7X8C

Crystal structure of a KTSC family protein from Euryarchaeon Methanolobus vulcani

Summary for 7X8C

• Entry DOI: 10.2210/pdb7x8c/pdb
• Descriptor: KTSC domain-containing protein, SODIUM ION (3 entities in total)
• Functional Keywords: archaea, ktsc domain-containing protein, single-stranded, dna binding protein
• Biological source: Methanolobus vulcani
• Total number of polymer chains: 4
• Total formula weight: 32749.89

Authors

Zhang, Z.F.,Zhu, K.L.,Chen, Y.Y.,Cao, P.,Gong, Y. (deposition date: 2022-03-12, release date: 2022-08-17, Last modification date: 2023-11-29)

Primary citation

Tian, L.,Zhu, K.,Chen, Y.,Zheng, X.,Zhang, H.,Geng, Z.,Li, W.,Ding, N.,Chen, J.,Dong, Y.,Cao, P.,Gong, Y.,Zhang, Z.
Biochemical and structural characterization of a KTSC family single-stranded DNA-binding protein from Euryarchaea.
Int.J.Biol.Macromol., 216:618-628, 2022

PubMed Abstract: The lysine (K) tRNA synthetase C-terminal (KTSC) domain containing proteins are widely spread in Bacteria, Archaea and Viruses, but the function of this short domain is unclear. The occurrence of the fusion of KTSC domain to a catalytic domain or domains related to DNA or RNA metabolisms suggests its potential role in DNA or RNA binding. Here, we report the characterization of Mvu8s from Methanolobus vulcani, which consists of a single KTSC domain. Mvu8s binds specifically to ssDNA with an affinity approximately 40- and 10-fold higher than those for dsDNA and ssRNA in vitro, respectively. It shows a slight preference to the G-rich DNA sequence but barely binds the A-stretch. Crystal structure of Mvu8s shows that it forms a homo-tetramer, with each monomer composed of a four-strand antiparallel β-sheet and a helix-turn-helix in the order of β1-β2-β3-α1-α2-β4. Four basic residues (R3, R7, K54 and K58) were found to serve important roles in ssDNA-binding. And, the spiral arrangement of the DNA interfaces in Mvu8s homo-tetramer presumably results in ssDNA wrapping. Our results not only offer clues of the functions of the KTSC domain containing proteins but also expand our knowledge on the non-oligonucleotide-binding (OB) fold single-stranded DNA-binding proteins in Archaea.

PubMed: 35809674
DOI: 10.1016/j.ijbiomac.2022.07.015

Experimental method

X-RAY DIFFRACTION (2.73 Å)