4G8Z

pcDHFR K37S/F69N double mutant TMP NADPH ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.259 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Kinetic and Structural Analysis for Potent Antifolate Inhibition of Pneumocystis jirovecii, Pneumocystis carinii, and Human Dihydrofolate Reductases and Their Active-Site Variants.

Cody, V.Pace, J.Queener, S.F.Adair, O.O.Gangjee, A.

(2013) Antimicrob.Agents Chemother. 57: 2669-2677

  • DOI: 10.1128/AAC.00172-13
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A major concern of immunocompromised patients, in particular those with AIDS, is susceptibility to infection caused by opportunistic pathogens such as Pneumocystis jirovecii, which is a leading cause of pneumonia in immunocompromised patients. We rep ...

    A major concern of immunocompromised patients, in particular those with AIDS, is susceptibility to infection caused by opportunistic pathogens such as Pneumocystis jirovecii, which is a leading cause of pneumonia in immunocompromised patients. We report the first kinetic and structural data for 2,4-diamino-6-[(2',5'-dichloro anilino)methyl]pyrido[2,3-d]pyrimidine (OAAG324), a potent inhibitor of dihydrofolate reductase (DHFR) from P. jirovecii (pjDHFR), and also for trimethoprim (TMP) and methotrexate (MTX) with pjDHFR, Pneumocystis carinii DHFR (pcDHFR), and human DHFR (hDHFR). OAAG324 shows a 9.0-fold selectivity for pjDHFR (Ki, 2.7 nM) compared to its selectivity for hDHFR (Ki, 24.4 nM), whereas there is only a 2.3-fold selectivity for pcDHFR (Ki, 6.3 nM). In order to understand the determinants of inhibitory potency, active-site mutations of pj-, pc-, and hDHFR were explored to make these enzymes more like each other. The most unexpected observations were that the variant pcDHFR forms with K37Q and K37Q/F69N mutations, which made the enzyme more like the human form, also made these enzymes more sensitive to the inhibitory activity of OAAG324, with Ki values of 0.26 and 0.71 nM, respectively. A similar gain in sensitivity was also observed for the hDHFR N64F variant, which showed a lower Ki value (0.58 nM) than native hDHFR, pcDHFR, or pjDHFR. Structural data are reported for complexes of OAAG324 with hDHFR and its Q35K and Q35S/N64F variants and for the complex of the K37S/F69N variant of pcDHFR with TMP. These results provide useful insight into the role of these residues in the optimization of highly selective inhibitors of DHFR against the opportunistic pathogen P. jirovecii.


    Organizational Affiliation

    Structural Biology Department, Hauptman Woodward Medical Research Institute, Buffalo, New York, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrofolate reductase
X
204Pneumocystis cariniiMutation(s): 2 
EC: 1.5.1.3
Find proteins for P16184 (Pneumocystis carinii)
Go to UniProtKB:  P16184
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TOP
Query on TOP

Download SDF File 
Download CCD File 
X
TRIMETHOPRIM
C14 H18 N4 O3
IEDVJHCEMCRBQM-UHFFFAOYSA-N
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
X
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TOPIC50: 12000 - 43000 nM (95) BINDINGDB
TOPKi: 151.4 - 152 nM (95) BINDINGDB
TOPKi: 227 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.259 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 37.157α = 90.00
b = 42.783β = 94.78
c = 59.172γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data collection
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-07-23 
  • Released Date: 2013-05-29 
  • Deposition Author(s): Cody, V.

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release