Crystal structure of uncharacterized protein TTHA1756 from <i>Thermus thermophilus</i> HB8: Structural variety in UPF0150 family proteins

Ebihara, Akio; Manzoku, Miho; Iino, Hitoshi; Kanagawa, Motoi; Shinkai, Akeo; Yokoyama, Shigeyuki; Kuramitsu, Seiki

doi:10.1002/prot.22018

Cited by 3 publications

(2 citation statements)

References 23 publications

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“…The other gene, PA1S_06920 , encoding a 140-aa protein that shares 30% identity with the E. coli HicB antitoxin, was named hicB . Protein homology modeling using CPHmodels predicted the structures of P. aeruginosa HicA and HicB based on the available solved three-dimensional structure of proteins TTHA1913 (PDB: 1WHZ) and TTHA1756 (PDB: 2YZT), respectively [ 23 , 24 ]. The secondary structure of HicA showed that it is likely to adopt an α1β1β2β3α2 fold characteristic of a double-stranded RNA (dsRNA)-binding domain ( Figure 1 A), and this fold is conserved in the HicA family.…”

Section: Resultsmentioning

confidence: 99%

Identification and Characterization of the HicAB Toxin-Antitoxin System in the Opportunistic Pathogen Pseudomonas aeruginosa

Shen

et al. 2016

Toxins

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Toxin-antitoxin (TA) systems are small genetic modules that are widely distributed in the genomes of bacteria and archaea and have been proposed to fulfill numerous functions. Here, we describe the identification and characterization of a type II TA system, comprising the hicAB locus in the human opportunistic pathogen Pseudomonas aeruginosa. The hicAB locus consists of genes hicA and hicB encoding a toxin and its cognate antitoxin, respectively. BLAST analysis revealed that hicAB is prevalent in approximately 36% of P. aeruginosa strains and locates in the same genomic region. RT-PCR demonstrated that hicAB forms a bicistronic operon that is cotranscribed under normal growth conditions. Overproduction of HicA inhibited the growth of Escherichia coli, and this effect could be counteracted by co-expression of HicB. The Escherichia coli kill/rescue assay showed that the effect of HicA is bacteriostatic, rather than bactericidal. Deletion of hicAB had no effect on the biofilm formation and virulence of P. aeruginosa in a mice infection model. Collectively, this study presents the first characterization of the HicAB system in the opportunistic pathogen P. aeruginosa.

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Section: Resultsmentioning

confidence: 99%

Identification and Characterization of the HicAB Toxin-Antitoxin System in the Opportunistic Pathogen Pseudomonas aeruginosa

Shen

et al. 2016

Toxins

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“…The putative protein from the gram-negative bacterium Thermus thermophilus [24] (PDB file 2YZT), crystallizes in a P 3 1 2 1 space group, which has 6 associated symmetry operations. Its small size (579 atoms) allows us to quickly analyze the asymmetric unit, unit cell (1x1x1), as well as 2x1x1 and 2x2x1 crystal lattices.…”

Section: Resultsmentioning

confidence: 99%

Rigidity analysis of protein biological assemblies and periodic crystal structures

et al. 2013

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Background: We initiate in silico rigidity-theoretical studies of biological assemblies and small crystals for protein structures. The goal is to determine if, and how, the interactions among neighboring cells and subchains affect the flexibility of a molecule in its crystallized state. We use experimental X-ray crystallography data from the Protein Data Bank (PDB). The analysis relies on an effcient graph-based algorithm. Computational experiments were performed using new protein rigidity analysis tools available in the new release of our KINARI-Web server http:// kinari.cs.umass.edu. Results: We provide two types of results: on biological assemblies and on crystals. We found that when only isolated subchains are considered, structural and functional information may be missed. Indeed, the rigidity of biological assemblies is sometimes dependent on the count and placement of hydrogen bonds and other interactions among the individual subchains of the biological unit. Similarly, the rigidity of small crystals may be affected by the interactions between atoms belonging to different unit cells. We have analyzed a dataset of approximately 300 proteins, from which we generated 982 crystals (some of which are biological assemblies). We identified two types of behaviors. (a) Some crystals and/or biological assemblies will aggregate into rigid bodies that span multiple unit cells/asymmetric units. Some of them create substantially larger rigid cluster in the crystal/biological assembly form, while in other cases, the aggregation has a smaller effect just at the interface between the units. (b) In other cases, the rigidity properties of the asymmetric units are retained, because the rigid bodies did not combine. We also identified two interesting cases where rigidity analysis may be correlated with the functional behavior of the protein. This type of information, identified here for the first time, depends critically on the ability to create crystals and biological assemblies, and would not have been observed only from the asymmetric unit. For the Ribonuclease A protein (PDB file 5RSA), which is functionally active in the crystallized form, we found that the individual protein and its crystal form retain the flexibility parameters between the two states. In contrast, a derivative of Ribonuclease A (PDB file 9RSA), has no functional activity, and the protein in both the asymmetric and crystalline forms, is very rigid. For the vaccinia virus D13 scaffolding protein (PDB file 3SAQ), which has two biological assemblies, we observed a striking asymmetry in the rigidity cluster decomposition of one of them, which seems implausible, given its symmetry. Upon careful investigation, we tracked the cause to a placement decision by the Reduce software concerning the hydrogen atoms, thus affecting the distribution of certain hydrogen bonds. The surprising result is that the presence or lack of a very few, but critical, hydrogen bonds, can drastically affect the rigid cluster decomposition of the biological assembly.

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Periodic rigidity of protein crystal structures

Clark

Grant

Monastra

et al. 2012

2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)

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Crystal structure of uncharacterized protein TTHA1756 from Thermus thermophilus HB8: Structural variety in UPF0150 family proteins

Cited by 3 publications

References 23 publications

Identification and Characterization of the HicAB Toxin-Antitoxin System in the Opportunistic Pathogen Pseudomonas aeruginosa

Identification and Characterization of the HicAB Toxin-Antitoxin System in the Opportunistic Pathogen Pseudomonas aeruginosa

Rigidity analysis of protein biological assemblies and periodic crystal structures

Periodic rigidity of protein crystal structures

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