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3bf7
From Proteopedia
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| , resolution 1.1Å | |||||||
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| Gene: | K12 (Escherichia coli) | ||||||
| Related: | 3BF8
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
1.1 resolution structure of ybfF, a new esterase from Escherichia coli: a unique substrate-binding crevice generated by domain arrangement
Overview
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.
About this Structure
3BF7 is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
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, J Mol Biol. 2008 Mar 7;376(5):1426-37. Epub 2008 Jan 4. PMID:18215690
Page seeded by OCA on Mon Mar 31 05:25:46 2008
Categories: Escherichia coli | Single protein | Kim, J S. | Park, S K. | Esterase | Helical cap | Hydrolase | Thioesterase | Ybff
