Biomedical subjects

Xiao Dong Su

Publications and source records attributed to Xiao Dong Su.

6 recordsLinked to original sources

PubMed2006

Preparation, crystallization and preliminary X-ray analysis of protein YtlP from Bacillus subtilis.

Bacillus subtilis YtlP is a protein that is predicted to belong to the bacterial and archael 2'-5' RNA-ligase family. It contains 183 residues and two copies of the HXTX sequence motif conserved among proteins belonging to this family. In order to determine the structure of YtlP and to compare it with the paralogue YjcG and identified 2'-5' RNA ligases, the gene ytlP was amplified from B. subtilis genomic DNA and cloned into expression vector pET-21a. The soluble protein was produced in Escherichia coli, purified to homogeneity and crystals suitable for X-ray analysis were obtained. The crystal diffracted to 2.0 A and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 34.16, b = 48.54, c = 105.75 A.

Amino Acid Sequence↗

PubMed2006

Preparation, crystallization and preliminary X-ray analysis of the methionine synthase (MetE) from Streptococcus mutans.

The Streptococcus mutans metE gene encodes methionine synthase (MetE), which catalyzes the direct transfer of a methyl group from methyltetrahydrofolate to homocysteine in the last step of methionine synthesis. metE was cloned into pET28a and the gene product was expressed at high levels in the Escherichia coli strain BL21 (DE3). MetE was purified to homogeneity using Ni(2+)-chelating chromatography followed by size-exclusion chromatography. Crystals of the protein were obtained by the hanging-drop vapour-diffusion method and diffracted to 2.2 A resolution. The crystal belongs to space group P2(1), with unit-cell parameters a = 52.85, b = 99.48, c = 77.88 A, beta = 94.55 degrees .

5-Methyltetrahydrofolate-Homocysteine S-Methyltran↗

PubMed2006

A large-scale, high-efficiency and low-cost platform for structural genomics studies.

A large-scale, high-efficiency and low-cost platform based on a Beckman Coulter Biomek FX and custom-made automation systems for structural genomics has been set up at Peking University, Beijing, People's Republic of China. This platform has the capacity to process up to 2000 genes per year for structural and functional analyses. Bacillus subtilis, a model organism for Gram-positive bacteria, and Streptococcus mutans, a major pathogen of dental caries, were selected as the main targets. To date, more than 470 B. subtilis and 1200 S. mutans proteins and hundreds of proteins from other sources, including human liver proteins, have been selected as targets for this platform. The selected genes are mainly related to important metabolism pathways and/or have potential relevance for drug design. To date, 40 independent structures have been determined; of these 11 are in the category of novel structures by the criterion of having less than 30% sequence identity to known structures. More than 13 structures were determined by SAD/MAD phasing. The macromolecular crystallography beamline at the Beijing Synchrotron Radiation Facility and modern phasing programs have been crucial components of the operation of the platform. The idea and practice of the genomic approach have been successfully adopted in a moderately funded structural biology program and it is believed this adaptation will greatly improve the production of protein structures. The goal is to be able to solve a protein structure of moderate difficulty at a cost about US 10,000 dollars.

Bacillus subtilis↗

PubMed2005

Preparation, crystallization and preliminary X-ray analysis of YjcG protein from Bacillus subtilis.

Bacillus subtilis YjcG is a functionally uncharacterized protein with 171 residues that has no structural homologue in the Protein Data Bank. However, it shows sequence homology to bacterial and archaeal 2'-5' RNA ligases. In order to identify its exact function via structural studies, the yjcG gene was amplified from B. subtilis genomic DNA and cloned into the expression vector pET21-DEST. The protein was expressed in a soluble form in Escherichia coli and was purified to homogeneity. Crystals suitable for X-ray analysis were obtained that diffracted to 2.3 A and belonged to space group C2, with unit-cell parameters a = 99.66, b = 73.93, c = 61.77 A, beta = 113.56 degrees.

Amino Acid Sequence↗

PubMed2004

Protein preparation, crystallization and preliminary X-ray analysis of human adrenal gland protein AD-004.

The adrenal gland protein AD-004 was identified in the human adrenal gland. Full-length AD-004 contains 172 amino acids, with a predicted molecular weight of about 20 kDa. In attempts to crystallize human AD-004, the gene was subcloned into a modified pET vector, pET21-DEST, with an N-terminal His(5) tag using the Gateway cloning system, followed by protein expression in Escherichia coli strain BL21(DE3). The protein was purified in two steps to near-homogeneity and was crystallized. The crystals belong to space group P6(1) or P6(5), with unit-cell parameters a = b = 99.56, c = 57.19 A. A complete 2.0 A data set has been collected at a rotating-anode X-ray source and structure determination is under way.

Adrenal Glands↗

PubMed2003

Crystallization and preliminary X-ray analysis of an alkaline serine protease from Nesterenkonia sp.

A novel calcium-independent serine protease from an alkaliphilic bacterium, Nesterenkonia sp. AL20, has been purified and crystallized at 296 K using sodium formate as the main precipitant. This enzyme is optimally active at pH 10, exhibits high stability towards autolytic digestion and its stability is not affected by the presence of EDTA or detergents. The triangular prism-shaped crystals diffracted X-rays to beyond 1.5 A at a synchrotron beamline, with space group R3 and unit-cell parameters a = b = 92.26, c = 137.88 A. A complete data set has been collected to 1.39 A resolution. The asymmetric unit is estimated and confirmed by self-rotation function calculation to contain two molecules, giving a crystal Volume per protein mass (V(M)) of 2.68 A(3) Da(-1) and a solvent content of 54%.

Actinomycetales↗