1h17: Difference between revisions

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-{{Seed}}
-[[Image:1h17.png|left|200px]]
-<!--
+==Pyruvate Formate-Lyase (E.coli) in complex with CoA and the substrate analog oxamate==
-The line below this paragraph, containing "STRUCTURE_1h17", creates the "Structure Box" on the page.
+<StructureSection load='1h17' size='340' side='right'caption='[[1h17]], [[Resolution|resolution]] 1.75&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'>[[1h17]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H17 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1H17 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]] 1.75&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=DTL:L-TREITOL'>DTL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OXM:OXAMIC+ACID'>OXM</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
-{{STRUCTURE_1h17|  PDB=1h17  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1h17 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h17 OCA], [https://pdbe.org/1h17 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h17 RCSB], [https://www.ebi.ac.uk/pdbsum/1h17 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h17 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PFLB_ECOLI PFLB_ECOLI]
+== 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/h1/1h17_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=1h17 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The glycyl radical enzyme pyruvate formate-lyase (PFL) synthesizes acetyl-CoA and formate from pyruvate and CoA. With the crystal structure of the non-radical form of PFL in complex with its two substrates, we have trapped the moment prior to pyruvate cleavage. The structure reveals how the active site aligns the scissile bond of pyruvate for radical attack, prevents non-radical side reactions of the pyruvate, and confines radical migration. The structure shows CoA in a syn conformation awaiting pyruvate cleavage. By changing to an anti conformation, without affecting the adenine binding mode of CoA, the thiol of CoA could pick up the acetyl group resulting from pyruvate cleavage.
-===PYRUVATE FORMATE-LYASE (E.COLI) IN COMPLEX WITH COA AND THE SUBSTRATE ANALOG OXAMATE===
+X-ray structure of pyruvate formate-lyase in complex with pyruvate and CoA. How the enzyme uses the Cys-418 thiyl radical for pyruvate cleavage.,Becker A, Kabsch W J Biol Chem. 2002 Oct 18;277(42):40036-42. Epub 2002 Aug 5. PMID:12163496<ref>PMID:12163496</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_12163496}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1h17" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 12163496 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12163496}}
+__TOC__
+</StructureSection>
-==About this Structure==
-H17 is a [[Single protein]] structure of sequence 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=1H17 OCA].
-==Reference==
-X-ray structure of pyruvate formate-lyase in complex with pyruvate and CoA. How the enzyme uses the Cys-418 thiyl radical for pyruvate cleavage., Becker A, Kabsch W, J Biol Chem. 2002 Oct 18;277(42):40036-42. Epub 2002 Aug 5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12163496 12163496]
 [[Category: Escherichia coli]]
-[[Category: Formate C-acetyltransferase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Becker A]]
-[[Category: Becker, A.]]
+[[Category: Kabsch W]]
-[[Category: Kabsch, W.]]
-[[Category: Acyltransferase acetylation]]
-[[Category: Glycyl radical enzyme]]
-[[Category: Lyase]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 06:27:13 2008''