Crystal structure of apo and copper bound HP0894 toxin from Helicobacter pylori 26695 and insight into mRNase activity

Pathak, Chinar; Im, Hyung‐Jun; Yang, Yeon-Jin; Yoon, Hye‐Jin; Kim, Hong-Man; Kwon, Ae‐Ran; Lee, Bong-Jin

doi:10.1016/j.bbapap.2013.09.006

Cited by 7 publications

(28 citation statements)

References 77 publications

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“…The sequence alignment showed that all these RelE superfamily members share high similarity in the C-terminal region. These proteins possess a highly conserved catalytic histidine residue, His86 in HP0892, 43 His84 in HP0894, 44,46 His87 in YafQ,…”

Section: Resonance Assignment and Chemical Shift Perturbation Experimmentioning

confidence: 99%

“…Unfortunately, molecular replacement did not yield satisfactory results. Therefore, the structure of HP0894 L66S (sequence identity 53.33%, PDB code 4LS4) 46 was used as a search model, and molecular replacement was performed successfully (we used this mutant protein structure because at this time native HP0894 [PDB code 4LTT] was not available yet).…”

Section: Structure Determination Of Hp0892mentioning

confidence: 99%

“…Highly positive charged residues (His47 and His60 in case of HP0892) might be required for efficient protonation in an acid-base catalysis reaction and thus serve as a general acid in the reaction. 11,43,44,46 Mutation of Glu58 in HP0892 (E58A HP0892 and E58A/H60A HP0892) resulted in complete loss of metal affinity towards HP0892 protein (Supporting Information Fig. S2 and Supporting Information Table SI).…”

mentioning

confidence: 99%

“…This Glu58 along with Asp64 in HP0892 coincides with Asp61 and Asp67 in YafQ, and Glu58 and Asp64 in HP0894, suggesting that they may have similar roles. Asp61 and Asp67 of YafQ and Glu58 of HP0894 were reported to be general bases in the acid-base catalysis reaction, 11,46 while Lys52 and Asp64 of HP0894 were proposed to be involved in substrate binding and specific sequence recognition. 44 Taken together, these data indicate that Glu58 46 Considering the sequential and structural homology, it appears that Arg83 in HP0892 also serves a similar role to that of Arg80 in HP0894 and Arg83 in YafQ.…”

mentioning

confidence: 99%

“…Asp61 and Asp67 of YafQ and Glu58 of HP0894 were reported to be general bases in the acid-base catalysis reaction, 11,46 while Lys52 and Asp64 of HP0894 were proposed to be involved in substrate binding and specific sequence recognition. 44 Taken together, these data indicate that Glu58 46 Considering the sequential and structural homology, it appears that Arg83 in HP0892 also serves a similar role to that of Arg80 in HP0894 and Arg83 in YafQ. Glu58 also acts as a general base in the acid-base catalysis reaction, and Arg83 of HP0892 is responsible for phosphate binding and the stabilization of transition state.…”

mentioning

confidence: 99%

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

Jang

Pathak

et al. 2014

Protein Science

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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.

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Section: Resonance Assignment and Chemical Shift Perturbation Experimmentioning

confidence: 99%

Section: Structure Determination Of Hp0892mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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

Jang

Pathak

et al. 2014

Protein Science

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

Boampong

Smith

Delahay

2020

Sci Rep

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Prokaryotic and archaeal chromosomes encode a diversity of toxin–antitoxin (TA) systems that contribute to a variety of stress-induced cellular processes in addition to stability and maintenance of mobile elements. Here, we find DinJ-YafQ family TA systems to be broadly distributed amongst diverse phyla, consistent with other ParE/RelE superfamily TAs, but more unusually occurring as a multiplicity of species-specific subtypes. In the gastric pathogen Helicobacter pylori we identify six distinct subtypes, of which three are predominantly associated with the mobilome, including the disease-associated integrative and conjugative element (ICE), tfs4. Whereas, the ICE-encoded proteins have characteristic features of DinJ-YafQ family Type II TA systems in general, the toxin component is distinguished by a broad metal-ion-dependent endonuclease activity with specificity for both RNA and DNA. We show that the remarkably rapid growth inhibitory activity of the ICE toxin is a correlate of a C-terminal lysine doublet which likely augments catalytic activity by increasing the positive electrostatic potential in the vicinity of the conserved active site. Our collective results reveal a structural feature of an ICE TA toxin that influences substrate catalysis and toxin function which may be relevant to specific TA-mediated responses in diverse genera of bacteria.

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Characterization of a Helicobacter pylori strain with high biofilm-forming ability

Wilkinson,

Alsharaf,

Thompson

et al. 2023

Journal of Medical Microbiology

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Introduction. Helicobacter pylori is highly polymorphic, and some strains are much more likely to cause disease than others. Biofilm formation can help bacteria to survive antibiotic treatment, immune attack and other stresses, promoting persistent infection. Hypothesis/Gap Statement. We hypothesized that H. pylori isolates from patients with more severe H. pylori-associated disease would be better at forming biofilms than isolates from patients with less severe disease. Aim. We initially aimed to determine whether or not the biofilm-forming ability of H. pylori isolates was associated with disease in the UK-based patients from whom the bacteria were isolated. Methodology. Biofilm-forming ability of H. pylori isolates was determined using a crystal violet assay on glass coverslips. The complete genome sequence of strain 444A was generated by hybrid assembly of Nanopore MinION and Illumina MiSeq data. Results. Although we found no associations between biofilm-forming ability of H. pylori and disease severity in patients, we discovered that strain 444A had particularly high biofilm-forming ability. This strain had been isolated from a patient with gastric ulcer disease and moderate to severe scores for H. pylori-induced histopathology. Analysis of the genome of the high biofilm-forming H. pylori strain 444A revealed that it possesses numerous biofilm- and virulence-associated genes and a small cryptic plasmid encoding a type II toxin–antitoxin system. Conclusion. There is substantial variation in biofilm-forming ability in H. pylori, but this was not significantly associated with disease severity in our study. We identified and characterized an interesting strain with high biofilm-forming ability, including generation and analysis of the complete genome.

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Crystal structure of apo and copper bound HP0894 toxin from Helicobacter pylori 26695 and insight into mRNase activity

Cited by 7 publications

References 77 publications

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

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

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

Characterization of a Helicobacter pylori strain with high biofilm-forming ability

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