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

Experimental Data Snapshot

  • Resolution: 1.68 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

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High-resolution structure of ybfF from Escherichia coli K12: a unique substrate-binding crevice generated by domain arrangement

Park, S.Y.Lee, S.H.Lee, J.Nishi, K.Kim, Y.S.Jung, C.H.Kim, J.S.

(2008) J Mol Biol 376: 1426-1437

  • DOI: https://doi.org/10.1016/j.jmb.2007.12.062
  • Primary Citation of Related Structures:  
    3BF7, 3BF8

  • 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.

  • Organizational Affiliation

    Department of Chemistry and Institute of Basic Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Esterase YbfF
A, B
255Escherichia coliMutation(s): 2 
EC: 3.1
Find proteins for P75736 (Escherichia coli (strain K12))
Explore P75736 
Go to UniProtKB:  P75736
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP75736
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.68 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.216α = 90
b = 91.061β = 90
c = 93.253γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-04-29
    Changes: Non-polymer description
  • Version 1.3: 2015-08-19
    Changes: Source and taxonomy
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations