Crystal structure of toxin HP0892 from Helicobacter pylori with two Zn(II) at 1.8 Å resolution

Abstract

Antibiotic resistance and microorganism virulence have been consistently exhibited by bacteria and archaea, which survive in conditions of environmental stress through toxin-antitoxin (TA) systems. The HP0892-HP0893 TA system is one of the two known TA systems belonging to Helicobacter pylori. The antitoxin, HP0893, binds and inhibits the HP0892 toxin and regulates the transcription of the TA operon. Here, we present the crystal structure of the zinc-bound HP0892 toxin at 1.8 Å resolution. Reorientation of residues at the mRNase active site was shown. The involved residues, namely E58A, H86A, and H58A/ H60A, were mutated and the binding affinity was monitored by ITC studies. Through the structural difference between the apo and the metal-bound state, and using a homology modeling tool, the involvement of the metal ion in mRNase active site could be identified. The most catalytically important residue, His86, reorients itself to exhibit RNase activity. His47, Glu58, and His60 are involved in metal binding where Glu58 acts as a general base and His47 and His60 may also act as a general acid in enzymatic activity. Glu58 and Asp64 are involved in substrate binding and specific sequence recognition. Arg83 is involved in phosphate binding and stabilization of the transition state, and Phe90 is involved in base packing and substrate orientation.

Transcriptional Profiling of Type II Toxin–Antitoxin Genes of Helicobacter pylori under Different Environmental Conditions: Identification of HP0967–HP0968 System

“…Three pairs of type II TA proteins have been described in H. pylori : HP0315–HP0316, HP0892–HP0893, and HP0894–HP0895 (Han et al, 2011, 2013; Kwon et al, 2012; Im et al, 2014). Searching for TA-encoding homolog genes of different families, we identified hp0967 , a gene that codes for a type II toxin belonging to the VapD protein family.…”

“…Three type II TA systems have been structurally and functionally characterized in H. pylori 26695: HP0315–HP0316, HP0892–HP0893, and HP0894–HP0895 (Han et al, 2011, 2013; Kwon et al, 2012; Pathak et al, 2013; Im et al, 2014). These TA systems belong to the Vap ( v irulence- a ssociated p rotein) family, found in Bacteria and Archaea (Makarova et al, 2006).…”

Rapid growth inhibitory activity of a YafQ-family endonuclease toxin of the Helicobacter pylori tfs4 integrative and conjugative element

“…The conserved Glu residue of the triad acts as a general base with His as a general acid in the acid–base catalysis reaction whereas Arg is involved in phosphate binding and stabilisation of the transition state 26 , 27 . In addition to these critical catalytic residues, aromatic side-chains of highly conserved Phe/Tyr residues in the extreme C-terminus of the toxins, including Phe88 in HP0894, Phe90 of HP0892, Phe91 of YafQ, and Tyr87 of RelE are involved in substrate orientation and facilitate the acid–base catalysis reaction 23 , 26 , 27 , 43 . The sequence and structural conservation of equivalent TfiT residues, including Phe91 (Fig.…”

“…These include several active site histidine residues, His50, His63, His87 in addition to Asp67, Phe91 and a subset of positively charged, mainly lysine residues, which comprise extended basic surface patches 19 . The catalytic residues in particular are highly conserved between YafQ and two structurally homologous endoribonuclease TA toxins, HP0892 and HP0894 of Helicobacter pylori [24][25][26][27] . Four different Type II TA systems have been described so far in H. pylori, HP0892-HP0893, HP0894-HP0895, HP0315-HP0316 and HP0968-HP0967, the latter two comprising toxins of the virulence-associated protein family, VapD 28,29 .…”

Effect of Divalent Metal Ions on the Ribonuclease Activity of the Toxin Molecule HP0894 from Helicobacter pylori

“…Our previous report [20] evidenced that copper binds to HP0894 (PDB code 4LSY) through His47, Glu58, His60, and His84 residues, which is consistent with the current results. In addition, Asp64 which is conserved in HP0894, HP0892, and E. coli YafQ [20] (Asp64 in HP0894, Asp64 in HP0892, and Asp67 in E. coli YafQ), evidenced notable changes, whereas no change was identified in Asp64 of HP0892 [33,39].…”