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Articles by Xu Shen
Total Records ( 6 ) for Xu Shen
  Claire d`Andre Hirwa , Paul Wallace , Xu Shen , Qinghua Nie , Guanfu Yang and Xiquan Zhang
  The candidate genes with important functions in animal metabolism can help to identify potential molecular markers for cattle production traits. The study of the genes related to economically traits is one important aspect of the breeding. This study reviews the genes related to economically important traits in beef cattle such as Peroxisome proliferatior-activated receptor-γ (PPAR-γ), Sterol regulatory element-binding protein 1(SREBP-1), leptin, stearoyl-CoA desaturase (SCD1), CCAAT-enhancer-binding proteins (or C/EBBS), calpastatin, thyroid hormone-responsive protein (THRSP), corticotrophin releasing hormone (CRH), fatty acid binding protein 4 (FABP4), DGAT1, FASN,… genes. In conclusion, this study will help in genetic improvement program in cattle.
  Shuai Chen , Tiancen Hu , Jian Zhang , Jing Chen , Kaixian Chen , Jianping Ding , Hualiang Jiang and Xu Shen
  SARS-CoV 3C-like protease (3CLpro) is an attractive target foranti-severe acute respiratory syndrome (SARS) drug discovery,and its dimerization has been extensively proved to be indispensablefor enzymatic activity. However, the reason why the dissociatedmonomer is inactive still remains unclear due to the absenceof the monomer structure. In this study, we showed that mutationof the dimer-interface residue Gly-11 to alanine entirely abolishedthe activity of SARS-CoV 3CLpro. Subsequently, we determinedthe crystal structure of this mutant and discovered a completecrystallographic dimer dissociation of SARS-CoV 3CLpro. Themutation might shorten the α-helix A` of domain I and cause amis-oriented N-terminal finger that could not correctly squeezeinto the pocket of another monomer during dimerization, thusdestabilizing the dimer structure. Several structural featuresessential for catalysis and substrate recognition are severelyimpaired in the G11A monomer. Moreover, domain III rotates dramaticallyagainst the chymotrypsin fold compared with the dimer, fromwhich we proposed a putative dimerization model for SARS-CoV3CLpro. As the first reported monomer structure for SARS-CoV3CLpro, the crystal structure of G11A mutant might provide insightinto the dimerization mechanism of the protease and supply directstructural evidence for the incompetence of the dissociatedmonomer.
  Liang Zhang , Weizhi Liu , Tiancen Hu , Li Du , Cheng Luo , Kaixian Chen , Xu Shen and Hualiang Jiang
  β-Hydroxyacyl-acyl carrier protein dehydratase (FabZ) is an important enzyme for the elongation cycles of both saturated and unsaturated fatty acids biosyntheses in the type II fatty acid biosynthesis system (FAS II) pathway. FabZ has been an essential target for the discovery of compounds effective against pathogenic microbes. In this work, to characterize the catalytic and inhibitory mechanisms of FabZ, the crystal structures of the FabZ of Helicobacter pylori (HpFabZ) and its complexes with two newly discovered inhibitors have been solved. Different from the structures of other bacterial FabZs, HpFabZ contains an extra short two-turn α-helix (α4) between α3 and β3, which plays an important role in shaping the substrate-binding tunnel. Residue Tyr-100 at the entrance of the tunnel adopts either an open or closed conformation in the crystal structure. The crystal structural characterization, the binding affinity determination, and the enzymatic activity assay of the HpFabZ mutant (Y100A) confirm the importance of Tyr-100 in catalytic activity and substrate binding. Residue Phe-83 at the exit tunnel was also refined in two alternative conformations, leading the tunnel to form an L-shape and U-shape. All these data thus contributed much to understanding the catalytic mechanism of HpFabZ. In addition, the co-crystal structures of HpFabZ with its inhibitors have suggested that the enzymatic activity of HpFabZ could be inhibited either by occupying the entrance of the tunnel or plugging the tunnel to prevent the substrate from accessing the active site. Our study has provided some insights into the catalytic and inhibitory mechanisms of FabZ, thus facilitating antibacterial agent development.
  Xiao-Ling Yu , Tiancen Hu , Jia-Mu Du , Jian-Ping Ding , Xiang-Min Yang , Jian Zhang , Bin Yang , Xu Shen , Zheng Zhang , Wei-De Zhong , Ning Wen , Hualiang Jiang , Ping Zhu and Zhi-Nan Chen
  CD147, a member of the immunoglobulin superfamily (IgSF), plays fundamental roles in intercellular interactions in numerous pathological and physiological processes. Importantly, our previous studies have demonstrated that HAb18G/CD147 is a novel hepatocellular carcinoma (HCC)-associated antigen, and HAb18G/CD147 stimulates adjacent fibroblasts and HCC cells to produce elevated levels of several matrix metalloproteinases, facilitating invasion and metastasis of HCC cells. In addition, HAb18G/CD147 has also been shown to be a novel universal cancer biomarker for diagnosis and prognostic assessment of a wide range of cancers. However, the structural basis underlying the multifunctional character of CD147 remains unresolved. We report here the crystal structure of the extracellular portion of HAb18G/CD147 at 2.8Å resolution. The structure comprises an N-terminal IgC2 domain and a C-terminal IgI domain, which are connected by a 5-residue flexible linker. This unique C2-I domain organization is distinct from those of other IgSF members. Four homophilic dimers exist in the crystal and adopt C2-C2 and C2-I dimerization rather than V-V dimerization commonly found in other IgSF members. This type of homophilic association thus presents a novel model for homophilic interaction between C2 domains of IgSF members. Moreover, the crystal structure of HAb18G/CD147 provides a good structural explanation for the established multifunction of CD147 mediated by homo/hetero-oligomerizations and should represent a general architecture of other CD147 family members.
  Tiancen Hu , Dalei Wu , Jing Chen , Jianping Ding , Hualiang Jiang and Xu Shen
  The meso-diaminopimelate decarboxylase (DAPDC, EC[EC]0) catalyzes the final step of L-lysine biosynthesis in bacteria and is regarded as a target for the discovery of antibiotics. Here we report the 2.3Å crystal structure of DAPDC from Helicobacter pylori (HpDAPDC). The structure, in which the product L-lysine forms a Schiff base with the cofactor pyridoxal 5'-phosphate, provides structural insight into the substrate specificity and catalytic mechanism of the enzyme, and implies that the carboxyl to be cleaved locates at the si face of the cofactor. To our knowledge, this might be the first reported external aldimine of DAPDC. Moreover, the active site loop of HpDAPDC is in a "down" conformation and shields the ligand from solvent. Mutations of Ile148 from the loop greatly impaired the catalytic efficiency. Combining the structural analysis of the I148L mutant, we hypothesize that HpDAPDC adopts an induced-fit catalytic mechanism in which this loop cycles through "down" and "up" conformations to stabilize intermediates and release product, respectively. Our work is expected to provide clues for designing specific inhibitors of DAPDC.
  Bingfa Sun , Jing Hong , Peng Zhang , Xianchi Dong , Xu Shen , Donghai Lin and Jianping Ding
  Eaf3 is a component of both NuA4 histone acetyltransferase and Rpd3S histone deacetylase complexes in Saccharomyces cerevisiae. It is involved in the regulation of the global pattern of histone acetylation that distinguishes promoters from coding regions. Eaf3 contains a chromo domain at the N terminus that can bind to methylated Lys-36 of histone H3 (H3K36). We report here the crystal structures of the Eaf3 chromo domain in two truncation forms. Unlike the typical HP1 and Polycomb chromo domains, which contain a large groove to bind the modified histone tail, the Eaf3 chromo domain assumes an autoinhibited chromo barrel domain similar to the human MRG15 chromo domain. Compared with other chromo domains, the Eaf3 chromo domain contains a unique 38-residue insertion that folds into two short β-strands and a long flexible loop to flank the β-barrel core. Both isothermal titration calorimetry and surface plasmon resonance studies indicate that the interaction between the Eaf3 chromo domain and the trimethylated H3K36 peptide is relatively weak, with a KD of ~10-4 M. NMR titration studies demonstrate that the methylated H3K36 peptide is bound to the cleft formed by the C-terminal α-helix and the β-barrel core. Site-directed mutagenesis study and in vitro binding assay results show that the conserved aromatic residues Tyr-23, Tyr-81, Trp-84, and Trp-88, which form a hydrophobic pocket at one end of the β-barrel, are essential for the binding of the methylated H3K36. These results reveal the molecular mechanism of the recognition and binding of the methylated H3K36 by Eaf3 and provide new insights into the functional roles of the Eaf3 chromo domain.
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