2JJE

Crystal structure of T330S mutant of Rv3290c from M. tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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: 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 ...

    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. Electronic address: r_ravishankar@cdri.res.in.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-LYSINE EPSILON AMINOTRANSFERASEA449Mycobacterium tuberculosisMutation(s): 1 
EC: 2.6.1.36
UniProt
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download Ideal Coordinates CCD File 
B [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.244α = 90
b = 103.244β = 90
c = 98.195γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2020-01-15
    Changes: Advisory, Derived calculations, Other