PDBsum entry 2fzh

Oxidoreductase

PDB id: 2fzh

Contents

Protein chain

206 a.a. *

Ligands

NDP

DH1

Waters ×94

* Residue conservation analysis

PDB id:

2fzh

Name:

Oxidoreductase

Title:

New insights into dihydrofolate reductase interactions: analysis of pneumocystis carinii and mouse dhfr complexes with NADPH and two highly potent trimethoprim derivatives

Structure:

Dihydrofolate reductase. Chain: a. Engineered: yes

Source:

Pneumocystis carinii. Organism_taxid: 4754. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.246 R-free: 0.295

Authors:

V.Cody,J.Pace,K.Chisum,A.Rosowsky

Key ref:

V.Cody et al. (2006). New insights into DHFR interactions: analysis of Pneumocystis carinii and mouse DHFR complexes with NADPH and two highly potent 5-(omega-carboxy(alkyloxy) trimethoprim derivatives reveals conformational correlations with activity and novel parallel ring stacking interactions. Proteins, 65, 959-969. PubMed id: 17019704 DOI: 10.1002/prot.21131

Date:

09-Feb-06 Release date: 26-Dec-06

Protein chain

P16184  (DYR_PNECA) -  Dihydrofolate reductase from Pneumocystis carinii

Seq: 206 a.a.

Struc: 206 a.a.

Enzyme reactions

• Enzyme class: E.C.1.5.1.3 - dihydrofolate reductase.
• Pathway: Folate Coenzymes
• Reaction: (6S)-5,6,7,8-tetrahydrofolate + NADP⁺ = 7,8-dihydrofolate + NADPH + H⁺

(6S)-5,6,7,8-tetrahydrofolate + NADP(+) (Bound ligand (Het Group name = NDP) corresponds exactly) = 7,8-dihydrofolate + NADPH + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1002/prot.21131

Proteins 65:959-969 (2006)

PubMed id: 17019704

New insights into DHFR interactions: analysis of Pneumocystis carinii and mouse DHFR complexes with NADPH and two highly potent 5-(omega-carboxy(alkyloxy) trimethoprim derivatives reveals conformational correlations with activity and novel parallel ring stacking interactions.

V.Cody, J.Pace, K.Chisum, A.Rosowsky.

ABSTRACT

Structural data are reported for two highly potent antifolates, 2,4-diamino-5-[3',4'-dimethoxy-5'-(5-carboxy-1-pentynyl)]benzylpyrimidine (PY1011), with 5000-fold selectivity for Pneumocystis carinii dihydrofolate reductase (pcDHFR), relative to rat liver DHFR, and 2,4-diamino-5-[2-methoxy-5-(4-carboxybutyloxy)benzyl]pyrimidine (PY957), that has 80-fold selectivity for pcDHFR. Crystal structures are reported for NADPH ternary complexes with PY957 and pcDHFR, refined to 2.2 A resolution; with PY1011 and pcDHFR, refined to 2.0 A resolution; and with PY1011 and mouse DHFR (mDHFR), refined to 2.2 A resolution. These results reveal that the carboxylate of the omega-carboxyalkyloxy side chain of these inhibitors form ionic interactions with the conserved Arg in the substrate binding pocket of DHFR. These data suggest that the enhanced inhibitory activity of PY1011 compared with PY957 is, in part, due to the favorable contacts with Phe69 of pcDHFR by the methylene carbons of the inhibitor side chain that are oriented by the triple bond of the 1-pentynyl side chain. These contacts are not present in the PY957 pcDHFR complex, or in the PY1011 mDHFR complex. In the structure of mDHFR the site of Phe69 in pcDHFR is occupied by Asn64. These data also revealed a preference for an unusual parallel ring stacking interaction between Tyr35 of the active site helix and Phe199 of the C-terminal beta sheet in pcDHFR and by Tyr33 and Phe179 in mDHFR that is independent of bound ligand. A unique His174-His187 parallel ring stacking interaction was also observed only in the structure of pcDHFR. These ring stacking interactions are rarely found in any other protein families and may serve to enhance protein stability.

Selected figure(s)

Figure 6.
Figure 6. (a) Conserved intermolecular contacts involving Arg75 of pcDHFR and inhibitor PY957. Residues Thr40, Ser41, and Lys73 make a series of hydrogen bond contacts to the N functions of Arg75. The carboxylate of PY957 also makes contact with the NH[2] of Arg-75, and through a water molecule, makes hydrogen bond contacts to the backbone carbonyl of Phe 69. (b) Similar intermolecular contacts with the conserved Arg70 of mDHFR and PY1011 are shown. Note that the conformation of Lys68 is such that its terminal NH2 goup can occupy the water position observed in the pcDHFR structures. Figure generated with DeepView.[41] (c) Stereoview of hydrogen bond contacts for PY1011 carboxylate side chain with pcDHFR NADPH PY1011 ternary complex.

Figure 8.
Figure 8. Superposition of pcDHFR PY1011 NADPH ternary complex (yellow/red) highlighting the stacking interactions of Tyr35/Phe199 and His174/His187 on mDHFR-PY1011 NADPH ternary complex (green) showing the differences in the loop conformation near the His stacking site.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 65, 959-969) copyright 2006.

Figures were selected by the author.