Crystal structure of the M. tuberculosis Lysine-epsilon aminotransferase (Rv3290c) complexed to an inhibitor

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.163 

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Mutational Analysis of Mycobacterium Tuberculosis Lysine Epsilon-Aminotransferase and Inhibitor Co-Crystal Structures, Reveals Distinct Binding Modes.

Tripathi, S.M.Agarwal, A.Ramachandran, R.

(2015) Biochem Biophys Res Commun 463: 154

  • DOI: https://doi.org/10.1016/j.bbrc.2015.05.055
  • Primary Citation of Related Structures:  
    2JJE, 2JJF, 2JJG, 2JJH

  • PubMed Abstract: 

    Lysine ɛ-aminotransferase (LAT) converts lysine to α-aminoadipate-δ-semialdehyde in a PLP-mediated reaction. We mutated active-site T330, N328 and E243, and structurally rationalized their properties. T330A and T330S mutants cannot bind PLP and are inactive. N328A although inactive, binds to PLP. E243A retains activity, but binds α-ketoglutarate in a different conformation. We had earlier identified 2-aminomethyl piperidine derivative as a LAT inhibitor. The co-crystal structure reveals that it mimics binding of C5 substrates and exhibits two binding modes. E243, that shields R422 in the apo enzyme, exhibits conformational changes to permit the binding of the inhibitor in one of the binding modes. Structure-based analysis of bound water in the active site suggests optimization strategies for synthesis of improved inhibitors.

  • Organizational Affiliation

    Molecular & Structural Biology Division, Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, U.P., India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-LYSINE EPSILON AMINOTRANSFERASE449Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WQ77 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQ77 
Go to UniProtKB:  P9WQ77
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WQ77
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on L18

Download Ideal Coordinates CCD File 
C [auth A](2S)-1-methyl-2-[(2S,4R)-2-methyl-4-phenylpentyl]piperidine
C18 H29 N
Query on PLP

Download Ideal Coordinates CCD File 
C8 H10 N O6 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.163 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.037α = 90
b = 103.037β = 90
c = 98.215γ = 120
Software Package:
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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2013-07-31
    Changes: Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2017-01-25
    Changes: Database references, Other, Structure summary