Structure of Dihydrofolate reductase from Mycobacterium tuberculosis in complex with NADPH and dihydrofolate

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

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Crystal structures of the closed form of Mycobacterium tuberculosis dihydrofolate reductase in complex with dihydrofolate and antifolates.

Ribeiro, J.A.Chavez-Pacheco, S.M.de Oliveira, G.S.Silva, C.D.S.Giudice, J.H.P.Libreros-Zuniga, G.A.Dias, M.V.B.

(2019) Acta Crystallogr D Struct Biol 75: 682-693

  • DOI: https://doi.org/10.1107/S205979831900901X
  • Primary Citation of Related Structures:  
    6NNC, 6NND, 6NNE, 6NNH, 6NNI

  • PubMed Abstract: 

    Tuberculosis is a disease caused by Mycobacterium tuberculosis and is the leading cause of death from a single infectious pathogen, with a high prevalence in developing countries in Africa and Asia. There still is a need for the development or repurposing of novel therapies to combat this disease owing to the long-term nature of current therapies and because of the number of reported resistant strains. Here, structures of dihydrofolate reductase from M. tuberculosis (MtDHFR), which is a key target of the folate pathway, are reported in complex with four antifolates, pyrimethamine, cycloguanil, diaverdine and pemetrexed, and its substrate dihydrofolate in order to understand their binding modes. The structures of all of these complexes were obtained in the closed-conformation state of the enzyme and a fine structural analysis indicated motion in key regions of the substrate-binding site and different binding modes of the ligands. In addition, the affinities, through K d measurement, of diaverdine and methotrexate have been determined; MtDHFR has a lower affinity (highest K d ) for diaverdine than pyrimethamine and trimethoprim, and a very high affinity for methotrexate, as expected. The structural comparisons and analysis described in this work provide new information about the plasticity of MtDHFR and the binding effects of different antifolates.

  • Organizational Affiliation

    Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrofolate reductase
A, B
159Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: folAdfrARv2763cMTV002.28c
Find proteins for P9WNX1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNX1 
Go to UniProtKB:  P9WNX1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WNX1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP (Subject of Investigation/LOI)
Query on NDP

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
C21 H30 N7 O17 P3
DHF (Subject of Investigation/LOI)
Query on DHF

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F [auth A],
M [auth B]
C19 H21 N7 O6
Query on SO4

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G [auth A]
H [auth A]
I [auth A]
J [auth A]
N [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B]
O4 S
Query on CO

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D [auth A],
E [auth A],
L [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.981α = 90
b = 70.863β = 90
c = 72.11γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Database references
  • Version 1.2: 2019-11-20
    Changes: Derived calculations
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations, Refinement description