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1PT5

Crystal structure of gene yfdW of E. coli

Summary for 1PT5
Entry DOI10.2210/pdb1pt5/pdb
DescriptorHypothetical protein yfdW, ACETYL COENZYME *A (3 entities in total)
Functional Keywordstransferase, coenzyme binding, acetylcoa, structural genomics, unknown function
Biological sourceEscherichia coli, Shigella flexneri (,)
Total number of polymer chains2
Total formula weight98444.74
Authors
Gruez, A.,Roig-Zamboni, V.,Valencia, C.,Campanacci, V.,Cambillau, C. (deposition date: 2003-06-23, release date: 2003-09-09, Last modification date: 2024-04-03)
Primary citationGruez, A.,Roig-Zamboni, V.,Valencia, C.,Campanacci, V.,Cambillau, C.
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
J.Biol.Chem., 278:34582-34586, 2003
Cited by
PubMed Abstract: 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.
PubMed: 12844490
DOI: 10.1074/jbc.C300282200
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2 Å)
Structure validation

237735

数据于2025-06-18公开中

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