Biomedical subjects

Zui Fujimoto

Publications and source records attributed to Zui Fujimoto.

31 records · Page 2Linked to original sources

PubMed2003

Crystal structures of decorated xylooligosaccharides bound to a family 10 xylanase from Streptomyces olivaceoviridis E-86.

The family 10 xylanase from Streptomyces olivaceoviridis E-86 (SoXyn10A) consists of a GH10 catalytic domain, which is joined by a Gly/Pro-rich linker to a family 13 carbohydrate-binding module (CBM13) that interacts with xylan. To understand how GH10 xylanases and CBM13 recognize decorated xylans, the crystal structure of SoXyn10A was determined in complex with alpha-l-arabinofuranosyl- and 4-O-methyl-alpha-d-glucuronosyl-xylooligosaccharides. The bound sugars were observed in the subsites of the catalytic cleft and also in subdomains alpha and gamma of CBM13. The data reveal that the binding mode of the oligosaccharides in the active site of the catalytic domain is entirely consistent with the substrate specificity and, in conjunction with the accompanying paper, demonstrate that the accommodation of the side chains in decorated xylans is conserved in GH10 xylanases of SoXyn10A against arabinoglucuronoxylan. CBM13 was shown to bind xylose or xylooligosaccharides reversibly by using nonsymmetric sugars as the ligands. The independent multiple sites in CBM13 may increase the probability of substrate binding.

Binding Sites↗

PubMed2003

Expression, crystallization and preliminary X-ray crystallographic studies of Arthrobacter globiformis inulin fructotransferase.

A recombinant form of Arthrobacter globiformis inulin fructotransferase (DFAIII-producing) has been overexpressed in Escherichia coli and purified to homogeneity. Crystals were obtained at 293 K by the hanging-drop vapour-diffusion technique using 0.1 M Na HEPES pH 7.5 buffer containing 1.5 M lithium sulfate as a precipitant. Crystals of the recombinant wild-type enzyme diffracted to better than 1.5 A at 100 K using a synchrotron-radiation source at the Photon Factory. The crystal belonged to space group R32, with unit-cell parameters a = b = 92.02, c = 229.82 A in the hexagonal axes. Assuming the presence of one molecule in the asymmetric unit, the V(M) value for the crystal was 2.15 A(3) Da(-1), indicating a solvent content of 42.8%. Selenomethionine-derivative crystals belonged to a different space group, C2, with unit-cell parameters a = 159.32, b = 91.92, c = 92.58 A, beta = 125.06. Matthews coefficient calculations suggested that the C2 selenomethionine-derivative crystal contained three molecules per asymmetric unit.

Arthrobacter↗

PubMed2003

Crystallization and preliminary X-ray crystallographic studies of alpha-galactosidase I from Mortierella vinacea.

alpha-Galactosidases catalyze the hydrolysis of a galactosyl residue from galactooligosaccharides and galactopolysaccharides. alpha-Galactosidase I from Mortierella vinacea was crystallized in two crystal forms using the hanging-drop vapour-diffusion method. Type 1 crystals belonged to space group I422, with unit-cell parameters a = b = 142.4, c = 131.5 A, and diffracted to beyond 2.1 A resolution, while type 2 crystals belonged to space group P4, with unit-cell parameters a = b = 100.9, c = 102.7 A, and diffracted to beyond 1.6 A resolution. This enzyme crystallized as a glycoprotein tetramer and the tetrameric structure was located around the crystallographic fourfold axis.

Bacterial Proteins↗

PubMed2003

Crystal structure of trimestatin, a disintegrin containing a cell adhesion recognition motif RGD.

Disintegrins are a family of small proteins containing an Arg-Gly-Asp (RGD) sequence motif that binds specifically to integrin receptors. Since the integrin is known to serve as the final common pathway leading to aggregation via formation of platelet-platelet bridges, disintegrins act as fibrinogen receptor antagonists. Here, we report the first crystal structure of a disintegrin, trimestatin, found in snake venom. The structure of trimestatin at 1.7A resolution reveals that a number of turns and loops form a rigid core stabilized by six disulfide bonds. Electron densities of the RGD sequence are visible clearly at the tip of a hairpin loop, in such a manner that the Arg and Asp side-chains point in opposite directions. A docking model using the crystal structure of integrin alphaVbeta3 suggests that the Arg binds to the propeller domain, and Asp to the betaA domain. This model indicates that the C-terminal region is another potential binding site with integrin receptors. In addition to the RGD sequence, the structural evidence of a C-terminal region (Arg66, Trp67 and Asn68) important for disintegrin activity allows understanding of the high affinity and selectiveness of snake venom disintegrin for integrin receptors. The crystal structure of trimestatin should provide a useful framework for designing and developing more effective drugs for controlling platelet aggregation and anti-angiogenesis cancer.

Amino Acid Motifs↗

PubMed2003

Crystal structure of Mg2+- and Ca2+-bound Gla domain of factor IX complexed with binding protein.

Factor IX is an indispensable protein required in the blood coagulation cascade. It binds to the surface of phospholipid membrane by means of a gamma-carboxyglutamic acid (Gla) domain situated at the N terminus. Recently, we showed that physiological concentrations of Mg2+ ions affect the native conformation of the Gla domain and in doing so augment the biological activity of factor IXa and binding affinity with its binding protein even in the presence of Ca2+ ions. Here we report on the crystal structures of the Mg2+/Ca2+-bound and Ca2+-bound (Mg2+-free) factor IX Gla domain (IXGD1-46) in complex with its binding protein (IX-bp) at 1.55 and 1.80 A resolutions, respectively. Three Mg2+ and five Ca2+ ions were bound in the Mg2+/Ca2+-bound IXGD1-46, and the Mg2+ ions were replaced by Ca2+ ions in Mg2+-free IXGD1-46. Comparison of Mg2+/Ca2+-bound with Ca2+-bound structures of the complexes showed that Mg2+ ion, which formed a bridge between IXGD1-46 and IX-bp, forced IXGD1-46 to rotate 4 degrees relative to IX-bp and hence might be the cause of a more tight interaction between the molecules than in the case of the Mg2+-free structure. The results clearly suggest that Mg2+ ions are required to maintain native conformation and in vivo function of factor IX Gla domain during blood coagulation.

1-Carboxyglutamic Acid↗

PubMed2003

Crystal structure of rice alpha-galactosidase complexed with D-galactose.

alpha-Galactosidases catalyze the hydrolysis of alpha-1,6-linked galactosyl residues from galacto-oligosaccharides and polymeric galacto-(gluco)mannans. The crystal structure of rice alpha-galactosidase has been determined at 1.5A 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 alpha-N-acetylgalactosaminidase, which is the same member of glycosyl hydrolase family 27. The catalytic domain had a (beta/alpha)8-barrel structure, and the C-terminal domain was made up of eight beta-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 beta-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 alpha-galactosidase with chicken alpha-N-acetylgalactosaminidase provided further understanding of the substrate recognition mechanism in these enzymes.

Amino Acid Sequence↗

PubMed2003

The atomic structure of rice dwarf virus reveals the self-assembly mechanism of component proteins.

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.

Bluetongue virus↗

PubMed2003

Crystal structure of Bacillus subtilis alpha-amylase in complex with acarbose.

The crystal structure of Bacillus subtilis alpha-amylase, in complex with the pseudotetrasaccharide inhibitor acarbose, revealed an hexasaccharide in the active site as a result of transglycosylation. After comparison with the known structure of the catalytic-site mutant complexed with the native substrate maltopentaose, it is suggested that the present structure represents a mimic intermediate in the initial stage of the catalytic process.

Acarbose↗

PubMed2002

Crystallization and preliminary crystallographic analysis of the terminal oxygenase component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10.

The terminal oxygenase component (CarAa) of carbazole 1,9a-dioxygenase from Pseudomonas resinovorans strain CA10 was crystallized at 293 K using the sitting-drop vapour-diffusion method under the following conditions: 0.1 M sodium citrate pH 5.6 in the presence of 0.5 M ammonium sulfate and 1.0 M lithium sulfate. By using additive reagents with the crystallizing condition, improved diffraction was obtained from the crystals. Preliminary X-ray diffraction analysis indicated that CarAa crystals are hexagonal and belong to space group P6(2) or P6(4), with unit-cell parameters a = b = 244.5, c = 65.7 A, alpha = beta = 90.0, gamma = 120.0 degrees. Diffraction data were collected to 3.0 A resolution. The V(M) value is 2.16 A(3) Da(-1), which indicates a solvent content of 43.0%. This is the first report of crystallization of the terminal oxygenase component of an angular-type dioxygenase.

Bacterial Proteins↗

PubMed2002

Crystallization and preliminary X-ray crystallographic studies of rice alpha-galactosidase.

alpha-Galactosidases catalyze the hydrolysis of galactooligosaccharides and galactopolysaccharides to alpha-galactose residues and are widely distributed in microorganisms, plants and animals. alpha-Galactosidase from rice (Oryza sativa L. ssp. japonica) was crystallized by the hanging-drop vapour-diffusion method. The crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 63.1, b = 71.3, c = 85.6 A, and diffract beyond 1.9 A resolution.

Crystallization↗

PubMed2002

Crystal structures of the sugar complexes of Streptomyces olivaceoviridis E-86 xylanase: sugar binding structure of the family 13 carbohydrate binding module.

The family 10 xylanase from Streptomyces olivaceoviridis E-86 contains a (beta/alpha)(8)-barrel as a catalytic domain, a family 13 carbohydrate binding module (CBM) as a xylan binding domain (XBD) and a Gly/Pro-rich linker between them. The crystal structure of this enzyme showed that XBD has three similar subdomains, as indicated by the presence of a triple-repeated sequence, forming a galactose binding lectin fold similar to that found in the ricin toxin B-chain. Comparison with the structure of ricin/lactose complex suggests three potential sugar binding sites in XBD. In order to understand how XBD binds to the xylan chain, we analyzed the sugar-complex structure by the soaking experiment method using the xylooligosaccharides and other sugars. In the catalytic cleft, bound sugars were observed in the xylobiose and xylotriose complex structures. In the XBD, bound sugars were identified in subdomains alpha and gamma in all of the complexes with xylose, xylobiose, xylotriose, glucose, galactose and lactose. XBD binds xylose or xylooligosaccharides at the same sugar binding sites as in the case of the ricin/lactose complex but its binding manner for xylose and xylooligosaccharides is different from the galactose binding mode in ricin, even though XBD binds galactose in the same manner as in the ricin/galactose complex. These different binding modes are utilized efficiently and differently to bind the long substrate to xylanase and ricin-type lectin. XBD can bind any xylose in the xylan backbone, whereas ricin-type lectin recognizes the terminal galactose to sandwich the large sugar chain, even though the two domains have the same family 13 CBM structure. Family 13 CBM has rather loose and broad sugar specificities and is used by some kinds of proteins to bind their target sugars. In such enzyme, XBD binds xylan, and the catalytic domain may assume a flexible position with respect to the XBD/xylan complex, inasmuch as the linker region is unstructured.

Binding Sites↗

PubMed2002

Crystallization and preliminary X-ray diffraction studies of HutP protein: an RNA-binding protein that regulates the transcription of hut operon in Bacillus subtilis.

HutP is an RNA-binding protein and regulates the expression of the histidine utilization (hut) operon in Bacillus subtilis by binding to cis-acting regulatory sequences on hut mRNA. A single point mutant (Val51Ile), which has increased affinity for the regulatory sequences, were purified and crystallized by the hanging drop vapor diffusion method. The space group was P2(1)3 with unit cell dimension a = b = c = 95.60 A resolution, and contain two molecules in the asymmetric unit. A complete MAD data set of 3.0 A resolution were collected at the LIII edge of Hg.

Bacillus subtilis↗

PubMed2001

Crystallization and preliminary crystallographic studies of dimeric disintegrins from the venom of two Agkistrodon snakes.

Piscivostatin (PVS) and acostatin are members of the disintegrin family of platelet-aggregation inhibitors found in snake venoms and are dimeric disintegrins which play different roles to the monomeric disintegrins. The crystals of PVS belonged to the P2(1)2(1)2(1) space group, with unit-cell parameters a = 34.3, b = 54.4, c = 115.9 A, and diffracted to 2.0 A resolution. The crystals of acostatin belonged to the P2(1) space group, with unit-cell parameters a = 55.4, b = 69.3, c = 63.5 A, beta = 111.7 degrees, and diffracted to 2.8 A resolution.

Agkistrodon↗