3di0: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3di0.png|left|200px]]
-<!--
+==Crystal Structure of Dihydrodipicolinate synthase from Staphylococcus aureus==
-The line below this paragraph, containing "STRUCTURE_3di0", creates the "Structure Box" on the page.
+<StructureSection load='3di0' size='340' side='right'caption='[[3di0]], [[Resolution|resolution]] 2.38&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'>[[3di0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_COL Staphylococcus aureus subsp. aureus COL]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DI0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DI0 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]] 2.38&#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></td></tr>
-{{STRUCTURE_3di0|  PDB=3di0  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3di0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3di0 OCA], [https://pdbe.org/3di0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3di0 RCSB], [https://www.ebi.ac.uk/pdbsum/3di0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3di0 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DAPA_STAAC DAPA_STAAC] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).<ref>PMID:18671976</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/di/3di0_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=3di0 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Lysine biosynthesis is crucial for cell-wall formation in bacteria. Enzymes involved in lysine biosynthesis are thus potential targets for anti-microbial therapeutics. Dihydrodipicolinate synthase (DHDPS) catalyzes the first step of this pathway. Unlike its homologues, Staphylococcus aureus DHDPS is a dimer both in solution and in the crystal and is not feedback inhibited by lysine. The crystal structure of S. aureus DHDPS in the free and substrate bound forms provides a structural rationale for its catalytic mechanism. The structure also reveals unique conformational features of the S. aureus enzyme that could be crucial for the design of specific non-competitive inhibitors.
-===Crystal Structure of Dihydrodipicolinate synthase from Staphylococcus aureus===
+Structural and functional characterization of Staphylococcus aureus dihydrodipicolinate synthase.,Girish TS, Sharma E, Gopal B FEBS Lett. 2008 Aug 20;582(19):2923-30. Epub 2008 Jul 29. PMID:18671976<ref>PMID:18671976</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3di0" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18671976}}, adds the Publication Abstract to the page
+*[[Dihydrodipicolinate synthase|Dihydrodipicolinate synthase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18671976 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18671976}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-DI0 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_col Staphylococcus aureus subsp. aureus col]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DI0 OCA].
+[[Category: Staphylococcus aureus subsp. aureus COL]]
+[[Category: Tavarekere GS]]
-==Reference==
-<ref group="xtra">PMID:18671976</ref><references group="xtra"/>
-[[Category: Dihydrodipicolinate synthase]]
-[[Category: Staphylococcus aureus subsp. aureus col]]
-[[Category: Tavarekere, G S.]]
-[[Category: Amino-acid biosynthesis]]
-[[Category: Cytoplasm]]
-[[Category: Diaminopimelate biosynthesis]]
-[[Category: Dihydrodipicolinate synthase]]
-[[Category: Feeb-back inhibition]]
-[[Category: Lyase]]
-[[Category: Lysine biosynthesis]]
-[[Category: Ping-pong mechanism]]
-[[Category: Schiff base]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:21:13 2009''