1xpm: 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:1xpm.png|left|200px]]
-<!--
+==Crystal Structure of Staphylococcus aureus HMG-COA Synthase with HMG-CoA and Acetoacetyl-COA and Acetylated Cysteine==
-The line below this paragraph, containing "STRUCTURE_1xpm", creates the "Structure Box" on the page.
+<StructureSection load='1xpm' size='340' side='right'caption='[[1xpm]], [[Resolution|resolution]] 1.60&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'>[[1xpm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XPM 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]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAA:ACETOACETYL-COENZYME+A'>CAA</scene>, <scene name='pdbligand=HMG:3-HYDROXY-3-METHYLGLUTARYL-COENZYME+A'>HMG</scene>, <scene name='pdbligand=SCY:S-ACETYL-CYSTEINE'>SCY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1xpm|  PDB=1xpm  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xpm OCA], [https://pdbe.org/1xpm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xpm RCSB], [https://www.ebi.ac.uk/pdbsum/1xpm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xpm ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A0H3K1U2_STAAW A0A0H3K1U2_STAAW]
+== 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/xp/1xpm_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=1xpm ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The formation of carbon-carbon bonds via an acyl-enzyme intermediate plays a central role in fatty acid, polyketide, and isoprenoid biosynthesis. Uniquely among condensing enzymes, 3-hydroxy-3-methylglutaryl (HMG)-CoA synthase (HMGS) catalyzes the formation of a carbon-carbon bond by activating the methyl group of an acetylated cysteine. This reaction is essential in Gram-positive bacteria, and represents the first committed step in human cholesterol biosynthesis. Reaction kinetics, isotope exchange, and mass spectroscopy suggest surprisingly that HMGS is able to catalyze the "backwards" reaction in solution, where HMG-CoA is cleaved to form acetoacetyl-CoA (AcAc-CoA) and acetate. Here, we trap a complex of acetylated HMGS from Staphylococcus aureus and bound acetoacetyl-CoA by cryo-cooling enzyme crystals at three different times during the course of its back-reaction with its physiological product (HMG-CoA). This nonphysiological "backwards" reaction is used to understand the details of the physiological reaction with regards to individual residues involved in catalysis and substrate/product binding. The structures suggest that an active-site glutamic acid (Glu-79) acts as a general base both in the condensation between acetoacetyl-CoA and the acetylated enzyme, and the hydrolytic release of HMG-CoA from the enzyme. The ability to trap this enzyme-intermediate complex may suggest a role for protein dynamics and the interplay between protomers during the normal course of catalysis.
-===Crystal Structure of Staphylococcus aureus HMG-COA Synthase with HMG-CoA and Acetoacetyl-COA and Acetylated Cysteine===
+-hydroxy-3-methylglutaryl-CoA synthase intermediate complex observed in "real-time".,Theisen MJ, Misra I, Saadat D, Campobasso N, Miziorko HM, Harrison DH Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16442-7. Epub 2004 Oct 21. PMID:15498869<ref>PMID:15498869</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_15498869}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1xpm" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 15498869 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15498869}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-XPM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus Staphylococcus aureus subsp. aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XPM OCA].
+[[Category: Staphylococcus aureus]]
+[[Category: Campobasso N]]
-==Reference==
+[[Category: Harrison DHT]]
--hydroxy-3-methylglutaryl-CoA synthase intermediate complex observed in "real-time"., Theisen MJ, Misra I, Saadat D, Campobasso N, Miziorko HM, Harrison DH, Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16442-7. Epub 2004 Oct 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15498869 15498869]
+[[Category: Misra I]]
-[[Category: Hydroxymethylglutaryl-CoA synthase]]
+[[Category: Miziorko HM]]
-[[Category: Single protein]]
+[[Category: Saadat D]]
-[[Category: Staphylococcus aureus subsp. aureus]]
+[[Category: Theisen MJ]]
-[[Category: Campobasso, N.]]
-[[Category: Harrison, D H.T.]]
-[[Category: Misra, I.]]
-[[Category: Miziorko, H M.]]
-[[Category: Saadat, D.]]
-[[Category: Theisen, M J.]]
-[[Category: Cholesterol biosynthesis]]
-[[Category: Coenzyme some]]
-[[Category: Condensing enzyme]]
-[[Category: Hmg-coa synthase]]
-[[Category: Hmg]]
-[[Category: Thiolase fold]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 15:11:53 2008''