1qhm: Difference between revisions

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:1qhm.jpg|left|200px]]<br /><applet load="1qhm" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1qhm, resolution 2.80&Aring;" />
-'''ESCHERICHIA COLI PYRUVATE FORMATE LYASE LARGE DOMAIN'''<br />
-==Overview==
+==ESCHERICHIA COLI PYRUVATE FORMATE LYASE LARGE DOMAIN==
-BACKGROUND: Pyruvate formate lyase (PFL) catalyses a key step in, Escherichia coli anaerobic glycolysis by converting pyruvate and CoA to, formate and acetylCoA. The PFL mechanism involves an unusual radical, cleavage of pyruvate, involving an essential C alpha radical of Gly734 and, two cysteine residues, Cys418 and Cys419, which may form thiyl radicals, required for catalysis. We undertook this study to understand the, structural basis for catalysis. RESULTS: The first structure of a fragment, of PFL (residues 1-624) at 2.8 A resolution shows an unusual barrel-like, structure, with a catalytic beta finger carrying Cys418 and Cys419, inserted into the centre of the barrel. Several residues near the, active-site cysteines can be ascribed roles in the catalytic mechanism:, Arg176 and Arg435 are positioned near Cys419 and may bind pyruvate/formate, and Trp333 partially buries Cys418. Both cysteine residues are accessible, to each other owing to their cis relationship at the tip of the beta, finger. Finally, two clefts that may serve as binding sites for CoA and, pyruvate have been identified. CONCLUSIONS: PFL has striking structural, homology to the aerobic ribonucleotide reductase (RNR): the superposition, of PFL and RNR includes eight of the ten strands in the unusual RNR, alpha/beta barrel as well as the beta finger, which carries key catalytic, residues in both enzymes. This provides the first structural proof that, RNRs and PFLs are related by divergent evolution from a common ancestor.
+<StructureSection load='1qhm' size='340' side='right'caption='[[1qhm]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1qhm]] is a 2 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=1QHM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QHM FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</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=1qhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qhm OCA], [https://pdbe.org/1qhm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qhm RCSB], [https://www.ebi.ac.uk/pdbsum/1qhm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qhm 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/qh/1qhm_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=1qhm ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+BACKGROUND: Pyruvate formate lyase (PFL) catalyses a key step in Escherichia coli anaerobic glycolysis by converting pyruvate and CoA to formate and acetylCoA. The PFL mechanism involves an unusual radical cleavage of pyruvate, involving an essential C alpha radical of Gly734 and two cysteine residues, Cys418 and Cys419, which may form thiyl radicals required for catalysis. We undertook this study to understand the structural basis for catalysis. RESULTS: The first structure of a fragment of PFL (residues 1-624) at 2.8 A resolution shows an unusual barrel-like structure, with a catalytic beta finger carrying Cys418 and Cys419 inserted into the centre of the barrel. Several residues near the active-site cysteines can be ascribed roles in the catalytic mechanism: Arg176 and Arg435 are positioned near Cys419 and may bind pyruvate/formate and Trp333 partially buries Cys418. Both cysteine residues are accessible to each other owing to their cis relationship at the tip of the beta finger. Finally, two clefts that may serve as binding sites for CoA and pyruvate have been identified. CONCLUSIONS: PFL has striking structural homology to the aerobic ribonucleotide reductase (RNR): the superposition of PFL and RNR includes eight of the ten strands in the unusual RNR alpha/beta barrel as well as the beta finger, which carries key catalytic residues in both enzymes. This provides the first structural proof that RNRs and PFLs are related by divergent evolution from a common ancestor.
-==About this Structure==
+Pyruvate formate lyase is structurally homologous to type I ribonucleotide reductase.,Leppanen VM, Merckel MC, Ollis DL, Wong KK, Kozarich JW, Goldman A Structure. 1999 Jul 15;7(7):733-44. PMID:10425676<ref>PMID:10425676</ref>
-QHM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Active as [http://en.wikipedia.org/wiki/Formate_C-acetyltransferase Formate C-acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.54 2.3.1.54] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1QHM OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Pyruvate formate lyase is structurally homologous to type I ribonucleotide reductase., Leppanen VM, Merckel MC, Ollis DL, Wong KK, Kozarich JW, Goldman A, Structure. 1999 Jul 15;7(7):733-44. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10425676 10425676]
+</div>
+<div class="pdbe-citations 1qhm" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Formate C-acetyltransferase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Goldman A]]
-[[Category: Goldman, A.]]
+[[Category: Kozarich JW]]
-[[Category: Kozarich, J.W.]]
+[[Category: Leppanen V-M]]
-[[Category: Leppanen, V.M.]]
+[[Category: Merckel MC]]
-[[Category: Merckel, M.C.]]
+[[Category: Ollis DL]]
-[[Category: Ollis, D.L.]]
+[[Category: Wong KK]]
-[[Category: Wong, K.K.]]
-[[Category: anaerobic]]
-[[Category: enzyme mechanism]]
-[[Category: homodimer]]
-[[Category: pyruvate formate lyase]]
-[[Category: x-ray crystallography]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:42:33 2007''