Dissecting the Unique Nucleotide Specificity of Mimivirus Nucleoside Diphosphate Kinase

Abstract

The analysis of the Acanthamoeba polyphaga mimivirus genome revealed the first virus-encoded nucleoside diphosphate kinase (NDK), an enzyme that is central to the synthesis of RNA and DNA, ubiquitous in cellular organisms, and well conserved among the three domains of life. In contrast with the broad specificity of cellular NDKs for all types of ribo-and deoxyribonucleotides, the mimivirus enzyme exhibits a strongly preferential affinity for deoxypyrimidines. In order to elucidate the molecular basis of this unique substrate specificity, we determined the three-dimensional (3D) structure of the Acanthamoeba polyphaga mimivirus NDK alone and in complex with various nucleotides. As predicted from a sequence comparison with cellular NDKs, the 3D structure of the mimivirus enzyme exhibits a shorter Kpn loop, previously recognized as a main feature of the NDK active site. The structure of the viral enzyme in complex with various nucleotides also pinpointed two residue changes, both located near the active site and specific to the viral NDK, which could explain its stronger affinity for deoxynucleotides and pyrimidine nucleotides. The role of these residues was explored by building a set of viral NDK variants, assaying their enzymatic activities, and determining their 3D structures in complex with various nucleotides. A total of 26 crystallographic structures were determined at resolutions ranging from 2.8 Å to 1.5 Å. Our results suggest that the mimivirus enzyme progressively evolved from an ancestral NDK under the constraints of optimizing its efficiency for the replication of an AT-rich (73%) viral genome in a thymidine-limited host environment.

Signaling transcript profile of the asexual intraerythrocytic development cycle of Plasmodium falciparum induced by melatonin and cAMP

“…This enzyme was found to bind a broad range of ribo- and deoxyribonucleotides; thus, it can produce all precursors of DNA and RNA synthesis. NDK produces NTP for nucleic acid synthesis, CTP for lipid synthesis, UTP for polysaccharide synthesis and GTP for protein synthesis, signal transduction or microtubule polymerization [38]. …”

Structure and analysis of nucleoside diphosphate kinase fromBorrelia burgdorferiprepared in a transition-state complex with ADP and vanadate moieties

“…Of these structures, roughly one third contain bound ligands such as (d)NTPs, (d)NDPs or other small molecules (Mg 2+ , sulfate or vanadate). Some examples include H. sapiens NDK bound to ADP (Giraud et al, 2006), Thermus thermophilus NDK complexed with GDP (PDB entry 1wkk; RIKEN Structural Genomics/Proteomics Initiative, unpublished work) and even Mimivirus NDK bound to Mg 2+ , phosphate, TDP and many other ligands (Jeudy et al, 2009). We were primarily interested in showing the transition state during substrate turnover, and so we chose to attempt cocrystallization with both ADP and vanadate.…”

Horizontal Gene Transfers with or without Cell Fusions in All Categories of the Living Matter

“…The Acantamoeba (A. castellani) enzyme clusters with fungal, and metazoan sequences. The viral enzyme was not acquired from a eukaryotic organism by horizontal gene transfer [182].…”