2qmw: Difference between revisions

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-[[Image:2qmw.png|left|200px]]
-<!--
+==The crystal structure of the prephenate dehydratase (PDT) from Staphylococcus aureus subsp. aureus Mu50==
-The line below this paragraph, containing "STRUCTURE_2qmw", creates the "Structure Box" on the page.
+<StructureSection load='2qmw' size='340' side='right'caption='[[2qmw]], [[Resolution|resolution]] 2.30&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'>[[2qmw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staam Staam]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2iq8 2iq8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QMW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QMW 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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
--->
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_2qmw|  PDB=2qmw  |  SCENE=  }}
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SAV1915 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=158878 STAAM])</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=2qmw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qmw OCA], [https://pdbe.org/2qmw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qmw RCSB], [https://www.ebi.ac.uk/pdbsum/2qmw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qmw ProSAT], [https://www.topsan.org/Proteins/MCSG/2qmw TOPSAN]</span></td></tr>
+</table>
+== 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/qm/2qmw_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=2qmw ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The enzyme prephenate dehydratase (PDT) converts prephenate to phenylpyruvate in L-phenylalanine biosynthesis. PDT is allosterically regulated by L-Phe and other amino acids. We report the first crystal structures of PDT from Staphylococcus aureus in a relaxed (R) state and PDT from Chlorobium tepidum in a tense (T) state. The two enzymes show low sequence identity (27.3%) but the same prototypic architecture and domain organization. Both enzymes are tetramers (dimer of dimers) in crystal and solution while a PDT dimer can be regarded as a basic catalytic unit. The N-terminal PDT domain consists of two similar subdomains with a cleft in between, which hosts the highly conserved active site. In one PDT dimer two clefts are aligned to form an extended active site across the dimer interface. Similarly at the interface two ACT regulatory domains create two highly conserved pockets. Upon binding of the L-Phe inside the pockets, PDT transits from an open to a closed conformation.
-===The crystal structure of the prephenate dehydratase (PDT) from Staphylococcus aureus subsp. aureus Mu50===
+Structures of open (R) and close (T) states of prephenate dehydratase (PDT)--implication of allosteric regulation by L-phenylalanine.,Tan K, Li H, Zhang R, Gu M, Clancy ST, Joachimiak A J Struct Biol. 2008 Apr;162(1):94-107. Epub 2007 Nov 29. PMID:18171624<ref>PMID:18171624</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18171624}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2qmw" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18171624 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18171624}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[2qmw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus Staphylococcus aureus subsp. aureus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2iq8 2iq8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QMW OCA].
+[[Category: Staam]]
+[[Category: Gu, M]]
-==Reference==
+[[Category: Joachimiak, A]]
-<ref group="xtra">PMID:018171624</ref><references group="xtra"/>
+[[Category: Li, H]]
-[[Category: Staphylococcus aureus subsp. aureus]]
+[[Category: Structural genomic]]
-[[Category: Gu, M.]]
+[[Category: Tan, K]]
-[[Category: Joachimiak, A.]]
+[[Category: Zhang, R]]
-[[Category: Li, H.]]
-[[Category: MCSG, Midwest Center for Structural Genomics.]]
-[[Category: Tan, K.]]
-[[Category: Zhang, R.]]
 [[Category: Apc85812]]
 [[Category: Mcsg]]
-[[Category: Midwest center for structural genomic]]
+[[Category: PSI, Protein structure initiative]]
-[[Category: Protein structure initiative]]
-[[Category: Psi-2]]
 [[Category: Staphylococcus aureus subsp. aureus mu50]]
-[[Category: Structural genomic]]
 [[Category: Unknown function]]