PDBsum entry 1f6t

Transferase

PDB id: 1f6t

Contents

Protein chains

150 a.a. *

Ligands

TBD ×3

Metals

_MG ×3

Waters ×377

* Residue conservation analysis

PDB id:

1f6t

Name:

Transferase

Title:

Structure of the nucleoside diphosphate kinase/alpha-borano(rp)-tdp.Mg complex

Structure:

Protein (nucleoside diphosphate kinase). Chain: a, b, c. Synonym: ndk, ndp kinase. Engineered: yes

Source:

Dictyostelium discoideum. Organism_taxid: 44689. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Hexamer (from PDB file)

Resolution:

1.92Å R-factor: 0.228 R-free: 0.274

Authors:

C.Guerreiro,J.Boretto,J.Janin,M.Veron,B.Canard,B.Schneider,S.Sarfati, D.Deville-Bonne

Key ref:

P.Meyer et al. (2000). Structural basis for activation of alpha-boranophosphate nucleotide analogues targeting drug-resistant reverse transcriptase. EMBO J, 19, 3520-3529. PubMed id: 10899107 DOI: 10.1093/emboj/19.14.3520

Date:

23-Jun-00 Release date: 13-Sep-00

Protein chains

P22887  (NDKC_DICDI) -  Nucleoside diphosphate kinase, cytosolic from Dictyostelium discoideum

Seq: 155 a.a.

Struc: 150 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.4.6 - nucleoside-diphosphate kinase.
• Reaction:
  1. a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP
  2. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP

ribonucleoside 5'-diphosphate + ATP = ribonucleoside 5'-triphosphate + ADP (Bound ligand (Het Group name = TBD) matches with 67.74% similarity)

2'-deoxyribonucleoside 5'-diphosphate + ATP = 2'-deoxyribonucleoside 5'-triphosphate + ADP (Bound ligand (Het Group name = TBD) matches with 67.74% similarity)

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

reference

DOI no: 10.1093/emboj/19.14.3520

EMBO J 19:3520-3529 (2000)

PubMed id: 10899107

Structural basis for activation of alpha-boranophosphate nucleotide analogues targeting drug-resistant reverse transcriptase.

P.Meyer, B.Schneider, S.Sarfati, D.Deville-Bonne, C.Guerreiro, J.Boretto, J.Janin, M.Véron, B.Canard.

ABSTRACT

AIDS chemotherapy is limited by inadequate intracellular concentrations of the active triphosphate form of nucleoside analogues, leading to incomplete inhibition of viral replication and the appearance of drug-resistant virus. Drug activation by nucleoside diphosphate kinase and inhibition of HIV-1 reverse transcriptase were studied comparatively. We synthesized analogues with a borano (BH(3)(-)) group on the alpha-phosphate, and found that they are substrates for both enzymes. X-ray structures of complexes with nucleotide diphosphate kinase provided a structural basis for their activation. The complex with d4T triphosphate displayed an intramolecular CH.O bond contributing to catalysis, and the R(p) diastereoisomer of thymidine alpha-boranotriphosphate bound like a normal substrate. Using alpha-(R(p))-boranophosphate derivatives of the clinically relevant compounds AZT and d4T, the presence of the alpha-borano group improved both phosphorylation by nucleotide diphosphate kinase and inhibition of reverse transcription. Moreover, repair of blocked DNA chains by pyrophosphorolysis was reduced significantly in variant reverse transcriptases bearing substitutions found in drug-resistant viruses. Thus, the alpha-borano modification of analogues targeting reverse transcriptase may be of generic value in fighting viral drug resistance.

Selected figure(s)

Figure 1.
Figure 1 Chemical formula of the -(R[p])-borano-d4T triphosphate diastereoisomer.

Figure 4.
Figure 4 Conformation of the nucleotide substrate in NDPK, T7 DNA polymerase and HIV reverse transcriptase. d4T triphosphate from the NDPK complex in Figure 2B is shown in atom-type coloured bonds superimposed onto (A) dideoxyGTP in the ternary complex with bacteriophage T7 DNA polymerase–DNA (PDB file 1T7P) and (B) deoxyTTP in the ternary complex with HIV reverse transcriptase–DNA (PDB file 1RTD). Least-square fitting was performed on atom N1 of the base and common atoms in the sugar and the -phosphate. In T7 polymerase and reverse transcriptase, relevant active site residues, DNA and the ligand are in blue bonds, and blue spheres represent two Mg^2+ ions bound. In NDPK, the red sphere is the single Mg^2+ ion bound to d4T triphosphate. It is located <1 Å away from one of the two Mg^2+ of the polymerases.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 3520-3529) copyright 2000.

Figures were selected by an automated process.