Structure Report for: 3BF7

Park, S.Y., Lee, S.H., Lee, J., Kosuke, N., Kim, Y.S., Jung, C.H., Kim, J.S.

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


ESTHER: Park_2008_J.Mol.Biol_376_1426
PubMedSearch: Park 2008 J.Mol.Biol 376 1426
PubMedID: 18215690
Gene_locus related to this paper: ecoli-ybff

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.



        

Title: Crystallization and preliminary X-ray diffraction analysis of ybfF, a new esterase from Escherichia coli K12
Park SY, Lee SH, Lee J, Jung CH, Kim JS
Ref: Acta Crystallographica Sect F Struct Biol Cryst Commun, 63:1051, 2007 : PubMed
Abstract


ESTHER: Park_2007_Acta.Crystallogr.Sect.F.Struct.Biol.Cryst.Commun_63_1051
PubMedSearch: Park 2007 Acta.Crystallogr.Sect.F.Struct.Biol.Cryst.Commun 63 1051
PubMedID: 18084091
Gene_locus related to this paper: ecoli-ybff

Abstract

The product of the recently discovered ybfF gene, which belongs to the esterase family, does not show high sequence similarity to other esterases. To provide the molecular background to the enzymatic mechanism of the ybfF esterase, the ybfF protein from Escherichia coli K12 (Ec_ybfF) was cloned, expressed and purified. The Ec_ybfF protein was crystallized from 60% Tacsimate and 0.1 M bis-Tris propane buffer pH 7.0. Diffraction data were collected to 1.10 A resolution using synchrotron radiation. The crystal belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 66.09, b = 90.71, c = 92.88 A. With two Ec_ybfF molecules in the asymmetric unit, the crystal volume per unit protein weight is 2.17 A(3) Da(-1), corresponding to a solvent content of 42%.