PDBsum entry 5fo4

Ligase

PDB id: 5fo4

Contents

Protein chains

302 a.a.

317 a.a.

Waters ×256

PDB id:

5fo4

Name:

Ligase

Title:

Crystal structure of the p.Falciparum cytosolic leucyl-tRNA synthetase editing domain (space group p1)

Structure:

Leucyl tRNA synthase. Chain: a, b. Fragment: editing domain, unp residues 272-687. Engineered: yes. Mutation: yes. Other_details: deletion of residues 475-519, c273s substitution to prevent disulfide bonds, gam inserted at n- term (expression vector)

Source:

Plasmodium falciparum. Organism_taxid: 5833. Strain: isolate 3d7. Gene: pff1095w. Expressed in: escherichia coli k-12. Expression_system_taxid: 83333. Expression_system_variant: de3 ril.

Resolution:

1.85Å R-factor: 0.197 R-free: 0.252

Authors:

A.Palencia,E.Sonoiki,D.Guo,V.Ahyong,C.Dong,X.Li,V.S.Hernandez,J.Gut, J.Legac,R.Cooper,M.R.K.Alley,Y.R.Freund,J.Derisi,S.Cusack, P.J.Rosenthal

Key ref:

E.Sonoiki et al. (2016). Antimalarial Benzoxaboroles Target Plasmodium falciparum Leucyl-tRNA Synthetase. Antimicrob Agents Chemother, 60, 4886-4895. PubMed id: 27270277 DOI: 10.1128/AAC.00820-16

Date:

18-Nov-15 Release date: 22-Jun-16

Protein chain

C6KT64  (C6KT64_PLAF7) -  leucine--tRNA ligase from Plasmodium falciparum (isolate 3D7)

Seq: 1447 a.a.

Struc: 302 a.a.*

Protein chain

C6KT64  (C6KT64_PLAF7) -  leucine--tRNA ligase from Plasmodium falciparum (isolate 3D7)

Seq: 1447 a.a.

Struc: 317 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.6.1.1.4 - leucine--tRNA ligase.
• Reaction: tRNA(Leu) + L-leucine + ATP = L-leucyl-tRNA(Leu) + AMP + diphosphate

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

reference

DOI no: 10.1128/AAC.00820-16

Antimicrob Agents Chemother 60:4886-4895 (2016)

PubMed id: 27270277

Antimalarial Benzoxaboroles Target Plasmodium falciparum Leucyl-tRNA Synthetase.

E.Sonoiki, A.Palencia, D.Guo, V.Ahyong, C.Dong, X.Li, V.S.Hernandez, Y.K.Zhang, W.Choi, J.Gut, J.Legac, R.Cooper, M.R.Alley, Y.R.Freund, J.DeRisi, S.Cusack, P.J.Rosenthal.

ABSTRACT

There is a need for new antimalarials, ideally with novel mechanisms of action. Benzoxaboroles have been shown to be active against bacteria, fungi, and trypanosomes. Therefore, we investigated the antimalarial activity and mechanism of action of 3-aminomethyl benzoxaboroles against Plasmodium falciparum Two 3-aminomethyl compounds, AN6426 and AN8432, demonstrated good potency against cultured multidrug-resistant (W2 strain) P. falciparum (50% inhibitory concentration [IC50] of 310 nM and 490 nM, respectively) and efficacy against murine Plasmodium berghei infection when administered orally once daily for 4 days (90% effective dose [ED90], 7.4 and 16.2 mg/kg of body weight, respectively). To characterize mechanisms of action, we selected parasites with decreased drug sensitivity by culturing with stepwise increases in concentration of AN6426. Resistant clones were characterized by whole-genome sequencing. Three generations of resistant parasites had polymorphisms in the predicted editing domain of the gene encoding a P. falciparum leucyl-tRNA synthetase (LeuRS; PF3D7_0622800) and in another gene (PF3D7_1218100), which encodes a protein of unknown function. Solution of the structure of the P. falciparum LeuRS editing domain suggested key roles for mutated residues in LeuRS editing. Short incubations with AN6426 and AN8432, unlike artemisinin, caused dose-dependent inhibition of [(14)C]leucine incorporation by cultured wild-type, but not resistant, parasites. The growth of resistant, but not wild-type, parasites was impaired in the presence of the unnatural amino acid norvaline, consistent with a loss of LeuRS editing activity in resistant parasites. In summary, the benzoxaboroles AN6426 and AN8432 offer effective antimalarial activity and act, at least in part, against a novel target, the editing domain of P. falciparum LeuRS.