1E26

Design, Synthesis and X-ray Crystal Structure of a Potent Dual Inhibitor of Thymidylate Synthase and Dihydrofolate Reductase as an Antitumor Agent.

PDB DOI: 10.2210/pdb1E26/pdb

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

Deposited: 2000-05-17 Released: 2001-05-17
Deposition Author(s): Gangjee, A., Yu, J., McGuire, J.J., Cody, V., Galitsky, N., Kisliuk, R.L., Queener, S.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.297
R-Value Work: 0.218
R-Value Observed: 0.218

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

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

PubMed: 10194348 Search on PubMed
DOI: 10.1021/bi982728m
Primary Citation of Related Structures:
1CD2, 1E26, 2CD2, 3CD2, 4CD2

PubMed Abstract:

Structural data from two independent crystal forms (P212121 and P21) of the folate (FA) binary complex and from the ternary complex with the oxidized coenzyme, NADP+, and recombinant Pneumocystis carinii dihydrofolate reductase (pcDHFR) refined to an average of 2.15 A resolution, show the first evidence of ligand-induced conformational changes in the structure of pcDHFR. These data are also compared with the crystal structure of the ternary complex of methotrexate (MTX) with NADPH and pcDHFR in the monoclinic lattice with data to 2.5 A resolution. Comparison of the data for the FA binary complex of pcDHFR with those for the ternary structures reveals significant differences, with a >7 A movement of the loop region near residue 23 that results in a new "flap-open" position for the binary complex, and a "closed" position in the ternary complexes, similar to that reported for Escherichia coli (ec) DHFR complexes. In the orthorhombic lattice for the binary FA pcDHFR complex, there is also an unwinding of a short helical region near residue 47 that places hydrophobic residues Phe-46 and Phe-49 toward the outer surface, a conformation that is stabilized by intermolecular packing contacts. The pyrophosphate moiety of NADP+ in the ternary folate pcDHFR complexes shows significant differences in conformation compared with that observed in the MTX-NADPH-pcDHFR ternary complex. Additionally, comparison of the conformations among these four pcDHFR structures reveals evidence for subdomain movement that correlates with cofactor binding states. The larger binding site access in the new "flap-open" loop 23 conformation of the binary FA complex is consistent with the rapid release of cofactor from the product complex during catalysis as well as the more rapid release of substrate product from the binary complex as a result of the weaker contacts of the closed loop 23 conformation, compared to ecDHFR.

Organizational Affiliation:

Hauptman-Woodward Medical Research Institute, Inc., Buffalo, New York, 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	206	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
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Ligand Interaction
GPB Query on GPB Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	N-[4-[2-(2-AMINO-4-METHYL-7H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYL]GLUTAMIC ACID C₂₁ H₂₃ N₅ O₅ FICRNCFTTZHHPO-HNNXBMFYSA-N		Ligand Interaction