正標数の特異点における重複度と密着閉包の研究

科学研究費補助金 研究種目：基盤研究(C)　課題番号：16540021　研究代表者：吉田健一　研究期間：2004-2006年度research repor

歴史的土木資産の保全手法 : 震災復興橋梁における標準的仕様の実態 <平成12年度 共同研究の概要>

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Search for D0-D̅0 Mixing in D0→K+π- Decays and Measurement of the Doubly-Cabibbo-Suppressed Decay Rate

journal articl

第3章 資源管理は可能か

application/pdf図書の一部寶田康弘, 馬奈木俊介. 資源経済学への招待 : ケーススタディとしての水産業. 2010年, 268p.boo

Schematic representations of the primary structures of ChiW proteins.

ChiW denotes the full-length protein of Paenibacillus sp. str. FPU-7 ChiW; ChiW-SLHd (CBM-54, Ig-1, Cat-1, Ig-2 and Cat-2 domains), ChiW-CD (Cat-1, Ig-2 and Cat-2 domains) and CBM-54 of ChiW (CBM-54 domain) denote the truncated versions of ChiW. Boxes denote annotated structural elements. The numbers indicate the amino acid residue numbers. ChiW is specifically cleaved between Asn282 and Ser283. The position is pointed out as the cleavage site. Glu691 and Glu1177 are predicted to be catalytic residues and act as generic acids.</p

Crystal Structure of Chitinase ChiW from <i>Paenibacillus</i> sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery

<div><p>The Gram-positive bacterium <i>Paenibacillus</i> sp. str. FPU-7 effectively hydrolyzes chitin by using a number of chitinases. A unique chitinase with two catalytic domains, ChiW, is expressed on the cell surface of this bacterium and has high activity towards various chitins, even crystalline chitin. Here, the crystal structure of ChiW at 2.1 Å resolution is presented and describes how the enzyme degrades chitin on the bacterial cell surface. The crystal structure revealed a unique multi-modular architecture composed of six domains to function efficiently on the cell surface: a right-handed β-helix domain (carbohydrate-binding module family 54, CBM-54), a Gly-Ser-rich loop, 1st immunoglobulin-like (Ig-like) fold domain, 1st β/α-barrel catalytic domain (glycoside hydrolase family 18, GH-18), 2nd Ig-like fold domain and 2nd β/α-barrel catalytic domain (GH-18). The structure of the CBM-54, flexibly linked to the catalytic region of ChiW, is described here for the first time. It is similar to those of carbohydrate lyases but displayed no detectable carbohydrate degradation activities. The CBM-54 of ChiW bound to cell wall polysaccharides, such as chin, chitosan, β-1,3-glucan, xylan and cellulose. The structural and biochemical data obtained here also indicated that the enzyme has deep and short active site clefts with endo-acting character. The affinity of CBM-54 towards cell wall polysaccharides and the degradation pattern of the catalytic domains may help to efficiently decompose the cell wall chitin through the contact surface. Furthermore, we clarify that other Gram-positive bacteria possess similar cell-surface-expressed multi-modular enzymes for cell wall polysaccharide degradation.</p></div

Active site of ChiW.

<p>(<b>A</b> and <b>B</b>) The reaction product is located in the binding cleft of ChiW Cat-1. Electron density of the reaction product (GlcNAc)₂ (stick model: carbon atoms, yellow; oxygen atoms, red; and nitrogen atoms, blue) in the omit (<i>F</i>o–<i>F</i>c) map (cyan) (<b>A</b>) was calculated without the substrate and contoured at the 3.0-σ level. The ChiW residues (<b>B</b>) that interact with the product are represented by pink stick models (oxygen atoms, red and nitrogen atoms, blue). The numbers (−2 and −1) indicate the subsite positions. Other numbers indicate the amino acid residues. (<b>C</b>) The comparison of the catalytic cleft residues at the 5 subsites (−3 to +2) of ChiW Cat-1 (pink), Cat-2 (green) and SerChiA (cyan). The numbers indicate the amino acid residues of ChiW Cat-1.</p

Data collection and refinement statistics for ChiW structures.

<p>Data collection and refinement statistics for ChiW structures.</p

Close-up views of the structure of the catalytic region of ChiW.

<p><b>(A</b>) The overall catalytic region is shown as a ribbon model; front view (left figure) and side view (right figure). (<b>B</b>) Left figure, top view of the ChiW Cat-1 domain. The secondary structure elements (α-helices and β-strands) of the β₈/α₇-barrel are indicated by numbers. Right figure, side view of the ChiW Cat-1 domain. The secondary structure elements (α-helices and β-strands) of the extra subdomains (ID-1 and ID-2) are indicated by numbers. (<b>C</b>) Structural comparison of Cat-1 (orange) and Cat-2 (cyan). The three-dimensional structures are very similar (rmsd = 1.0 Å) with high amino acid sequence similarity (56% identity). (<b>D</b>) A comparison of the catalytic cleft of ChiW Cat-1 (orange ribbon model), and Cat-2 (cyan ribbon model). The amino acid residues (stick models), Trp568/Trp1055, Trp652/Trp1138, Asp687/Asp1173, Asp689/Asp1175, Glu691/Glu1177, Tyr766/Tyr1252, Trp772/Trp1258, Trp905/Trp1396, are near identical in the two active clefts. The amino acid residues (stick models), Lys573/Asn1060, Asp610/Glu1097, Ile613/Phe1098, Lys620/Gln1106, Trp698/Phe1184, Lys743/Pro1229 and Leu790/Phe1278, are located at the edge of the clefts. (<b>E</b>) Structural comparison of ChiW (orange) and BaChiA1CD (PDB ID: 1ITX; cyan). Their β₈/α₇-barrel core structures and ID-1 are similar, but significant differences exist in ID-2. The ChiW ID-2 forms the wall of the cleft, whereas the identical area of BaChiA1CD is positioned outside of the cleft.</p

Surface structure of ChiW catalytic domain.

<p>(<b>A-C</b>) The surface models of SmChiA (<b>A</b>), Cat-1 of ChiW (<b>B</b>) and BaChiA1CD (<b>C</b>). The side chains of the aromatic residues (Trp, Phe and Tyr) are shown in magenta. Electrostatic potentials at pH 7 are also represented. The +8 to –8 kT/e potential isocontours are shown as blue to red surfaces, respectively. ChiW catalytic domains have characteristic subdomains (ID-1 and ID-2) that form deep and short clefts surrounded by negative charges.</p