E. coli Thioesterase I/Protease I/Lysophospholipase L1 in complexed with diethyl phosphono moiety

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.239 

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This is version 1.3 of the entry. See complete history


Crystal Structure of Escherichia coli Thioesterase I/Protease I/Lysophospholipase L1: Consensus Sequence Blocks Constitute the Catalytic Center of SGNH-hydrolases through a Conserved Hydrogen Bond Network

Lo, Y.-C.Lin, S.-C.Shaw, J.-F.Liaw, Y.-C.

(2003) J Mol Biol 330: 539-551

  • DOI: https://doi.org/10.1016/s0022-2836(03)00637-5
  • Primary Citation of Related Structures:  
    1IVN, 1J00, 1JRL

  • PubMed Abstract: 

    Escherichia coli thioesterase I (TAP) is a multifunctional enzyme possessing activities of thioesterase, esterase, arylesterase, protease, and lysophospholipase. In particular, TAP has stereoselectivity for amino acid derivative substrates, hence it is useful for the kinetic resolution of racemic mixtures of industrial chemicals. In the present work, the crystal structure of native TAP was determined at 1.9A, revealing a minimal SGNH-hydrolase fold. The structure of TAP in complex with a diethyl phosphono moiety (DEP) identified its catalytic triad, Ser10-Asp154-His157, and oxyanion hole, Ser10-Gly44-Asn73. The oxyanion hole of TAP consists of three residues each separated from the other by more than 3.5A, implying that all of them are highly polarized when substrate bound. The catalytic (His)C(epsilon1)-H...O=C hydrogen bond usually plays a role in the catalytic mechanisms of most serine hydrolases, however, there were none present in SGNH-hydrolases. We propose that the existence of the highly polarized tri-residue-constituted oxyanion hole compensates for the lack of a (His)C(epsilon1)-H...O=C hydrogen bond. This suggests that members of the SGNH-hydrolase family may employ a unique catalytic mechanism. In addition, most SGNH-hydrolases have low sequence identities and presently there is no clear criterion to define consensus sequence blocks. Through comparison of TAP and the three SGNH-hydrolase structures currently known, we have identified a unique hydrogen bond network which stabilizes the catalytic center: a newly discovered structural feature of SGNH-hydrolases. We have defined these consensus sequence blocks providing a basis for the sub-classification of SGNH-hydrolases.

  • Organizational Affiliation

    Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Neihu 114, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thioesterase I190Escherichia coliMutation(s): 1 
Gene Names: tesA/apeA/pldC
EC: 3.1.2 (PDB Primary Data), (PDB Primary Data)
Find proteins for P0ADA1 (Escherichia coli (strain K12))
Explore P0ADA1 
Go to UniProtKB:  P0ADA1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADA1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on SDP
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.239 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.907α = 90
b = 49.907β = 90
c = 171.898γ = 90
Software Package:
Software NamePurpose
XPRESSdata reduction
DIP2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description