1pt7: Difference between revisions
New page: left|200px<br /><applet load="1pt7" size="450" color="white" frame="true" align="right" spinBox="true" caption="1pt7, resolution 1.80Å" /> '''Crystal structure of... |
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[[Image:1pt7.jpg|left|200px]]<br /><applet load="1pt7" size=" | [[Image:1pt7.jpg|left|200px]]<br /><applet load="1pt7" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1pt7, resolution 1.80Å" /> | caption="1pt7, resolution 1.80Å" /> | ||
'''Crystal structure of the apo-form of the yfdW gene product of E. coli'''<br /> | '''Crystal structure of the apo-form of the yfdW gene product of E. coli'''<br /> | ||
==Overview== | ==Overview== | ||
Because of its toxicity, oxalate accumulation from amino acid catabolism | Because of its toxicity, oxalate accumulation from amino acid catabolism leads to acute disorders in mammals. Gut microflora are therefore pivotal in maintaining a safe intestinal oxalate balance through oxalate degradation. Oxalate catabolism was first identified in Oxalobacter formigenes, a specialized, strictly anaerobic bacterium. Oxalate degradation was found to be performed successively by two enzymes, a formyl-CoA transferase (frc) and an oxalate decarboxylase (oxc). These two genes are present in several bacterial genomes including that of Escherichia coli. The frc ortholog in E. coli is yfdW, with which it shares 61% sequence identity. We have expressed the YfdW open reading frame product and solved its crystal structure in the apo-form and in complex with acetyl-CoA and with a mixture of acetyl-CoA and oxalate. YfdW exhibits a novel and spectacular fold in which two monomers assemble as interlaced rings, defining the CoA binding site at their interface. From the structure of the complex with acetyl-CoA and oxalate, we propose a putative formyl/oxalate transfer mechanism involving the conserved catalytic residue Asp169. The similarity of yfdW with bacterial orthologs (approximately 60% identity) and paralogs (approximately 20-30% identity) suggests that this new fold and parts of the CoA transfer mechanism are likely to be the hallmarks of a wide family of CoA transferases. | ||
==About this Structure== | ==About this Structure== | ||
1PT7 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli,_and_shigella_flexneri Escherichia coli, and shigella flexneri] with PO4 and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | 1PT7 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli,_and_shigella_flexneri Escherichia coli, and shigella flexneri] with <scene name='pdbligand=PO4:'>PO4</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PT7 OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: structural genomics]] | [[Category: structural genomics]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:32:18 2008'' | ||
Revision as of 15:32, 21 February 2008
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Crystal structure of the apo-form of the yfdW gene product of E. coli
OverviewOverview
Because of its toxicity, oxalate accumulation from amino acid catabolism leads to acute disorders in mammals. Gut microflora are therefore pivotal in maintaining a safe intestinal oxalate balance through oxalate degradation. Oxalate catabolism was first identified in Oxalobacter formigenes, a specialized, strictly anaerobic bacterium. Oxalate degradation was found to be performed successively by two enzymes, a formyl-CoA transferase (frc) and an oxalate decarboxylase (oxc). These two genes are present in several bacterial genomes including that of Escherichia coli. The frc ortholog in E. coli is yfdW, with which it shares 61% sequence identity. We have expressed the YfdW open reading frame product and solved its crystal structure in the apo-form and in complex with acetyl-CoA and with a mixture of acetyl-CoA and oxalate. YfdW exhibits a novel and spectacular fold in which two monomers assemble as interlaced rings, defining the CoA binding site at their interface. From the structure of the complex with acetyl-CoA and oxalate, we propose a putative formyl/oxalate transfer mechanism involving the conserved catalytic residue Asp169. The similarity of yfdW with bacterial orthologs (approximately 60% identity) and paralogs (approximately 20-30% identity) suggests that this new fold and parts of the CoA transfer mechanism are likely to be the hallmarks of a wide family of CoA transferases.
About this StructureAbout this Structure
1PT7 is a Single protein structure of sequence from Escherichia coli, and shigella flexneri with and as ligands. Full crystallographic information is available from OCA.
ReferenceReference
The crystal structure of the Escherichia coli YfdW gene product reveals a new fold of two interlaced rings identifying a wide family of CoA transferases., Gruez A, Roig-Zamboni V, Valencia C, Campanacci V, Cambillau C, J Biol Chem. 2003 Sep 5;278(36):34582-6. Epub 2003 Jul 3. PMID:12844490
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