Park_2008_J.Mol.Biol_376_1426

Reference

Title : High-resolution structure of ybfF from Escherichia coli K12: a unique substrate-binding crevice generated by domain arrangement. - Park_2008_J.Mol.Biol_376_1426
Author(s) : Park SY , Lee SH , Lee J , Nishi K , Kim YS , Jung CH , Kim JS
Ref : Journal of Molecular Biology , 376 :1426 , 2008
Abstract :

Esterases are one of the most common enzymes and are involved in diverse cellular functions. ybfF protein from Escherichia coli (Ec_ybfF) belongs to the esterase family for the large substrates, palmitoyl coenzyme A and malonyl coenzyme A, which are important cellular intermediates for energy conversion and biomolecular synthesis. To obtain molecular information on ybfF esterase, which is found in a wide range of microorganisms, we elucidated the crystal structures of Ec_ybfF in complexes with small molecules at resolutions of 1.1 and 1.68 A, respectively. The structure of Ec_ybfF is composed of a globular alpha/beta hydrolase domain with a three-helical bundle cap, which is linked by a kinked helix to the alpha/beta hydrolase domain. It contains a catalytic tetrad of Ser-His-Asp-Ser with the first Ser acting as a nucleophile. The unique spatial arrangement and orientation of the helical cap with respect to the alpha/beta hydrolase domain form a substrate-binding crevice for large substrates. The helical cap is also directly involved in catalysis by providing a substrate anchor, viz., the conserved residues of Arg123 and Tyr208. The high-resolution structure of Ec_ybfF shows that the inserted helical bundle structure and its spatial orientation with respect to the alpha/beta hydrolase domain are critical for creating a large inner space and constituting a specific active site, thereby providing the broad substrate spectrum toward large biomolecules.

PubMedSearch : Park_2008_J.Mol.Biol_376_1426
PubMedID: 18215690
Gene_locus related to this paper: ecoli-ybff

Related information

Substrate Malonyl-CoA    Palmitoyl-CoA
Gene_locus Malonyl-CoA    Palmitoyl-CoA    ecoli-ybff
Family Malonyl-CoA    Palmitoyl-CoA    ecoli-ybff    ABHD11-Acetyl_transferase
Structure Malonyl-CoA    Palmitoyl-CoA    ecoli-ybff    ABHD11-Acetyl_transferase    3BF7    3BF8

Citations formats

Park SY, Lee SH, Lee J, Nishi K, Kim YS, Jung CH, Kim JS (2008)
High-resolution structure of ybfF from Escherichia coli K12: a unique substrate-binding crevice generated by domain arrangement.
Journal of Molecular Biology 376 :1426

Park SY, Lee SH, Lee J, Nishi K, Kim YS, Jung CH, Kim JS (2008)
Journal of Molecular Biology 376 :1426