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Ping-Chiang Lyu

Publications and source records attributed to Ping-Chiang Lyu.

At least 19 recordsLinked to original sources
PubMed2007

Solution structure of family 21 carbohydrate-binding module from Rhizopus oryzae glucoamylase.

CBMs (carbohydrate-binding modules) function independently to assist carbohydrate-active enzymes. Family 21 CBMs contain approx. 100 amino acid residues, and some members have starchbinding functions or glycogen-binding activities. We report here the first structure of a family 21 CBM from the SBD (starch-binding domain) of Rhizopus oryzae glucoamylase (RoCBM21) determined by NMR spectroscopy. This CBM has a beta-sandwich fold with an immunoglobulin-like structure. Ligand-binding properties of RoCBM21 were analysed by chemical-shift perturbations and automated docking. Structural comparisons with previously reported SBDs revealed two types of topologies, namely type I and type II, with CBM20, CBM25, CBM26 and CBM41 showing type I topology, with CBM21 and CBM34 showing type II topology. According to the chemical-shift perturbations, RoCBM21 contains two ligand-binding sites. Residues in site II are similar to those found in the family 20 CBM from Aspergillus niger glucoamylase (AnCBM20). Site I, however, is embedded in a region with unique sequence motifs only found in some members of CBM21s. Additionally, docking of beta-cyclodextrin and malto-oligosaccharides highlights that side chains of Y83 and W47 (one-letter amino acid code) form the central part of the conserved binding platform in the SBD. The structure of RoCBM21 provides the first direct evidence of the structural features and the basis for protein-carbohydrate recognition from an SBD of CBM21.

Binding Sites↗
PubMed2006

Preliminary X-ray analysis of XC5848, a hypothetical ORFan protein with an Sm-like motif from Xanthomonas campestris.

XC5848, a hypothetical protein from the pathogenic bacterium Xanthomonas campestris that causes black rot, has been chosen as a potential target for the discovery of novel folds. It is unique to the Xanthomonas genus and has significant sequence identity mainly to corresponding proteins from the Xanthomonas genus. In this paper, the cloning, overexpression, purification and crystallization of the XC5848 protein are reported. The XC5848 crystals diffracted to a resolution of at least 1.68 A. They belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 48.13, b = 51.62, c = 82.32 A. Two molecules were found in each asymmetric unit. Preliminary structural studies nevertheless indicate that XC5848 belongs to the highly conserved Sm-like alpha-beta-beta-beta-beta fold. However, significant differences in sequence and structure were observed. It therefore represents a novel variant of the crucial Sm-like motif that is heavily involved in mRNA splicing and degradation.

Amino Acid Motifs↗
PubMed2006

Crystallization and preliminary X-ray analysis of XC1015, a histidine triad-like protein from Xanthomonas campestris.

Histidine-triad (HIT) proteins are a superfamily of nucleotide hydrolases and transferases that contain a conserved Hphi Hphi Hphi phi motif (where phi is a hydrophobic amino acid) and are found in a variety of organisms. In addition to binding to a variety of nucleotides, other biological functions of the HIT superfamily proteins have been discovered and HIT malfunction has been implicated in several human diseases. Structural studies of HIT superfamily proteins are thus of particular interest. In this manuscript, the cloning, expression, crystallization and preliminary X-ray analysis of XC1015, a HIT protein present in the plant pathogen Xanthomonas campestris pathovar campestris, are reported. The XC1015 crystals diffracted to a resolution of 1.3 A. They are tetragonal and belong to space group P4(3)2(1)2, with unit-cell parameters a = 40.52, b = 40.52, c = 126.89 A.

Bacterial Proteins↗
PubMed2006

Cloning, crystallization and preliminary X-ray studies of XC2981 from Xanthomonas campestris, a putative CutA1 protein involved in copper-ion homeostasis.

Divalent metal ions play key roles in all living organisms, serving as cofactors for many proteins involved in a variety of electron-transfer activities. However, copper ions are highly toxic when an excessive amount is accumulated in a cell. CutA1 is a protein found in all kingdoms of life that is believed to participate in copper-ion tolerance in Escherichia coli, although its specific function remains unknown. Several crystal structures of multimeric CutA1 with different rotation angles and degrees of interaction between trimer interfaces have been reported. Here, the cloning, expression, crystallization and preliminary X-ray analysis of XC2981, a possible CutA1 protein present in the plant pathogen Xanthomonas campestris, are reported. The XC2981 crystals diffracted to a resolution of 2.6 A. They are cubic and belong to space group I23, with unit-cell parameters a = b = c = 130.73 A.

Bacterial Proteins↗
PubMed2006

Structural basis for the structure-activity relationships of peroxisome proliferator-activated receptor agonists.

Type 2 diabetes has rapidly reached an epidemic proportion becoming a major threat to global public health. PPAR agonists have emerged as a leading class of oral antidiabetic drugs. We report a structure biology analysis of novel indole-based PPAR agonists to explain the structure-activity relationships and present a critical analysis of reasons for change in selectivity with change in the orientation of the same scaffolds. The results would be helpful in designing novel PPAR agonists.

Acetates↗
PubMed2006

Cloning, crystallization and preliminary X-ray study of XC1258, a CN-hydrolase superfamily protein from Xanthomonas campestris.

CN-hydrolase superfamily proteins are involved in a wide variety of non-peptide carbon-nitrogen hydrolysis reactions, producing some important natural products such as auxin, biotin, precursors of antibiotics etc. These reactions all involve attack on a cyano or carbonyl carbon by a conserved novel catalytic triad Glu-Lys-Cys through a thiol acylenzyme intermediate. However, classification into the CN-hydrolase superfamily based on sequence similarity alone is not straightforward and further structural data are necessary to improve this categorization. Here, the cloning, expression, crystallization and preliminary X-ray analysis of XC1258, a CN-hydrolase superfamily protein from the plant pathogen Xanthomonas campestris (Xcc), are reported. The SeMet-substituted XC1258 crystals diffracted to a resolution of 1.73 A. They are orthorhombic and belong to space group P2(1)2(1)2, with unit-cell parameters a = 143.8, b = 154.63, c = 51.3 A, respectively.

Amino Acid Sequence↗
PubMed2006

The cloning, crystallization and preliminary X-ray analysis of XC2113, a YaeQ protein from Xanthomonas campestris.

Xanthomonas campestris is a Gram-negative bacterium that is phytopathogenic to cruciferous plants and causes worldwide agricultural loss. It is therefore important to identify potential pathogenic factors involved in this plant disease. Here, the cloning, expression, crystallization and preliminary X-ray analysis of XC2113, a YaeQ protein possibly involved in the production of virulence factors in Xanthomonas campestris pathovar campestris, are reported. The XC2113 crystals diffracted well to a resolution of at least 1.28 A. They are orthorhombic and belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 32.86, b = 62.69, c = 79.96 A.

Bacterial Proteins↗
PubMed2006

Human pancreatitis-associated protein forms fibrillar aggregates with a native-like conformation.

Human pancreatitis-associated protein was identified in pathognomonic lesions of Alzheimer disease, a disease characterized by the presence of filamentous protein aggregates. Here, we showed that at physiological pH, human pancreatitis-associated protein forms non-Congo Red-binding, proteinase K-resistant fibrillar aggregates with diameters from 6 up to as large as 68 nm. Interestingly, circular dichroism and Fourier transform infrared spectra showed that, unlike typical amyloid fibrils, which have a cross-beta-sheet structure, these aggregates have a very similar secondary structure to that of the native protein, which is composed of two alpha-helices and eight beta-strands, as determined by NMR techniques. Surface structure analysis showed that the positively charged and negatively charged residues were clustered on opposite sides, and strong electrostatic interactions between molecules were therefore very likely, which was confirmed by cross-linking experiments. In addition, several hydrophobic residues were found to constitute a continuous hydrophobic surface. These results and protein aggregation prediction using the TANGO algorithm led us to synthesize peptide Thr(84) to Ser(116), which, very interestingly, was found to form amyloid-like fibrils with a cross-beta structure. Thus, our data suggested that human pancreatitis-associated protein fibrillization is initiated by protein aggregation primarily because of electrostatic interactions, and the loop from residues 84 to 116 may play an important role in the formation of fibrillar aggregates with a native-like conformation.

Amino Acid Sequence↗
PubMed2006

Biosynthesis of fluorescent allophycocyanin alpha-subunits by autocatalytic bilin attachment.

Allophycocyanin (APC) is one of the phycobiliproteins expressed in cyanobacteria. Phycobiliproteins contain a covalently bound chromophore, and thus, they are valuable as fluorescent probes. Biosynthesis of a functional phycobiliprotein is achieved by a bilin attachment process between the chromophore and apoprotein. Chromophore lyases are necessary to catalyze the chromophorylation of cyanobacterial phycobiliproteins, such as C-phycocyanin, and phycoerythrocyanin. To identify the lyase that catalyzes the chromophorylation of the APC alpha-subunit (ApcA), we searched the entire genomes of two cyanobacteria, Synechocystis sp. PCC6803 and Anabaena sp. PCC 7120; however, these genomes do not appear to encode an APC-specific chromophore lyase. In this study, chromophorylated ApcA (chromo-ApcA) was obtained via a spontaneous bilin attachment reaction. The absorption and fluorescence characteristics of chromo-ApcA were similar to those of the native APC alpha-subunit. The extent of chromophore attachment to apo-ApcA was comparable to that of the lyase-catalyzed reactions for other phycobiliproteins. These results indicate that ApcA has autocatalytic bilin:biliprotein lyase activity.

Base Sequence↗
PubMed2006

Solution structure of the plant defensin VrD1 from mung bean and its possible role in insecticidal activity against bruchids.

Vigna radiata plant defensin 1 (VrD1) is the first reported plant defensin exhibiting insecticidal activity. We report herein the nuclear magnetic resonance solution structure of VrD1 and the implication on its insecticidal activity. The root-mean-square deviation values are 0.51 +/- 0.35 and 1.23 +/- 0.29 A for backbone and all heavy atoms, respectively. The VrD1 structure comprises a triple-stranded antiparallel beta-sheet, an alpha-helix, and a 3(10) helix stabilized by four disulfide bonds, forming a typical cysteine-stabilized alphabeta motif. Among plant defensins of known structure, VrD1 is the first to contain a 3(10) helix. Glu26 is highly conserved among defensins; VrD1 contains an arginine at this position, which may induce a shift in the orientation of Trp10, thereby promoting the formation of this 3(10) helix. Moreover, VrD1 inhibits Tenebrio molitor alpha-amylase. Alpha-amylase has an essential role in the digestion of plant starch in the insect gut, and expression of the common bean alpha-amylase inhibitor 1 in transgenic pea imparts complete resistance against bruchids. These results imply that VrD1 insecticidal activity has its basis in the inhibition of a polysaccharide hydrolase. Sequence and structural comparisons between two groups of plant defensins having different specificity toward insect alpha-amylase reveal that the loop between beta2 and beta3 is the probable binding site for the alpha-amylase. Computational docking experiments were used to study VrD1-alpha-amylase interactions, and these results provide information that may be used to improve the insecticidal activity of VrD1.

Amino Acid Sequence↗
PubMed2006

Indol-1-yl acetic acids as peroxisome proliferator-activated receptor agonists: design, synthesis, structural biology, and molecular docking studies.

A series of novel indole-based PPAR agonists is described leading to discovery of 10k, a highly potent PPAR pan-agonist. The structural biology and molecular docking studies revealed that the distances between the acidic group and the linker, when a ligand was complexed with PPARgamma protein, were important for the potent activity. The hydrophobic tail part of 10k makes intensive hydrophobic interaction with the PPARgamma protein resulting in potent activity.

Binding Sites↗
PubMed2005

Japanese encephalitis virus NS2B-NS3 protease binding to phage-displayed human brain proteins with the domain of trypsin inhibitor and basic region leucine zipper.

Flavivirus NS2B-NS3 proteases are associated with neurovirulence, becoming an important target for insight into the virus-induced pathogenesis. In this study, a phage-displayed human brain cDNA library was used to detect possible interaction between brain proteins and the Japanese encephalitis virus (JEV) NS2B-NS3 protease. After six rounds of biopanning, eight high-affinity NS2B-NS3 protease-interacting phages were identified. Identified NS2B-NS3 protease-interacting brain proteins contained several repeats of the consensus motifs E(R/K)(R/K)K and G(R/K)(R/K) with the dibasic residues, being similar to the conserved cleavage sites among flavivirus proteases. In addition, three identified brain proteins (phage-24, 34, and 44) were predicted as the domain of trypsin inhibitor and basic region leucine zipper (bZIP) using the SMART genome search. Immunoprecipitation and cleavage of two brain fusion proteins (phage-24 and phage-46) by the NS2B-NS3 protease confirmed the specific interaction between identified brain proteins and the JEV NS2B-NS3 protease. Fluorogenic peptide substrate assays revealed dose-manner inhibitory effects of these two brain fusion proteins on the trans-cleavage activity of NS2B-NS3 protease. Moreover, in vitro signaling pathway assay revealed that the JEV NS2B-NS3 protease significantly inhibited the signaling pathway of activator protein 1(AP1), a member of the bZIP family. Our results provide an insight into the protein interaction network of the JEV NS2B-NS3 protease in human brain.

Amino Acid Sequence↗
PubMed2005

Cloning, purification, crystallization and preliminary X-ray crystallographic analysis of XC847, a 3'-5' oligoribonuclease from Xanthomonas campestris.

Oligoribonucleases are essential components of RNA and DNA metabolism and close homologues of genes encoding them are found not only in prokaryotes but also in a wide range of eukaryotes, including yeast and humans. Inactivation of the oligoribonuclease gene (orn) can result in cellular lethality. Despite their important biological function, they have been studied little from a structural point of view. In this report, the cloning, expression, crystallization and preliminary X-ray analysis of XC847, a DEDDh-type 3'-5' oligoribonuclease from the plant pathogen Xanthomonas campestris pv. campestris, a Gram-negative bacterium causing major worldwide disease of cruciferous crops, is described. The XC847 crystals diffracted to a resolution of at least 2.1 A. They are tetragonal and belong to space group P4(3)2(1)2, with unit-cell parameters a = b = 67.5, c = 89.8 A. One molecule is present per asymmetric unit.

Amino Acid Motifs↗
PubMed2005

Preparation, crystallization and preliminary X-ray characterization of a conserved hypothetical protein XC1692 from Xanthomonas campestris.

Xanthomonas campestris pv. campestris strain 17 is a Gram-negative yellow-pigmented pathogenic bacterium that causes black rot, one of the major worldwide diseases of cruciferous crops. Its genome contains approximately 4500 genes, one third of which have no known structure and/or function yet are highly conserved among several different bacterial genuses. One of these gene products is XC1692 protein, containing 141 amino acids. It was overexpressed in Escherichia coli, purified and crystallized in a variety of forms using the hanging-drop vapour-diffusion method. The crystals diffract to at least 1.45 A resolution. They are hexagonal and belong to space group P6(3), with unit-cell parameters a = b = 56.9, c = 71.0 A. They contain one molecule per asymmetric unit.

Bacterial Proteins↗
PubMed2005

Cloning, purification, crystallization and preliminary X-ray analysis of XC229, a conserved hypothetical protein from Xanthomonas campestris.

Xanthomonas campestris pv. campestris is a Gram-negative yellow-pigmented pathogenic bacterium that causes black rot, one of the major worldwide diseases of cruciferous crops. Its genome contains approximately 4500 genes, roughly one third of which have no known structure and/or function. However, some of these unknown genes are highly conserved among several different bacterial genuses. XC229 is one such protein containing 134 amino acids. It was overexpressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystal diffracted to a resolution of at least 1.80 A. It is cubic and belongs to space group I2(x)3, with unit-cell parameters a = b = c = 106.8 A. It contains one or two molecules per asymmetric unit.

Bacterial Proteins↗
PubMed2005

Preparation, crystallization and preliminary X-ray analysis of XC2382, an ApaG protein of unknown structure from Xanthomonas campestris.

Xanthomonas campestris pv. campestris is the causative agent of black rot, one of the major worldwide diseases of cruciferous crops. Its genome encodes approximately 4500 proteins, roughly one third of which have unknown function. XC2382 is one such protein, with a MW of 14.2 kDa. Based on a bioinformatics study, it was annotated as an ApaG gene product that serves multiple functions. The ApaG protein has been overexpressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystals diffracted to a resolution of at least 2.30 A. They are tetragonal and belong to space group P4(1/3), with unit-cell parameters a = b = 57.6, c = 122.9 A. There are two, three or four molecules in the asymmetric unit.

Bacterial Proteins↗
PubMed2005

A putative polyketide-synthesis protein XC5357 from Xanthomonas campestris: heterologous expression, crystallization and preliminary X-ray analysis.

Xanthomonas campestris pv. campestris (Xcc) is a Gram-negative yellow-pigmented bacterium and is the causative agent of black rot, one of the major worldwide diseases of cruciferous crops. It also synthesizes a variety of polyketide metabolites that lead to important antibiotics. XC5357 is a putative 12.2 kDa protein of unknown structure from Xcc that is likely to be essential for polyketide synthesis. It was overexpressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystals belong to the triclinic space group P1, with unit-cell parameters a = 43.7, b = 43.7, c = 46.5 A, alpha = 65.0, beta = 64.9, gamma = 73.4 degrees, and diffracted to a resolution of 1.85 A.

Bacterial Proteins↗