yxc]]</div></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapA, b2478, JW2463 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/4-hydroxy-tetrahydrodipicolinate_synthase 4-hydroxy-tetrahydrodipicolinate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.3.7 4.3.3.7] </span></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=3du0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3du0 OCA], [https://pdbe.org/3du0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3du0 RCSB], [https://www.ebi.ac.uk/pdbsum/3du0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3du0 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/du/3du0_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=3du0 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Dihydrodipicolinate synthase (DHDPS) mediates the key first reaction common to the biosynthesis of (S)-lysine and meso-diaminopimelate, molecules which play a crucial cross-linking role in bacterial cell walls. An effective inhibitor of DHDPS would represent a useful antibacterial agent; despite extensive effort, a suitable inhibitor has yet to be found. In an attempt to examine the specificity of the active site of DHDPS, the enzyme was cocrystallized with the substrate analogue oxaloacetate. The resulting crystals diffracted to 2.0 A resolution, but solution of the protein structure revealed that pyruvate was bound in the active site rather than oxaloacetic acid. Kinetic analysis confirmed that the decarboxylation of oxaloacetate was not catalysed by DHDPS and was instead a slow spontaneous chemical process.
-===E. coli dihydrodipicolinate synthase with first substrate, pyruvate, bound in active site===
+The high-resolution structure of dihydrodipicolinate synthase from Escherichia coli bound to its first substrate, pyruvate.,Devenish SR, Gerrard JA, Jameson GB, Dobson RC Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Dec 1;64(Pt 12):1092-5., doi: 10.1107/S1744309108033654. Epub 2008 Nov 28. PMID:19052357<ref>PMID:19052357</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3du0" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-DU0 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DU0 OCA].
+*[[Dihydrodipicolinate synthase|Dihydrodipicolinate synthase]]
-[[Category: Dihydrodipicolinate synthase]]
+== References ==
-[[Category: Escherichia coli]]
+<references/>
-[[Category: Devenish, S R.A.]]
+__TOC__
-[[Category: Dobson, R C.J.]]
+</StructureSection>
-[[Category: Gerrard, J A.]]
+[[Category: 4-hydroxy-tetrahydrodipicolinate synthase]]
-[[Category: Jameson, G B.]]
+[[Category: Ecoli]]
+[[Category: Large Structures]]
+[[Category: Devenish, S R.A]]
+[[Category: Dobson, R C.J]]
+[[Category: Gerrard, J A]]
+[[Category: Jameson, G B]]
 [[Category: Alpha/beta barrel]]
 [[Category: Amino-acid biosynthesis]]
-[[Category: Cytoplasm]]
 [[Category: Diaminopimelate biosynthesis]]
 [[Category: Lyase]]
@@ Line 29: / Line 53: @@
 [[Category: Schiff base]]
 [[Category: Tim barrel]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Nov 20 07:44:52 2008''