Crystal structure of transaminase CC1012 complexed with PLP and L-alanine

Experimental Data Snapshot

  • Resolution: 1.98 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

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Mechanism-Guided Computational Design of omega-Transaminase by Reprograming of High-Energy-Barrier Steps.

Yang, L.Zhang, K.Xu, M.Xie, Y.Meng, X.Wang, H.Wei, D.

(2022) Angew Chem Int Ed Engl 61: e202212555-e202212555

  • DOI: https://doi.org/10.1002/anie.202212555
  • Primary Citation of Related Structures:  
    7YPM, 7YPN

  • PubMed Abstract: 

    ω-Transaminases (ω-TAs) show considerable potential for the synthesis of chiral amines. However, their low catalytic efficiency towards bulky substrates limits their application, and complicated catalytic mechanisms prevent precise enzyme design. Herein, we address this challenge using a mechanism-guided computational enzyme design strategy by reprograming the transition and ground states in key reaction steps. The common features among the three high-energy-barrier steps responsible for the low catalytic efficiency were revealed using quantum mechanics (QM). Five key residues were simultaneously tailored to stabilize the rate-limiting transition state with the aid of the Rosetta design. The 14 top-ranked variants showed 16.9-143-fold improved catalytic activity. The catalytic efficiency of the best variant, M9 (Q25F/M60W/W64F/I266A), was significantly increased, with a 1660-fold increase in k cat /K m and a 1.5-26.8-fold increase in turnover number (TON) towards various indanone derivatives.

  • Organizational Affiliation

    State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology East China University of Science and Technology, Shanghai, P. R. China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate aminotransferase family protein
A, B, C, D
474Caulobacter sp. D5Mutation(s): 5 
Gene Names: DMC18_08975
Find proteins for A0A318BC23 (Caulobacter sp. D5)
Explore A0A318BC23 
Go to UniProtKB:  A0A318BC23
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A318BC23
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PLP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
C8 H10 N O6 P
Query on PEG

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C4 H10 O3
Query on ALA

Download Ideal Coordinates CCD File 
F [auth A]
I [auth B]
J [auth B]
M [auth C]
O [auth D]
F [auth A],
I [auth B],
J [auth B],
M [auth C],
O [auth D],
P [auth D]
C3 H7 N O2
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A]1,2-ETHANEDIOL
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.98 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.968α = 90
b = 79.272β = 100.31
c = 173.845γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description