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Biomedical subjects

Nobuhisa Watanabe

Publications and source records attributed to Nobuhisa Watanabe.

At least 19 recordsLinked to original sources
PubMed2007

Correlation of low-volatile organic chlorine (LVOCl) and PCDD/Fs in various municipal waste incinerators (MWIs).

Medium- and low-volatile organic chlorine (M/LVOCl) and PCDD/Fs in flue gas from various municipal waste incinerators (MWIs) were monitored. The sample for M/LVOCl was collected in an adsorption tube which was thermally desorbed and the amount of chlorine was measured by atomic emission spectrometry (AES) detection using radiofrequency helium plasma. The helium plasma excited chlorine having an optical emission line of 837.6 nm was monitored. The MVOCl and LVOCl were organic chlorine groups whose boiling points (bp) ranged from 70-120 degrees C and 170-270 degrees C, respectively. The compounds having bp 120-170 degrees C were distributed in two tubes. LVOCl correlated well with PCDD/Fs (ng/Nm3, r=0.81) in a wide range of 0.01-100 ng/Nm3 of PCDD/Fs, while the correlation of LVOCl vs. TEQ was less related (r=0.69). These results agreed with the fact that LVOCl monitored the amount of organic chlorine without molecular structure information, which is critical to toxicity. Since the bp of LVOCl was not identical with that of PCDD/Fs, the regression was effected by the conditions of the gas treatment devices. Because most data of 2001 were collected just after the installation of PCDD/Fs in MWIs, the regression of 2001 was slightly different from that of 2002-2003. Eliminating these initial unsteady data, the regression of LVOCl vs. PCDD/Fs became better, giving r= 0.86. Besides having PCDD/Fs as surrogates, M/LVOCl is valuable as a versatile element-selective organic chlorine monitor to improve thermal process control.

Air Pollutants↗
PubMed2007

DNA recognition mechanism of the ONECUT homeodomain of transcription factor HNF-6.

Hepatocyte nuclear factor-6 (HNF-6), a liver-enriched transcription factor, controls the development of various tissues, such as the pancreas and liver, and regulates the expression of several hepatic genes. This protein belongs to the ONECUT class of homeodomain proteins and contains a bipartite DNA-binding domain composed of a single cut domain and a characteristic homeodomain. This transcription factor has two distinct modes of DNA binding and transcriptional activation that use different coactivators depending on the target gene. The crystal structure of the bipartite DNA-binding domain of HNF-6alpha complexed with the HNF-6-binding site of the TTR promoter revealed the DNA recognition mechanism of this protein. Comparing our structure with the DNA-free structure of HNF-6 or the structure of Oct-1, we discuss characteristic features associated with DNA binding and the structural basis for the dual mode of action of this protein, and we suggest a strategy for variability of transcriptional activation of the target gene.

Amino Acid Sequence↗
PubMed2006

Structural and mutational analyses of Drp35 from Staphylococcus aureus: a possible mechanism for its lactonase activity.

Drp35 is a protein induced by cell wall-affecting antibiotics or detergents; it possesses calcium-dependent lactonase activity. To determine the molecular basis of the lactonase activity, we first solved the crystal structures of Drp35 with and without Ca(2+); these showed that the molecule has a six-bladed beta-propeller structure with two calcium ions bound at the center of the beta-propeller and surface region. Mutational analyses of evolutionarily conserved residues revealed that the central calcium-binding site is essential for the enzymatic activity of Drp35. Substitution of some other amino acid residues for the calcium-binding residues demonstrated the critical contributions of Glu(48), Asp(138), and Asp(236) to the enzymatic activity. Differential scanning calorimetric analysis revealed that the loss of activity of E48Q and D236N, but not D138N, was attributed to their inability to hold the calcium ion. Further structural analysis of the D138N mutant indicates that it lacks a water molecule bound to the calcium ion rather than the calcium ion itself. Based on these observations and structural information, a possible catalytic mechanism in which the calcium ion and its binding residues play direct roles was proposed for the lactonase activity of Drp35.

Amino Acid Substitution↗
PubMed2006

SAD phasing by OASIS-2004: case studies of dual-space fragment extension.

The principle of dual-space phasing is used in dealing with protein SAD data. Four programs are involved in iterative dual-space fragment extension to improve automatic model building. OASIS-2004 is used to break the phase ambiguity intrinsic in the SAD experiment. In the initial cycle, discrimination of SAD phase doublets is performed by the direct method incorporating the known anomalous-scattering substructure. In subsequent cycles, discrimination is performed by the direct method incorporating both the known anomalous-scattering substructure and the partial protein structure obtained from model building in the preceding cycle. DM is used to improve direct-method phases via density modification. RESOLVE is used for initial model building and ARP/wARP is used to complete the structure. Case studies with three sets of difficult SAD data showed that the procedure is beneficial to high-throughput protein-structure determination and all of the four programs involved make their unique contribution to the process.

Models, Molecular↗
PubMed2006

From phasing to structure refinement in-house: Cr/Cu dual-wavelength system and a loopless free crystal-mounting method.

The practical applicability of in-house structure determination using Cr K alpha X-rays (2.29 A) and a loopless free crystal-mounting method was examined using five novel proteins. Proteins from 9.6 to 84 kDa have been solved using this method without any derivatization. In all cases, more than 90% of structures were constructed automatically with side chains by use of the Cr SAD method. The free crystal-mounting technique increases the accuracy of the anomalous differences between Bijvoet mates and makes the in-house single-wavelength SAD method with a Cr K alpha X-ray source a very useful tool for high-throughput structure determination. In addition, a Cr/Cu dual-wavelength system makes it possible to perform structure analysis from phasing to refinement of the structure in-house.

Chromium↗
PubMed2006

Structure of the catalytic nucleotide-binding subunit A of A-type ATP synthase from Pyrococcus horikoshii reveals a novel domain related to the peripheral stalk.

H(+)-transporting ATP synthase is a multi-subunit enzyme involved in the production of ATP, which is an essential molecule for living organisms as a source of energy. Archaeal A-type ATPase (A-ATPase) is thought to act as a functional ATP synthase in archaea and is thought to have chimeric properties of F-ATPase and V-ATPase. Previous structural studies of F-ATPase indicated that the major nucleotide-binding subunits alpha and beta consist of three domains. The catalytic nucleotide-binding subunit A of V/A-ATPase contains an insertion of about 90 residues which is absent from the F(1)-ATPase beta subunit. Here, the first X-ray structure of the catalytic nucleotide-binding subunit A of an A(1)-ATPase is described, determined at 2.55 A resolution. A(1)-ATPase subunit A from Pyrococcus horikoshii consists of four domains. A novel domain, including part of the insertion, corresponds to the 'knob-like structure' observed in electron microscopy of A(1)-ATPase. Based on the structure, it is highly likely that this inserted domain is related to the peripheral stalk common to the A- and V-ATPases. The arrangement of this inserted domain suggests that this region plays an important role in A-ATPase as well as in V-ATPase.

Amino Acid Sequence↗
PubMed2006

Crystallization and preliminary X-ray studies of the DNA-binding domain of hepatocyte nuclear factor-6alpha complexed with DNA.

Hepatocyte nuclear factor 6 (HNF-6)/OC-1, a part of liver-enriched transcription factor, controls pancreas and liver development and regulates expression of several hepatic genes. DNA-binding region of HNF-6alpha bound to a 14-mer DNA fragment has been crystallized by the hanging drop vapor diffusion method. The crystals belong to space group P2 with unit cell parameters of a = 73.0 A, b = 39.0 A, c = 106.5 A, beta = 107.6 degrees. X-ray diffraction data were collected to 2.0 A resolution.

Base Sequence↗
PubMed2006

Estimation and control of atmospheric emissions of chloroform and dichloromethane due to laboratory activity.

In Japanese universities, the management of chemical reagents has become an important issue in preserving the environment and the health of students and researchers. It is thus necessary to estimate the levels of chemical emissions into the environment and to measure working-environment chemical levels in laboratories. However, there are many laboratories in universities using many chemical reagents for their own needs. Hence, it is difficult for universities to quantitate the amount of chemicals on campus, and there is a lack of information about laboratory environment chemical levels. In this study, the material balance of chloroform and dichloromethane (DCM) in Kyoto University was examined, and the emission rates of chloroform and DCM were estimated to be 37-50% and 50-70%, respectively. These chemicals were thought to be volatilized mainly through reduced-pressure distillation. However, it was found that there was a loss of chemicals due to volatility, which researchers were unaware of, such as that during solvent recovery under reduced pressure and volatilization from containers of organic waste liquid. On the other hand, working-environment chemical levels were measured in several laboratories which used chloroform and DCM frequently. Even in such laboratories, the average concentrations of these chemicals were approximately 1 ppm at most measurement points.

Air Pollution↗
PubMed2005

Comparison of phasing methods for sulfur-SAD using in-house chromium radiation: case studies for standard proteins and a 69 kDa protein.

Phasing of the crystal structures of four standard proteins (lysozyme, trypsin, glucose isomerase and thaumatin) and a novel 69 kDa protein from Thermus thermophilus, TT0570, was performed using the single-wavelength anomalous diffraction of S atoms intrinsically present within the native protein molecules. To utilize the sulfur anomalous diffraction, the data sets were collected using the loopless data-collection method with chromium Kalpha X-rays of wavelength 2.29 A. Three phasing methods, MLPHARE, SHARP and OASIS-2004, were tested in combination with the DM or SOLOMON density-modification method. The results showed that the solvent contents are still an important factor for phasing with the S-SAD method, even when longer wavelength Cr Kalpha radiation is used. Of the three procedures, the improved direct phasing of OASIS-2004 with its implemented fragment feedback to the direct-method probability calculation gave the best results in determining the initial phases. For all five proteins, almost the entire models could be built automatically.

Aldose-Ketose Isomerases↗
PubMed2005

The CGL2612 protein from Corynebacterium glutamicum is a drug resistance-related transcriptional repressor: structural and functional analysis of a newly identified transcription factor from genomic DNA analysis.

The emergence of antibiotic-resistant bacteria often causes serious clinical problems. The TetR family is one of the major transcription factor families that regulate expression of genes involved in bacterial antimicrobial resistance systems. CGL2612 protein is a transcription factor newly identified by genomic DNA analysis on Corynebacterium glutamicum, which belongs to the mycolic acid-containing Actinomycetales, including the well known pathogens Corynebacterium diphtheriae and Mycobacterium tuberculosis. Crystal structure analysis showed that the CGL2612 protein exhibits significant structural similarity to the multidrug resistance (MDR)-related transcription factor QacR from Staphylococcus aureus, despite poor amino acid sequence similarity between these proteins. Binding DNA sequence analysis of CGL2612 protein using the systematic evolution of ligands by the exponential enrichment (systematic evolution of ligands by exponential enrichment, or SELEX) method revealed that this protein is a new member of the TetR family, which regulates expression of the immediately upstream gene, cgl2611, probably encoding a major facilitator superfamily permease. Subsequent functional analyses confirmed a function of the CGL2612 as a transcriptional repressor responsible for the antimicrobial resistance system in C. glutamicum. The strategy used in the present study is one of the most convenient and powerful methods to analyze functionally unknown transcription factors, and the results obtained here will contribute to our understanding of the drug resistance mechanism not only in C. glutamicum but also in the related bacteria, C. diphtheriae and M. tuberculosis.

Amino Acid Sequence↗
PubMed2005

Structure determination of a novel protein by sulfur SAD using chromium radiation in combination with a new crystal-mounting method.

A novel and easy crystal-mounting technique was developed for the sulfur SAD method using Cr Kalpha radiation (2.29 A). Using this technique, the cryo-buffer and cryoloop around the protein crystal can be removed before data collection in order to eliminate their X-ray absorption. The superiority and reproducibility of the data sets with this mounting technique were demonstrated using tetragonal hen egg-white lysozyme crystals. The structure of a novel protein, PH1109, from Pyrococcus horikoshii OT3 was solved using this technique. At the wavelength of Cr Kalpha radiation, the anomalous signal |DeltaF|/|F| of PH1109 is expected to be 1.72% as this protein of 144 residues includes four methionines and two cysteines. Sulfur SAD phasing was performed using SHELXD and SHELXE. In the case of the data set obtained using this novel crystal-mounting technique, 54.9% of all residues were built with side chains automatically by RESOLVE. On the other hand, only 16.0% were built with side chains for the data set collected using the standard cryoloop. These results indicated that this crystal-mounting technique was superior to the standard loop-mounting method for the measurement of small anomalous differences at longer wavelength and yielded better results in sulfur-substructure solution and initial phasing. The present study demonstrates that the sulfur SAD method with a chromium source becomes enhanced and more practical for macromolecular structure determination using the new crystal-mounting technique.

Absorption↗
PubMed2004

Structural and enzymatic properties of 1-aminocyclopropane-1-carboxylate deaminase homologue from Pyrococcus horikoshii.

1-Aminocyclopropane-l-carboxylate deaminase (ACCD) is a pyridoxal 5/-phosphate dependent enzyme that shows deaminase activity toward ACC, a precursor of plant hormone ethylene. ACCD from some soil bacteria has been reported to be able to break the cyclopropane ring of ACC to yield a-ketobutyrate and ammonia. We reported the crystal structure of ACCD from the yeast Hansenula saturnus in the absence/presence of substrate ACC, and proposed its ingenious reaction mechanisms. In order to study the enzyme further, we overexpressed the ACCD homologue protein (phAHP) from the fully decoded hyperthermophilic archearon, Pyrococcus horikoshii OT3. However, phAHP does not show ACCD activity at high temperature as well as at room temperature, though it has significant sequence similarity. Instead of ACCD activity, the GC-MS analysis and enzymatic method show that phAHP has deaminase activity toward L and D-serine. Here, we present the crystal structures of the native and ACC-complexed phAHP. The overall topology of the phAHP structure is very similar to that of ACCD; however, critical differences were observed around the active site. Here, the differences of enzymatic activity between phAHP and ACCD are discussed based on the structural differences of these two proteins. We suggest that the catalytic disagreement between these two enzymes comes from the difference of the residues near the pyridine ring of pyridoxal 5'-phosphate (PLP), not the difference of the catalytic residues themselves. We also propose a condition necessary in the primary sequence to have ACCD activity.

Amino Acid Sequence↗
PubMed2004

Preparation and preliminary X-ray analysis of the catalytic module of beta-1,3-xylanase from the marine bacterium Vibrio sp. AX-4.

Beta-1,3-xylanase (1,3-beta-D-xylan xylanohydrolase; EC 3.2.1.32) is an enzyme capable of hydrolyzing beta-1,3-xylan. The newly cloned beta-1,3-xylanase from the marine bacterium Vibrio sp. AX-4 (XYL4) exhibited a modular structure consisting of three modules: an N-terminal catalytic module belonging to glycoside hydrolase family 26 and two C-terminal xylan-binding modules belonging to carbohydrate-binding module family 31. Despite substantial crystallization screening, crystallization of the recombinant XYL4 was not accomplished. However, the deletion mutant of XYL4, composed of a catalytic module without a xylan-binding module, was crystallized. The crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 51.6, b = 75.8, c = 82.0 A. X-ray diffraction data were collected to 1.44 A resolution.

Catalytic Domain↗