Hydrocinnamic acid-bound structure of SRHEPT mutant of E. coli aspartate aminotransferase

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

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Narrowing substrate specificity in a directly evolved enzyme: the A293D mutant of aspartate aminotransferase

Chow, M.A.McElroy, K.E.Corbett, K.D.Berger, J.M.Kirsch, J.F.

(2004) Biochemistry 43: 12780-12787

  • DOI: https://doi.org/10.1021/bi0487544
  • Primary Citation of Related Structures:  
    1TOE, 1TOG, 1TOI, 1TOJ, 1TOK

  • PubMed Abstract: 

    Several mutant Escherichia coli aspartate aminotransferases (eAATases) have been characterized in the attempt to evolve or rationally redesign the substrate specificity of eAATase into that of E. coli tyrosine aminotransferase (eTATase). These include HEX (designed), HEX + A293D (design followed by directed evolution), and SRHEPT (directed evolution). The A293D mutation realized from directed evolution of HEX is here imported into the SRHEPT platform by site-directed mutagenesis, resulting in an enzyme (SRHEPT + A293D) with nearly the same ratio of k(cat)/K(m)(Phe) to k(cat)/K(m)(Asp) as that of wild-type eTATase. The A293D substitution is an important specificity determinant; it selectively disfavors interactions with dicarboxylic substrates and inhibitors compared to aromatic ones. Context dependence analysis is generalized to provide quantitative comparisons of a common substitution in two or more different protein scaffolds. High-resolution crystal structures of ligand complexes of HEX + A293D, SRHEPT, and SRHEPT + A293D were determined. We find that in both SRHEPT + A293D and HEX + A293D, the additional mutation holds the Arg 292 side chain away from the active site to allow increased specificity for phenylalanine over aspartate. The resulting movement of Arg 292 allows greater flexibility of the small domain in HEX + A293D. While HEX is always in the closed conformation, HEX + A293D is observed in both the closed and a novel open conformation, allowing for more rapid product release.

  • Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3206, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate aminotransferase396Escherichia coliMutation(s): 8 
Gene Names: ASPCB0928
Find proteins for P00509 (Escherichia coli (strain K12))
Explore P00509 
Go to UniProtKB:  P00509
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00509
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HCI

Download Ideal Coordinates CCD File 
C9 H10 O2
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on LLP
Binding Affinity Annotations 
IDSourceBinding Affinity
HCI PDBBind:  1TOJ Kd: 4.10e+5 (nM) from 1 assay(s)
Binding MOAD:  1TOJ Kd: 4.10e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.412α = 90
b = 156.03β = 90
c = 77.865γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-23
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-11-15
    Changes: Data collection