3BF8

1.1 resolution structure of ybfF, a new esterase from Escherichia coli: a unique substrate-binding crevice generated by domain arrangement

Summary for 3BF8

• Entry DOI: 10.2210/pdb3bf8/pdb
• Related: 3BF7
• Descriptor: Esterase YbfF, MALONIC ACID (3 entities in total)
• Functional Keywords: esterase, thioesterase, ybff, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 57412.87

Authors

Park, S.K.,Kim, J.S. (deposition date: 2007-11-21, release date: 2008-01-15, Last modification date: 2024-03-13)

Primary citation

Park, S.Y.,Lee, S.H.,Lee, J.,Nishi, K.,Kim, Y.S.,Jung, C.H.,Kim, J.S.
High-resolution structure of ybfF from Escherichia coli K12: a unique substrate-binding crevice generated by domain arrangement
J.Mol.Biol., 376:1426-1437, 2008

PubMed 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.

PubMed: 18215690
DOI: 10.1016/j.jmb.2007.12.062

Experimental method

X-RAY DIFFRACTION (1.68 Å)