1VJ3

STRUCTURAL STUDIES ON BIO-ACTIVE COMPOUNDS. CRYSTAL STRUCTURE AND MOLECULAR MODELING STUDIES ON THE PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE COFACTOR COMPLEX WITH TAB, A HIGHLY SELECTIVE ANTIFOLATE.

PDB DOI: 10.2210/pdb1VJ3/pdb
Entry: 1VJ3 supersedes: 1D8R

Classification: OXIDOREDUCTASE
Organism(s): Pneumocystis carinii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-01-13 Released: 2004-01-20
Deposition Author(s): Cody, V., Galitsky, N., Rak, D., Luft, J.R., Queener, S.F., Laughton, C.A., Malcolm, F.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural studies on bioactive compounds. 30. Crystal structure and molecular modeling studies on the Pneumocystis carinii dihydrofolate reductase cofactor complex with TAB, a highly selective antifolate.

Cody, V., Chan, D., Galitsky, N., Rak, D., Luft, J.R., Pangborn, W., Queener, S.F., Laughton, C.A., Stevens, M.F.

(2000) Biochemistry 39: 3556-3564

PubMed: 10736154 Search on PubMed
DOI: 10.1021/bi9924563
Primary Citation of Related Structures:
1VJ3

PubMed Abstract:

The crystal structure of the ternary complex of NADPH, the potent antifolate [2, 4-diamino-5-¿3-[3-(2-acetyloxyethyl)-3-benzyltriazen-1-yl]-4 -chloroph enyl¿-6-ethylpyrimidine] (TAB, 1) and Pneumocystis carinii dihydrofolate reductase (pcDHFR), refined to 2.1 A resolution, reveals that TAB binds similar to the antifolates trimethoprim and methotrexate. These data also reveal multiple conformations for the binding geometry of TAB with two preferred orientations of the acetyloxy and benzyl groups that results from a 180 degrees rotation about the N2-N3 triazenyl bond. The methyl of the acetyloxy and benzyl ring of TAB probes large hydrophobic regions of the p-aminobenzoyl folate binding pocket of the active site, in particular the region near Phe69, which is unique to the pcDHFR sequence. These results confirm prior molecular modeling investigations of the binding of TAB to pcDHFR that identified four low-energy binding geometries, two involving rotations about the terminal N(2)-N(3) triazenyl linkage and two involving atropisomerism about the pivotal pyrimethamine-phenyl bond. The primary differences in the molecular dynamics (MD) models and those observed in this crystal complex result from small conformational changes in active-site residues on energy minimization. However, two MD models place the acetyloxy and benzyl ring groups in a region of the active site between the cofactor-binding region and the p-aminobenzoyl folate pocket; an orientation never observed in any DHFR crystal structure to date. These conformers interact with solvent near the enzyme surface and are probably not observed due to the loss of specific hydrogen bonds with the enzyme. The high species pcDHFR selectivity of TAB could be the result of ligand flexibility that enables multiple binding orientations at the enzyme active site. Further modification of the acetyloxy region of TAB could increase its potency and selectivity for pcDHFR.

Related Citations:

Ligand-Induced Conformational Changes in the Crystal Structures of Pneumocystis Carinii Dihydrofolate Reductase Complexes with Folate and Nadp+
Cody, V., Galitsky, N., Rak, D., Luft, J.R., Pangborn, W., Queener, S.F.
(1999) Biochemistry 38: 4303

The Structure of Pneumocystis Carinii Dihydrofolate Reductase to 1.9 A Resolution
Champness, J.N., Achari, A., Ballantine, S.P., Bryant, P.K., Delves, C.J., Stammers, D.K.
(1994) Structure 2: 915

Organizational Affiliation:

Hauptman-Woodward Medical Research Institute, Inc., Buffalo, New York 14203, USA. cody@hwi.buffalo.edu

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROFOLATE REDUCTASE	A	205	Pneumocystis carinii	Mutation(s): 0 Gene Names: C-DNA P.CARINII DHFR EC: 1.5.1.3
UniProt
Find proteins for P16184 (Pneumocystis carinii) Explore P16184 Go to UniProtKB: P16184
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P16184
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Ligand Interaction
TAB Query on TAB Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	ACETIC ACID N-[2-CHLORO-5-[6-ETHYL-2,4-DIAMINO-PYRIMID-5-YL]-PHENYL]-[BENZYL-TRIAZEN-3-YL]ETHYL ESTER C₂₃ H₂₆ Cl N₇ O₂ QKBISNUGIKKCIM-QVIHXGFCSA-N		Ligand Interaction