Nozomi Nagano

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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 highlight(More)
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 modified(More)
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 homologous genes(More)
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) database(More)
A preamplifier for 40-Gb/s optical transmission systems has been constructed using AlGaAs-InGaAs HBTs with p/sup +/ regrown extrinsic base layers. This preamplifier achieved a bandwidth of 34.6 GHz and a transimpedance gain of 41.6 dB/spl Omega/. This is the widest bandwidth in a preamplifier ever reported. These characteristics are suitable for use in a 40(More)
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 unique(More)
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 distinct(More)
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 small(More)
MOTIVATION 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. RESULTS The automatic selection of atoms so that site matches(More)
Vectors are denoted by boldfaced lower-case letters, and matrices by boldfaced upper-case letters. Elements of vectors and matrices are not bold-faced. The transposition of a matrix A is denoted by A and the inverse of A is denoted by A−1. The n × n identity matrix is denoted by In. We use Eij to denote a matrix in which (i, j) element is one and all the(More)