Crystal structure of Rv3772 encoded aminotransferase

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

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Crystal structures of Mycobacterium tuberculosis HspAT and ArAT reveal structural basis of their distinct substrate specificities

Nasir, N.Anant, A.Vyas, R.Biswal, B.K.

(2016) Sci Rep 6: 18880-18880

  • DOI: https://doi.org/10.1038/srep18880
  • Primary Citation of Related Structures:  
    4R2N, 4R5Z

  • PubMed Abstract: 

    Aminotransferases of subfamily Iβ, which include histidinol phosphate aminotransferases (HspATs) and aromatic amino acid aminotransferases (ArATs), are structurally similar but possess distinct substrate specificities. This study, encompassing structural and biochemical characterisation of HspAT and ArAT from Mycobacterium tuberculosis demonstrates that the residues lining the substrate binding pocket and N-terminal lid are the primary determinants of their substrate specificities. In mHspAT, hydrophilic residues in the substrate binding pocket and N-terminal lid allow the entry and binding of its preferential substrate, Hsp. On the other hand, the hydrophobic nature of both the substrate binding pocket and the N-terminal lid of mArAT is responsible for the discrimination of a polar substrate such as Hsp, while facilitating the binding of Phe and other aromatic residues such as Tyr and Trp. In addition, the present study delineates the ligand induced conformational rearrangements, providing insights into the plasticity of aminotransferases. Furthermore, the study also demonstrates that the adventitiously bound ligand 2-(N-morpholino)ethanesulfonic acid (MES) is indeed a specific inhibitor of HspAT. These results suggest that previously untapped morpholine-ring scaffold compounds could be explored for the design of new anti-TB agents.

  • Organizational Affiliation

    Protein Crystallography Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative phenylalanine aminotransferase
A, B, C, D
367Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: patP425_03929RVBD_3772
EC: 2.6.1
Find proteins for P9WML5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WML5 
Go to UniProtKB:  P9WML5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WML5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PMP

Download Ideal Coordinates CCD File 
EA [auth D],
F [auth A],
O [auth B],
X [auth C]
C8 H13 N2 O5 P
Query on EPE

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CA [auth C],
JA [auth D],
M [auth A],
V [auth B]
C8 H18 N2 O4 S
Query on SIN

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DA [auth D],
E [auth A],
N [auth B],
W [auth C]
C4 H6 O4
Query on GOL

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AA [auth C]
BA [auth C]
FA [auth D]
G [auth A]
GA [auth D]
AA [auth C],
BA [auth C],
FA [auth D],
G [auth A],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
K [auth A],
L [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
Y [auth C],
Z [auth C]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 256.92α = 90
b = 77.556β = 90
c = 117.914γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2016-12-07
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description