High-resolution structure of ybfF from Escherichia coli K12: A unique substrate-binding crevice generated by domain arrangement
SCOPUS
- Title
- High-resolution structure of ybfF from Escherichia coli K12: A unique substrate-binding crevice generated by domain arrangement
- Authors
- Park, SY; Lee, SH; Lee, J; Nishi, K; Kim, YS; Jung, CH; Kim, JS
- Date Issued
- 2008-03
- Publisher
- Academic Press
- 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 angstrom, 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. (c) 2007 Elsevier Ltd. All rights reserved.
- URI
- https://oasis.postech.ac.kr/handle/2014.oak/109128
- DOI
- 10.1016/j.jmb.2007.12.062
- ISSN
- 0022-2836
- Article Type
- Article
- Citation
- Journal of Molecular Biology, vol. 376, no. 5, page. 1426 - 1437, 2008-03
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