Function and X-ray crystal structure of Escherichia coli YfdE

Area of Science:

• Biochemistry
• Microbiology
• Structural Biology

Background:

• Oxalate is absorbed by humans but not metabolized, leading to urinary stone formation.
• The bacterium Oxalobacter formigenes metabolizes oxalate via oxalyl-CoA decarboxylase (OXC).
• Class III CoA-transferases, like formyl-CoA:oxalate CoA-transferase (FCOCT), are widespread in bacteria.

Purpose of the Study:

• To characterize the function and structure of the Escherichia coli protein YfdE.
• To investigate the role of YfdE in oxalate metabolism and acid tolerance.
• To expand understanding of bacterial oxalate catabolism pathways.

Main Methods:

• Protein purification and in vitro characterization of YfdE.
• X-ray crystallography to determine the 2.1-Å crystal structure of YfdE.
• Functional analysis of YfdE and its orthologue UctC.

Main Results:

• YfdE was identified as acetyl-CoA:oxalate CoA-transferase (ACOCT).
• YfdE and UctC catalyze the reversible conversion of acetyl-CoA and oxalate to oxalyl-CoA and acetate.
• Distinctive active site loops in FCOCT and ACOCT appear to determine substrate specificity.

Conclusions:

• The discovery of ACOCT expands the known metabolic pathways involved in oxalate catabolism.
• YfdE contributes to oxalate-induced acid tolerance in E. coli.
• Understanding ACOCT and FCOCT active site loops may reveal mechanisms of substrate specificity in CoA-transferases.