• Journal of the Korean Magnetic Resonance Society
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• v.21 no.2
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• pp.50-54
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• 2017

Cupin-superfamily proteins represent the most functionally diverse groups of proteins and include a huge number of functionally uncharacterized proteins. Recently, YaiE, a cupin protein from Escherichia coli has been suggested to be involved in a novel activity of pyrimidine/purine nucleoside phosphorylase (PPNP). In the present study, we achieved a complete backbone NMR assignments of YaiE, by a series of heteronuclear multidimensional NMR experiments on its [$^{13}C/^{15}N$]-enriched sample. Subsequently, secondary structure analysis using the assigned chemical shift values identified 10 obvious ${\beta}-strands$ and a tentative $3_{10}-helix$. Taken all together, the results constitute the first structural characterization of a putative PPNP cupin protein.

• BMB Reports
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• v.38 no.5
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• pp.591-594
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• 2005

One of the small proteins from Helicobacter pylori, HP1242, was investigated by the solution nuclear magnetic resonance (NMR) spectroscopy. HP1242 is known as a 76-residue conserved hypothetical protein and its function cannot be identified based on sequence homology. Here, the results of the backbone $^1H$, $^{15}N$, and $^{13}C$ resonance assignments of the HP1242 are reported using double- and triple-resonance techniques. About 95% of all of the $^1HN$, $^{15}N$, $^{13}CO$, $^{13}C{\alpha}$, and $^{13}C{\beta}$ resonances that cover 75 non- Proline residues of the 76 residues are clarified through sequential- and specific- assignments. In addition, three helical regions were clearly identified on the basis of the resonance assignments.

• Journal of the Korean Magnetic Resonance Society
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• v.24 no.3
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• pp.70-76
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• 2020

The CRISPR-Cas system provides an adaptive immunity for bacteria and archaea against invading phages or foreign plasmids. In the type II CRISPR-Cas system, a single effector protein Cas9 and a guide RNA form an RNA-guided endonuclease complex that can degrade DNA targets of foreign origin. To avoid the Cas9-mediated destruction, phages evolved anti-CRISPR (Acr) proteins that neutralize the host bacterial immunity by inactivating the CRISPR-Cas system. Here we report the backbone ¹H, ¹⁵N, and ¹³C resonance assignments of AcrIIA5 that inhibits the endonuclease activity of type II-A Streptococcus thermophilus Cas9 and also Streptococcus pyogenesis Cas9 using triple resonance nuclear magnetic resonance spectroscopy. The backbone chemical shifts of AcrIIA5 predict a disordered region at the N-terminus, followed by an αββββαβββ fold.

• Molecules and Cells
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• v.24 no.3
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• pp.437-440
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• 2007

$OGL-20P^T$-358 is a novel 66 amino acid residue protein from the hyperthermophile Thermococcus thioreducens sp. nov., strain $OGL-20P^T$, which was collected from the wall of the hydrothermal black smoker in the Rainbow Vent along the mid-Atlantic ridge. This protein, which has no detectable sequence homology with proteins or domains of known function, has a calculated pI of 4.76 and a molecular mass of 8.2 kDa. We report here the backbone $^1H$, $^{15}N$, and $^{13}C$ resonance assignments of $OGL-20P^T$-358. Assignments are 97.5% (316/324) complete. Chemical shift index was used to determine the secondary structure of the protein, which appears to consist of primarily ${\alpha}$-helical regions. This work is the foundation for future studies to determine the three-dimensional solution structure of the protein.

• Molecules and Cells
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• v.20 no.3
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• pp.442-445
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• 2005

HP0894 (SwissProt/TrEMBL ID O25554) is an 88-residue conserved hypothetical protein from Helicobacter pylori strain 26695 with a calculated pI of 8.5 and a molecular weight of 10.38 kDa. Proteins with sequence similarity to HP0894 exist in Vibrio choierae, Enterococcus faecalis, Campylobacter jejuni, Streptococcus pneumoniae, Haemophilus influenzae, Escherichia coli O157, etc. Here we report the sequence-specific backbone resonance assignments of HP0894. About 97.5% (418/429) of the HN, N, CO, $C{\alpha}$, $C{\beta}$ resonances of the 88 residues of HP0894 were assigned. On the basis of these assignments, three helical regions and four strand regions were identified using the CSI program. This study is a prerequisite for calculating the solution structure of HP0894, and studying its interaction with its substrates, if any, and/or with other proteins.

• Journal of the Korean Magnetic Resonance Society
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• v.19 no.3
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• pp.99-105
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• 2015

Hsp33 is a prokaryotic molecular chaperon that exerts a holdase activity upon response to an oxidative stress at raised temperature. In particular, intramolecular disulfide bond formation between the four conserved cysteines that bind a zinc ion in reduced state is known to be critically associated with the redox sensing. Here we report the backbone NMR assignment results of the half-oxidized Hsp33, where only two of the four cysteines form an intramolecular disulfide bond. Almost all of the resolved peaks could be unambiguously assigned, although the total assignments extent reached just about 50%. Majority of the missing assignments could be attributed to a significant spectral collapse, largely due to the oxidation-induced unfolding of the C-terminal redox-switch domain. These results support two previous suggestions: conformational change in the first oxidation step is localized mainly in the C-terminal zinc-binding domain, and the half-oxidized form would be still inactive. However, some additional regions appeared to be potentially changed from the reduced state, which suggest that the half-oxidized conformation would be an intermediate state that is more labile to heat and/or further oxidation.

• Journal of the Korean Magnetic Resonance Society
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• v.22 no.3
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• pp.64-70
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• 2018

Human Tid1, belonging to the family of the Hsp40/DnaJ, functions as a co-chaperone of cytosolic and mitochondrial Hsp70 proteins. In addition, the conserved J-domain and G/F-rich region of Tid1 has been suggested to interact with the p53 tumor suppressor protein, to translocate it to the mitochondria. Here, backbone NMR assignments were achieved for the putative p53-binding domain of Tid1. The obtained chemical shift information identified five ${\alpha}$-helices including four helices characteristic of J-domain, which are connected to a short ${\alpha}$-helix in the G/F-rich region via a flexible loop region. We expect that this structural information would contribute to our progressing studies to elucidate atomic structure and molecular interaction of the domain with p53.

• Journal of the Korean Magnetic Resonance Society
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• v.17 no.1
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• pp.59-66
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• 2013

BldD, a developmental transcription factor from Streptomyces coelicolor, is a homodimeric, DNA-binding protein with 167 amino acids in each subunit. Each monomer consists of two structurally distinct domains, the N-terminal domain (BldD-NTD) responsible for DNA-binding and dimerization and the C-terminal domain (BldD-CTD). In contrast to the BldD-NTD, of which crystal structure has been solved, the BldD-CTD has been characterized neither in structure nor in function. Thus, in terms of structural genomics, structural study of the BldD-CTD has been conducted in solution, and in the present work, mainchain NMR assignments of the recombinant BldD-CTD (residues 80-167 of BldD) could be achieved by a series of heteronuclear multidimensional NMR experiments on a [$^{13}C/^{15}N$]-enriched protein sample. Finally, the secondary structure prediction by CSI and TALOS+ analysis using the assigned chemical shifts data identified a ${\beta}-{\alpha}-{\alpha}-{\beta}-{\alpha}-{\alpha}-{\alpha}$ topology of the domain. The results will provide the most fundamental data for more detailed approach to the atomic structure of the BldD-CTD, which would be essential for entire understanding of the molecular function of BldD.

• Journal of the Korean Magnetic Resonance Society
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• v.21 no.1
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• pp.20-25
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• 2017

The cytoplasmic domains A and B of the mannitol transporter enzyme $II^{Mtl}$ are covalently linked in Escherichia coli, but separately expressed in Thermoanaerobacter Tengcongensis. The phosphorylation of domain B ($TtIIB^{Mtl}$) substantially increases the binding affinity to the domain A ($TtIIA^{Mtl}$) in T. Tengcongensis. To understand the structural basis of the enhanced domain-domain interaction by protein phosphorylation, we obtained NMR backbone assignments of the phospho-$TtIIB^{Mtl}$ using a standard suite of triple resonance experiments. Our results will be useful to monitor chemical shift changes at the active site of phosphorylation and the binding interfaces.

• Journal of the Korean Magnetic Resonance Society
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• v.19 no.1
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• pp.42-48
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• 2015

The mannitol transporter Enzyme $II^{Mtl}$ of the bacterial phosphotransferase system has two cytoplasmic phosphoryl transfer domains $IIA^{Mtl}$ and $IIB^{Mtl}$. The two domains are linked by a flexible peptide linker in mesophilic bacterial strains, whereas they are expressed as separated domains in thermophilic strains. Here, we carried out backbone assignment of $IIA^{Mtl}$ from thermophilic Thermoanaerobacter Tencongensis using a suite of heteronuclear triple resonance NMR spectroscopy. We have completed 94% of the backbone assignment, and obtained secondary structural information based on torsion angles derived from the chemical shifts. $IIA^{Mtl}$ of Thermoanaerobacter Tencongensis is predicted to have six ${\beta}$ strands and six ${\alpha}$ helices, which is analogous to $IIA^{Mtl}$ of Escherichia coli.