A Novel Structural Fold in Polysaccharide Lyases

Ochiai, Akihito; Itoh, Takafumi; Maruyama, Yukie; Kawamata, Akiko; Mikami, Bunzo; Hashimoto, Wataru; Murata, Kousaku

doi:10.1074/jbc.m704663200

Cited by 29 publications

(11 citation statements)

References 70 publications

(58 reference statements)

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“…Here we report similar motifs in differently sized propeller domains of two bacterial proteins, Bacillus subtilis rhamnogalacturonan lyase [24] and Pseudomonas aeruginosa PilY1 [25] and a fungal lectin [26]. The resemblance of the motif of the last to the EF-hand has not previously been noted.…”

Section: Resultsmentioning

confidence: 53%

New Structural and Functional Contexts of the Dx[DN]xDG Linear Motif: Insights into Evolution of Calcium-Binding Proteins

et al. 2011

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Binding of calcium ions (Ca2+) to proteins can have profound effects on their structure and function. Common roles of calcium binding include structure stabilization and regulation of activity. It is known that diverse families – EF-hands being one of at least twelve – use a Dx[DN]xDG linear motif to bind calcium in near-identical fashion. Here, four novel structural contexts for the motif are described. Existing experimental data for one of them, a thermophilic archaeal subtilisin, demonstrate for the first time a role for Dx[DN]xDG-bound calcium in protein folding. An integrin-like embedding of the motif in the blade of a β-propeller fold – here named the calcium blade – is discovered in structures of bacterial and fungal proteins. Furthermore, sensitive database searches suggest a common origin for the calcium blade in β-propeller structures of different sizes and a pan-kingdom distribution of these proteins. Factors favouring the multiple convergent evolution of the motif appear to include its general Asp-richness, the regular spacing of the Asp residues and the fact that change of Asp into Gly and vice versa can occur though a single nucleotide change. Among the known structural contexts for the Dx[DN]xDG motif, only the calcium blade and the EF-hand are currently found intracellularly in large numbers, perhaps because the higher extracellular concentration of Ca2+ allows for easier fixing of newly evolved motifs that have acquired useful functions. The analysis presented here will inform ongoing efforts toward prediction of similar calcium-binding motifs from sequence information alone.

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Section: Resultsmentioning

confidence: 53%

New Structural and Functional Contexts of the Dx[DN]xDG Linear Motif: Insights into Evolution of Calcium-Binding Proteins

et al. 2011

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“…Traoré's study reveals that the Zn(Cys)4 site locks the dimerization domain and stabilizes the dimer of protein PerR [34]. Ochiai and colleagues show that a calcium ion coordinated by Asp401, Glu422, His363, and His399 is required for the enzyme activity of rhamnogalacturonan lyase YesW [38]. Sankaranarayanan and colleagues point out that a zinc ion is directly involved in threonine recognition, forming a pentacoordinate intermediate with both the amino group and the side chain hydroxyl and mediated AA discrimination by threonyl-tRNA synthetase [39].…”

Section: Resultsmentioning

confidence: 99%

Investigation of Atomic Level Patterns in Protein—Small Ligand Interactions

Chen

Kurgan

2009

PLoS ONE

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BackgroundShape complementarity and non-covalent interactions are believed to drive protein-ligand interaction. To date protein-protein, protein-DNA, and protein-RNA interactions were systematically investigated, which is in contrast to interactions with small ligands. We investigate the role of covalent and non-covalent bonds in protein-small ligand interactions using a comprehensive dataset of 2,320 complexes.Methodology and Principal FindingsWe show that protein-ligand interactions are governed by different forces for different ligand types, i.e., protein-organic compound interactions are governed by hydrogen bonds, van der Waals contacts, and covalent bonds; protein-metal ion interactions are dominated by electrostatic force and coordination bonds; protein-anion interactions are established with electrostatic force, hydrogen bonds, and van der Waals contacts; and protein-inorganic cluster interactions are driven by coordination bonds. We extracted several frequently occurring atomic-level patterns concerning these interactions. For instance, 73% of investigated covalent bonds were summarized with just three patterns in which bonds are formed between thiol of Cys and carbon or sulfur atoms of ligands, and nitrogen of Lys and carbon of ligands. Similar patterns were found for the coordination bonds. Hydrogen bonds occur in 67% of protein-organic compound complexes and 66% of them are formed between NH- group of protein residues and oxygen atom of ligands. We quantify relative abundance of specific interaction types and discuss their characteristic features. The extracted protein-organic compound patterns are shown to complement and improve a geometric approach for prediction of binding sites.Conclusions and SignificanceWe show that for a given type (group) of ligands and type of the interaction force, majority of protein-ligand interactions are repetitive and could be summarized with several simple atomic-level patterns. We summarize and analyze 10 frequently occurring interaction patterns that cover 56% of all considered complexes and we show a practical application for the patterns that concerns interactions with organic compounds.

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“…The crystal structures of PLs in 18 families have been determined, and the structure and functional relationships of enzymes such as pectin lyase in family PL-1 (14); pectate lyases in families PL-2, PL-3, and PL-10 (15-17); alginate lyases in families PL-5, PL-7, and PL-14 (13,18,19); rhamnogalacturonan lyases in families PL-4 and PL-11 (20,21); chondroitin lyases in families PL-6 and PL-8 (22); hyaluronan lyases in families PL-8 and PL-16 (23,24); heparin lyases in families PL-13 and PL-21 (25,26); and xanthan lyase in family PL-8 (12) have been demonstrated. On the other hand, no structural information on family PL-15 alginate lyases has been accumulated, and the enzyme mechanism for releasing unsaturated monosaccharides from the polysaccharide main chain remains to be clarified.…”

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confidence: 99%

Crystal Structure of Exotype Alginate Lyase Atu3025 from Agrobacterium tumefaciens

Ochiai

Yamasaki

Mikami

et al. 2010

Journal of Biological Chemistry

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Alginate, a major component of the cell wall matrix in brown seaweeds, is degraded by alginate lyases through a ␤-elimination reaction. Almost all alginate lyases act endolytically on substrate, thereby yielding unsaturated oligouronic acids having 4-deoxy-L-erythro-hex-4-enepyranosyluronic acid at the nonreducing end. In contrast, Agrobacterium tumefaciens alginate lyase Atu3025, a member of polysaccharide lyase family 15, acts on alginate polysaccharides and oligosaccharides exolytically and releases unsaturated monosaccharides from the substrate terminal. The crystal structures of Atu3025 and its inactive mutant in complex with alginate trisaccharide (H531A/⌬GGG) were determined at 2.10-and 2.99-Å resolutions with final R-factors of 18.3 and 19.9%, respectively, by x-ray crystallography. The enzyme is comprised of an ␣/␣-barrel ؉ anti-parallel ␤-sheet as a basic scaffold, and its structural fold has not been seen in alginate lyases analyzed thus far. The structural analysis of H531A/⌬GGG and subsequent site-directed mutagenesis studies proposed the enzyme reaction mechanism, with His 311 and Tyr 365 as the catalytic base and acid, respectively. Two structural determinants, i.e. a short ␣-helix in the central ␣/␣-barrel domain and a conformational change at the interface between the central and C-terminal domains, are essential for the exolytic mode of action. This is, to our knowledge, the first report on the structure of the family 15 enzyme.Carbohydrate-active enzymes such as glycoside hydrolases, polysaccharide lyases, glycosyl transferases, and carbohydrate esterases are categorized into more than 200 families based on amino acid sequences in the Carbohydrate-Active enZYmes (CAZy) data base (1). Polysaccharide lyases (PLs) 2 are classified into 21 PL families and they play an important role in degrading acidic polysaccharides such as polygalacturonan, rhamnogalacturonan, alginate, chondroitin, hyaluronan, heparin, heparan, and xanthan. These lyases commonly recognize uronic acid residues in polysaccharides, catalyze ␤-elimination, and produce unsaturated saccharides with CϭC double bonds at nonreducing terminal uronate residues.Alginate, produced by brown seaweeds as a major component of the cell wall matrix, is a linear polysaccharide composed of ␣-L-guluronate (G) and its C5 epimer ␤-D-mannuronate (M). Three blocks, such as poly-␣-L-guluronate (poly(G)), poly-␤-D-mannuronate (poly(M)), and heteropolymeric random sequences (poly(MG)), constitute the alginate polymer (2). The alginate degradation pathway has been characterized in some bacteria, virus, and abalone. In the bacterium Sphingomonas sp. strain A1, alginate is directly incorporated into the cytoplasm by the cell surface pit, periplasmic binding proteins, and ATPbinding cassette transporter. The incorporated alginate is subsequently depolymerized into unsaturated disaccharides, trisaccharides, and tetrasaccharides through the action of three cytoplasmic endotype alginate lyases, A1-I, A1-II, and A1-III (Fig. 1A) (3). The unsaturated oligosaccha...

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A Novel Structural Fold in Polysaccharide Lyases

Cited by 29 publications

References 70 publications

New Structural and Functional Contexts of the Dx[DN]xDG Linear Motif: Insights into Evolution of Calcium-Binding Proteins

New Structural and Functional Contexts of the Dx[DN]xDG Linear Motif: Insights into Evolution of Calcium-Binding Proteins

Investigation of Atomic Level Patterns in Protein—Small Ligand Interactions

Crystal Structure of Exotype Alginate Lyase Atu3025 from Agrobacterium tumefaciens

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