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Introduction
Constructing enzyme reaction database (EzCatDB, URL:http://ezcatdb.cbrc.jp/EzCatDB/)
Current institution
Publications
Publications (52)
Ustiloxins were found recently to be the first example of cyclic peptidyl secondary metabolites that are ribosomally synthesized in filamentous fungi. In this work, two function-unknown genes (ustYa/ustYb) in the gene cluster for ustiloxins from Aspergillus flavus were found experimentally to be involved in cyclization of the peptide. Their homolog...
During 11–12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus
in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as
CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centr...
As the volume of data relating to proteins increases, researchers rely more and more on the analysis of published data, thus increasing the importance of good access to these data that vary from the supplemental material of individual papers, all the way to major reference databases with professional staff and long-term funding. Specialist protein...
The EzCatDB database (http://ezcatdb.cbrc.jp/EzCatDB/) has emphasized manual classification of enzyme reactions from the viewpoints of enzyme active-site structures and their
catalytic mechanisms based on literature information, amino acid sequences of enzymes (UniProtKB) and the corresponding tertiary
structures from the Protein Data Bank (PDB). R...
Catalytic mechanisms of 270 enzymes from 131 superfamilies, mainly hydrolases and transferases, were analyzed based on their enzyme structures. A method of systematic comparison and classification of the catalytic reactions was developed. Hydrolysis and transfer reactions closely resemble one another, displaying common mechanisms, single displaceme...
Idiopathic pulmonary fibrosis (IPF) is a severe and progressive chronic fibrosing interstitial lung disease with causes that have remained unclear to date. Development of effective treatments will require elucidation of the detailed pathogenetic mechanisms of IPF at both the molecular and cellular levels. With a biomedical corpus that includes IPF-...
We present Disease Network Constructor
(DNC)1, a system that extracts and visualizes a
disease network, in which nodes are entities
such as diseases, proteins, and genes, and
edges represent regulation relation. We
focused on the disease network derived
through regulation events found in scientific
articles on idiopathic pulmonary fibrosis
(IPF). T...
The biosynthetic machinery of the first fungal ribosomally synthesized and post-translationally modified peptide (RiPP) ustiloxin B was elucidated through a series of gene inactivation and heterologous expression studies. The results confirmed an essential requirement for novel oxidases possessing the DUF3328 motif for macrocyclization, and highly...
The biosynthetic machinery of the first fungal ribosomally synthesized and post-translationally modified peptide (RiPP) ustiloxin B was elucidated through a series of gene inactivation and heterologous expression studies. The results confirmed an essential requirement for novel oxidases possessing the DUF3328 motif for macrocyclization, and highly...
Ustiloxin B, originally isolated from the fungus Ustilaginoidea virens, is a known inhibitor of microtubule assembly. Ustiloxin B is also produced by Aspergillus flavus and is synthesized through the ribosomal peptide synthesis pathway. In A. flavus, the gene cluster associated with ustiloxin B production contains 15 genes including those encoding...
Although many 3D structures have been solved for proteins to date, functions of some proteins remain unknown. To predict protein functions, comparison of local structures of proteins with pre-defined model structures, whose functions have been elucidated, is widely performed. For the comparison, the root mean square deviation (RMSD) has been used a...
キノコ以外の糸状菌で初めて，化合物の骨格構造が遺伝子に直接書き込まれたリボソームペプチド生合成（RiPS）経路を見出した．この特徴的な新規二次代謝経路は，ペプチド化合物のデザイン・合成系としても可能性を秘めている．
(URL https://katosei.jsbba.or.jp/index.php?aid=370) 化学と生物、(2015) 53:273-276
Motivation: Ustiloxins A and B are toxic cyclic tetrapeptides, Tyr-Val/Ala-Ile-Gly (Y-V/A-I-G), that were originally identified from Ustilaginoidea virens, a pathogenic fungus affecting rice plants. Contrary to our report that ustiloxin B is ribosomally synthesised in Aspergillus flavus, a recent report suggested that ustiloxins are synthesised by...
Ustiloxin B is a secondary metabolite known to be produced by Ustilaginoidea virens. In our previous paper, we observed the production of this compound by Aspergillus flavus, and identified two A. flavus genes responsible for ustiloxin B biosynthesis (Umemura et al., 2013). The compound is a cyclic tetrapeptide of Tyr-Ala-Ile-Gly, whose tyrosine is...
Determining enzyme functions is essential for a thorough understanding of cellular processes. Although many prediction methods have been developed, it remains a significant challenge to predict enzyme functions at the fourth-digit level of the Enzyme Commission numbers. Functional specificity of enzymes often changes drastically by mutations of a s...
Many bioactive natural products are produced as “secondary metabolites” by plants, bacteria, and fungi. During the middle of the 20th century, several secondary metabolites from fungi revolutionized the pharmaceutical industry, for example, penicillin, lovastatin, and cyclosporine. They are generally biosynthesized by enzymes encoded by clusters of...
Supplementary Materials This file provides the mathematical notations, the post-processing methods, the abbreviations, Figure 5–8, and Tables 3–5.
Predicting enzyme active-sites in proteins is an important issue not only for protein sciences but also for a variety of practical applications such as drug design. Because enzyme reaction mechanisms are based on the local structures of enzyme active-sites, various template-based methods that compare local structures in proteins have been developed...
It is an important problem to find functionally analogous enzymes based on the local structures of active-sites. Conventional methods predict active-sites by computing the deviations from the local-structure templates with no statistical parameters. We present a new statistical algorithm that uses parametric templates to compute the deviations of l...
Finding functionally analogous enzymes based on the local structures of active sites is an important problem. Conventional methods use templates of local structures to search for analogous sites, but their performance depends on the selection of atoms for inclusion in the templates.
The automatic selection of atoms so that site matches can be discr...
Most proteins from higher organisms are known to be multi-domain proteins and contain substantial numbers of intrinsically disordered (ID) regions. To analyse such protein sequences, those from human for instance, we developed a special protein-structure-prediction pipeline and accumulated the products in the Structure Atlas of Human Genome (SAHG)...
To investigate the relationships between functional subclasses and sequence and structural information contained in the active-site and ligand-binding residues (LBRs), we performed a detailed analysis of seven diverse enzyme superfamilies: aldolase class I, TIM-barrel glycosidases, alpha/beta-hydrolases, P-loop containing nucleotide triphosphate hy...
ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
重要な酵素の全てが産業に活用されている訳ではないが、酵素の中には、産業に活用されるべき酵素が実に多いのに著者は感銘を受けてきた。本稿では、酵素関連のデータベースを紹介すると共に、従来の酵素研究の問題点、著者が開発している酵素触媒機構データベース（EzCatDB）、重要な酵素の例について解説する。
http://mol.medicalonline.jp/archive/search?jo=ec6sebut&ye=2007&vo=47&nu=5
A universal rule is found about nucleotide sequence complementarities between the regions 2653-2666 in the GTPase-binding site of 23S rRNA and 1064-1077 of 16S rRNA as well as between the region 1103-1107 of 16S rRNA and GUUCG (or GUUCA) of tRNAs. This rule holds for all species in the living kingdoms except for two protista mitochondrial rRNAs of...
酵素触媒機構データベースEzCatDBを構築し、酵素蛋白質の触媒部位やリガンドとの対応関係などをアノテーションし、酵素触媒反応分類などを行っている（URL: http://mbs.cbrc.jp/EzCatDB/）。本稿では、特に酵素触媒反応分類について紹介する。
http://www.enzyme-eng.com/modules/pico02/index.php?content_id=9
EzCatDBは酵素反応をその立体構造、触媒機構、活性部位の構造パターンの観点から新たに捉え直し，分類した酵素触媒機構データベースである。本稿では、EzCatDBの活用法と関連する酵素・立体構造データベースについて紹介する。
The EzCatDB (Enzyme Catalytic-mechanism Database) specifically includes catalytic mechanisms of enzymes in terms of sequences
and tertiary structures of enzymes, and proposed catalytic mechanisms, along with ligand structures. The EzCatDB groups enzyme
data in the Protein Data Bank (PDB) and the SWISS-PROT database with identical domain composition...
http://www.jsbi.org/pdfs/journal1/GIW04/GIW04P074.pdf
https://www.jsbi.org/pdfs/journal1/GIW03/GIW03P140.pdf
In this paper, we have analyzed systematically the sequences, structures and functions of P-loop containing NTP hydrolase superfamily, using various techniques, such as PSI-BLAST [1] and a structural comparison method, MATRAS [2]
The eightfold (betaalpha) barrel structure, first observed in triose-phosphate isomerase, occurs ubiquitously in nature. It is nearly always an enzyme and most often involved in molecular or energy metabolism within the cell. In this review we bring together data on the sequence, structure and function of the proteins known to adopt this fold. We h...
There are currently at least nine distinct glycosidase sequence families which are all known to adopt a TIM barrel fold [Henrissat,B. and Davies,G. (1997) CURR: Opin. Struct. Biol., 7, 637-644]. To explore the relationships between these enzymes and their evolution, comprehensive sequence and structure comparisons were performed, generating four di...
There are currently at least nine distinct glycosidase sequence families which are all known to adopt a TIM barrel fold [Henrissat,B. and Davies,G. (1997) CURR: Opin. Struct. Biol., 7, 637-644]. To explore the relationships between these enzymes and their evolution, comprehensive sequence and structure comparisons were performed, generating four di...
The differences between disulfide-bonding cystine (Cys_SS) and free cysteine (Cys_SH) residues were examined by analyzing the statistical distribution of both types of residue in proteins of known structure. Surprisingly, Cys_SH residues display stronger hydrophobicity than Cys_SS residues. A detailed survey of atoms which come into contact with th...
Automated methods for identifying and characterizing regular β-barrels from coordinate data have been developed to analyze and classify various kinds of barrel structures based on geometric parameters such as the barrel strand number (n) and shear number (S). In total, we find 1,316 barrels in the January 1998 release of Protein Data Bank. Of 1,316...
Motivation:
TOPS cartoons are a schematic ion of protein three-dimensional structures in two dimensions, and are used for understanding and manual comparison of protein folds. Recently, an algorithm that produces the cartoons automatically from protein structures has been devised and cartoons have been generated to represent all the structures in...
Various experimental data have been supporting an idea that the conformation of A-site tRNA is different from that of P-site tRNA and have led to a new tRNA docking pair model, in which the highly conserved G18 and G19 of D-loop in A-site tRNA and C56 and C61 of T psi C-loop in P-site tRNA base pair exist along with the conventional base pairs of a...
A consensus has been reached that the conformation of the anticodon—codon interactions of two adjacent tRNA molecules on the
ribosome is a Sundaralingam-type (S-type). Even if it is kept to the S-type, there are still various possibilities. Various
experimental data have been supporting an idea that the conformation of A-site tRNA is different from...
Melittin is known to be a major hydrophobic peptide component in honeybee venom that can cause as much elevation of fertilization membrane of sea urchin eggs as normal fertilization. The action of melittin has been thought to be closely related with its ability to facilitate the phospholipase A2 activity on the eggs. However, another peptide "masto...
