High-resolution crystal structure of RNA kinase ArK1 from G. acetivorans

Chulei Cao; Weizhen Zhang; Yanqing Gao; Jie Yang; Hehua Liu; Jianhua Gan

doi:10.1016/j.bbrc.2024.149966

High-resolution crystal structure of RNA kinase ArK1 from G. acetivorans

Biochem Biophys Res Commun. 2024 Jun 25:714:149966. doi: 10.1016/j.bbrc.2024.149966. Epub 2024 Apr 22.

Authors

Chulei Cao¹, Weizhen Zhang¹, Yanqing Gao¹, Jie Yang¹, Hehua Liu¹, Jianhua Gan²

Affiliations

¹ Shanghai Sci-Tech Inno Center for Infection & Immunity, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, PR China.
² Shanghai Sci-Tech Inno Center for Infection & Immunity, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, PR China. Electronic address: ganjhh@fudan.edu.cn.

PMID: 38657448
DOI: 10.1016/j.bbrc.2024.149966

Abstract

U47 phosphorylation (U^p47) is a novel tRNA modification discovered recently; it can confer thermal stability and nuclease resistance to tRNAs. U47 phosphorylation is catalyzed by Archaeal RNA kinase (Ark1) in an ATP-dependent manner. However, the structural basis for tRNA and/or ATP binding by Ark1 is unclear. Here, we report the expression, purification, and crystallization studies of Ark1 from G. acetivorans (GaArk1). In addition to the Apo-form structure, one GaArk1-ATP complex was also determined in atomic resolution and revealed the detailed basis for ATP binding by GaArk1. The GaArk1-ATP complex represents the only ATP-bound structure of the Ark1 protein. The majority of the ATP-binding residues are conserved, suggesting that GaArk1 and the homologous proteins share similar mechanism in ATP binding. Sequence and structural analysis further indicated that endogenous guanosine will only inhibit the activities of certain Ark1 proteins, such as Ark1 from T. kodakarensis.

Keywords: ATP binding; Ark1 protein; Complex structure; RNA kinase; U47 phosphorylation; tRNA modification.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adenosine Triphosphate* / metabolism
Amino Acid Sequence
Archaeal Proteins / chemistry
Archaeal Proteins / genetics
Archaeal Proteins / metabolism
Binding Sites
Crystallography, X-Ray
Models, Molecular*
Protein Binding
Protein Conformation

Substances

Adenosine Triphosphate
Archaeal Proteins