1qhm: Difference between revisions

Revision as of 06:17, 3 May 2008

ESCHERICHIA COLI PYRUVATE FORMATE LYASE LARGE DOMAIN

OverviewOverview

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 StructureAbout this Structure

1QHM is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.

ReferenceReference

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 Page seeded by OCA on Sat May 3 06:17:00 2008

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OCA

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 [[Image:1qhm.jpg|left|200px]]
- {{Structure
+<!--
-|PDB= 1qhm |SIZE=350|CAPTION= <scene name='initialview01'>1qhm</scene>, resolution 2.80&Aring;
+The line below this paragraph, containing "STRUCTURE_1qhm", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND=
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <span class='plainlinks'>[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] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE= PFL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+-->
-|DOMAIN=
+{{STRUCTURE_1qhm|  PDB=1qhm  |  SCENE=  }}
-|RELATEDENTRY=
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qhm OCA], [http://www.ebi.ac.uk/pdbsum/1qhm PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1qhm RCSB]</span>
-}}
 '''ESCHERICHIA COLI PYRUVATE FORMATE LYASE LARGE DOMAIN'''
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 [[Category: Ollis, D L.]]
 [[Category: Wong, K K.]]
-[[Category: anaerobic]]
+[[Category: Anaerobic]]
-[[Category: enzyme mechanism]]
+[[Category: Enzyme mechanism]]
-[[Category: homodimer]]
+[[Category: Homodimer]]
-[[Category: pyruvate formate lyase]]
+[[Category: Pyruvate formate lyase]]
-[[Category: x-ray crystallography]]
+[[Category: X-ray crystallography]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 06:17:00 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:13:42 2008''