title: High-resolution structure of ybfF from Escherichia coli K12: a unique substrate-binding crevice generated by domain arrangement.
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.
authors.affiliation: Department of Chemistry and Institute of Basic Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, Korea.
authors.forename: Suk-Youl
authors.initials: SY
authors.lastname: Park
authors.forename: Sang-Hak
authors.initials: SH
authors.lastname: Lee
authors.forename: Jieun
authors.initials: J
authors.lastname: Lee
authors.forename: Kosuke
authors.initials: K
authors.lastname: Nishi
authors.forename: Yong-Sung
authors.initials: YS
authors.lastname: Kim
authors.forename: Che-Hun
authors.initials: CH
authors.lastname: Jung
authors.forename: Jeong-Sun
authors.initials: JS
authors.lastname: Kim
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D048168:Escherichia coli K12 / Q000737:chemistry*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D004950:Esterases / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment
chemical_list: D029968:Escherichia coli Proteins; D004950:Esterases; C526138:ybfF protein, E coli