Rice dwarf virus (RDV), the causal agent of rice dwarf disease, is a member of the genus Phytoreovirus in the family Reoviridae. RDV is a double-shelled virus with a molecular mass of approximately 70 million Dalton. This virus is widely prevalent and is one of the viruses that cause the most economic damage in many Asian countries. The atomic structure of RDV was determined at 3.5 A resolution by X-ray crystallography. The double-shelled structure consists of two different proteins, the core protein P3 and the outer shell protein P8. The atomic structure shows structural and electrostatic complementarities between both homologous (P3-P3 and P8-P8) and heterologous (P3-P8) interactions, as well as overall conformational changes found in P3-P3 dimer caused by the insertion of amino-terminal loop regions of one of the P3 protein into the other. These interactions suggest how the 900 protein components are built into a higher-ordered virus core structure.

Coagulation factors IX/X-binding protein is an intertwined dimer with a central loop projecting into the adjoining subunit. Excluding this loop, each subunit has a fold similar to rat mannose-binding protein.

␣-Galactosidases catalyze the hydrolysis of ␣-1,6-linked galactosyl residues from galacto-oligosaccharides and polymeric galacto-(gluco)mannans. The crystal structure of rice ␣-galactosidase has been determined at 1.5Å resolution using the multiple isomorphous replacement method. The structure consisted of a catalytic domain and a C-terminal domain and was essentially the same as that of ␣-N-acetylgalactosaminidase, which is the same member of glycosyl hydrolase family 27. The catalytic domain had a (␤/␣) 8 -barrel structure, and the C-terminal domain was made up of eight ␤-strands containing a Greek key motif. The structure was solved as a complex with D-galactose, providing a mode of substrate binding in detail. The D-galactose molecule was found bound in the active site pocket on the C-terminal side of the central ␤-barrel of the catalytic domain. The D-galactose molecule consisted of a mixture of two anomers present in a ratio equal to their natural abundance. Structural comparisons of rice ␣-galactosidase with chicken ␣-N-acetylgalactosaminidase provided further understanding of the substrate recognition mechanism in these enzymes. ␣-Galactosidases (␣-Gals1 ; E.C. 3.2.1.22) catalyze the hydrolysis of ␣-1,6-linked galactosyl residues from galacto-oligosaccharides and polymeric galacto-(gluco)mannans. ␣-Gals are widely distributed in animals, plants, and microorganisms.In humans, ␣-Gal is a lysosomal exoglycosidase that cleaves the terminal ␣-galactose residue from glycolipids and glycoproteins. Mutations in the ␣-Gal gene cause incomplete degradation of carbohydrates, resulting in Fabry disease (1, 2). In plants, galactomannan is one of the major storage polysaccharides in seeds, and ␣-Gal is one of the key enzymes in the degradation of cell wall galactomannan during germination (3, 4). Raffinose and stachyose in beans are known to cause flatulence, and ␣-Gal has the potential to alleviate these symptoms (5). In the sugar beet industry, ␣-Gal has been used to increase the sucrose yield by eliminating raffinose, which prevents normal crystallization of beet sugar (6).We have purified and sequenced several ␣-Gals from Mortierella vinacea, Penicillium purpurogenum, Thermus sp. T2, and Oryza sativa L. and have elucidated the substrate specificities of these enzymes using two types of the galactomannooligosaccharides, 63 -mono-␣-D-galactopyranosyl-␤-1,4-mannotriose and 6 3 -mono-␣-D-galactopyranosyl-␤-1,4-mannotetraose (7-13). The results showed that ␣-Gals have a diverse preference for substrates. The M. vinacea ␣-Gal I and yeast ␣-Gals were specific only for 6 3 -mono-␣-D-galactopyranosyl-␤-1,4-mannotriose, which has an ␣-galactosyl residue (designated the terminal ␣-galactosyl residue) linked to the non-reducing end mannose of ␤-1,4-mannotriose (14, 15). Aspergillis niger ␣-Gal and P. purpurogenum ␣-Gal, however, showed a preference for 6 3 -mono-␣-D-galactopyranosyl-␤-1,4-mannotetraose, which has an ␣-galactosyl residue (designated the side-chain ␣-galactosyl residue) attached to the inner mannose of ␤-1,4-ma...

The ␥-carboxyglutamic acid (Gla) domain of blood coagulation factors is responsible for Ca 2؉ -dependent phospholipid membrane binding. Factor X-binding protein (X-bp), an anticoagulant protein from snake venom, specifically binds to the Gla domain of factor X. The crystal structure of X-bp in complex with the Gla domain peptide of factor X at 2.3-Å resolution showed that the anticoagulation is based on the fact that two patches of the Gla domain essential for membrane binding are buried in the complex formation. The Gla domain thus is expected to be a new target of anticoagulant drugs, and X-bp provides a basis for designing them. This structure also provides a membrane-bound model of factor X.

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2؉ion, which formed a bridge between IXGD1-46 and IXbp, forced IXGD1-46 to rotate 4°relative to IX-bp and hence might be the cause of a more tight interaction between the molecules than in the case of the Mg 2؉ -free structure. The results clearly suggest that Mg 2؉ ions are required to maintain native conformation and in vivo function of factor IX Gla domain during blood coagulation.

Carbazole 1,9a-dioxygenase (CARDO), a member of the Rieske nonheme iron oxygenase system (ROS), consists of a terminal oxygenase (CARDO-O) and electron transfer components (ferredoxin [CARDO-F] and ferredoxin reductase [CARDO-R]). We determined the crystal structures of the nonreduced, reduced, and substrate-bound binary complexes of CARDO-O with its electron donor, CARDO-F, at 1.9, 1.8, and 2.0 A resolutions, respectively. These structures provide the first structure-based interpretation of intercomponent electron transfer between two Rieske [2Fe-2S] clusters of ferredoxin and oxygenase in ROS. Three molecules of CARDO-F bind to the subunit boundary of one CARDO-O trimeric molecule, and specific binding created by electrostatic and hydrophobic interactions with conformational changes suitably aligns the two Rieske clusters for electron transfer. Additionally, conformational changes upon binding carbazole resulted in the closure of a lid over the substrate-binding pocket, thereby seemingly trapping carbazole at the substrate-binding site.

Ants are eusocial insects that are found in most regions of the world. Within its caste, worker ants are responsible for various tasks that are required for colony maintenance. In their chemical communication, α-helical carrier proteins, odorant-binding proteins, and chemosensory proteins, which accumulate in the sensillum lymph in the antennae, play essential roles in transferring hydrophobic semiochemicals to chemosensory receptors. It has been hypothesized that semiochemicals are recognized by α-helical carrier proteins. The number of these proteins, however, is not sufficient to interact with a large number of semiochemicals estimated from chemosensory receptor genes. Here we shed light on this conundrum by identifying a Niemann–Pick type C2 (NPC2) protein from the antenna of the worker Japanese carpenter ant, Camponotus japonicus (CjapNPC2). CjapNPC2 accumulated in the sensillum cavity in the basiconic sensillum. The ligand-binding pocket of CjapNPC2 was composed of a flexible β-structure that allowed it to bind to a wide range of potential semiochemicals. Some of the semiochemicals elicited electrophysiolgical responses in the worker antenna. In vertebrates, NPC2 acts as an essential carrier protein for cholesterol from late endosomes and lysosomes to other cellular organelles. However, the ants have evolved an NPC2 with a malleable ligand-binding pocket as a moderately selective carrier protein in the sensillum cavity of the basiconic sensillum. CjapNPC2 might be able to deliver various hydrophobic semiochemicals to chemosensory receptor neurons and plays crucial roles in chemical communication required to perform the worker ant tasks.