pcr-mutagenesis-cloning-expression-fast-protein-purification

PCR Mutagenesis, Cloning, Expression, Fast Protein Purification Protocols and Crystallization of the Wild Type and Mutant Forms of Tryptophan Synthase

Structural studies with tryptophan synthase (TS) bienzyme complex (&#945;2&#946;2 TS) from Salmonella typhimurium have been performed to better understand ...

University of California-Riverside

Xanthomonas citri pv. citri (Xac) causes citrus canker and affects citrus agriculture worldwide. Functional genetic analysis has indicated that a putative general stress protein (XacGSP) encoded by the Xac2369 gene is involved in the bacterial infection. In this report, the crystal structure of XacGSP was determined to 2.5 Å resolution. There are four XacGSP molecules in the crystal asymmetric unit. Each XacGSP monomer folds into a six-stranded antiparallel β-barrel flanked by five α-helices. A C-terminal extension protrudes from the sixth β-strand of the β-barrel and pairs with its counterpart from another monomer to form a bridge between the two subunits of an XacGSP dimer. Two XacGSP dimers cross over each other to form a tetramer; the β-barrels from one dimer contact the β-barrels of the other, while the two bridges are distant from each other and do not make contacts. The three-dimensional structure of the XacGSP monomer is very similar to those of pyridoxine 5-phosphate oxidases, a group of enzymes that use flavin mononucleotide (FMN) as a cofactor. Consistent with this, purified XacGSP protein binds to both FMN and flavin adenine dinucleotide (FAD), suggesting that XacGSP may help the bacteria to react against the oxidative stress induced by the defense mechanisms of the plant.

The structure of a Xanthomonas general stress protein involved in citrus canker reveals its flavin-binding property.

The acidic leucine aminopeptidase (LAP-A) from tomato is induced in response to wounding and insect feeding. Although LAP-A shows in vitro peptidase activity towards peptides and peptide analogs, it is not clear what kind of substrates LAP-A hydrolyzes in vivo. In the current study, the crystal structure of LAP-A was determined to 2.20 Å resolution. Like other LAPs in the M17 peptidase family, LAP-A is a dimer of trimers containing six monomers of bilobal structure. Each monomer contains two metal ions bridged by a water or a hydroxyl ion at the active site. Modeling of different peptides or peptide analogs in the active site of LAP-A reveals a spacious substrate-binding channel that can bind peptides of five or fewer residues with few geometric restrictions. The sequence specificity of the bound peptide is likely to be selected by the structural and chemical restrictions on the amino acid at the P1 and P1' positions because these two amino acids have to bind perfectly at the active site for hydrolysis of the first peptide bond to occur. The hexameric assembly results in the merger of the open ends of the six substrate-binding channels from the LAP-A monomers to form a spacious central cavity allowing the hexameric LAP-A enzyme to simultaneously hydrolyze six peptides containing up to six amino acids each. The hexameric LAP-A enzyme may also hydrolyze long peptides or proteins if only one such substrate is bound to the hexamer because the substrate can extend through the central cavity and the two major solvent channels between the two LAP-A trimers. 

Structure of tomato wound-induced leucine aminopeptidase sheds light on substrate specificity.

Tomato plants express acidic leucine aminopeptidase (LAP-A) in response to various environmental stressors. LAP-A not only functions as a peptidase for diverse peptide substrates, but also displays chaperone activity. A K354E mutation has been shown to abolish the peptidase activity but to enhance the chaperone activity of LAP-A. To better understand this moonlighting function of LAP-A, the crystal structure of the K354E mutant was determined at 2.15 Å resolution. The structure reveals that the K354E mutation destabilizes an active-site loop and causes significant rearrangement of active-site residues, leading to loss of the catalytic metal-ion coordination required for the peptidase activity. Although the mutant was crystallized in the same hexameric form as wild-type LAP-A, gel-filtration chromatography revealed an apparent shift from the hexamer to lower-order oligomers for the K354E mutant, showing a mixture of monomers to trimers in solution. In addition, surface-probing assays indicated that the K354E mutant has more accessible hydrophobic areas than wild-type LAP-A. Consistently, computational thermodynamic estimations of the interfaces between LAP-A monomers suggest that increased exposure of hydrophobic surfaces occurs upon hexamer breakdown. These results suggest that the K354E mutation disrupts the active-site loop, which also contributes to the hexameric assembly, and destabilizes the hexamers, resulting in much greater hydrophobic areas accessible for efficient chaperone activity than in the wild-type LAP-A.

Structural insights into chaperone-activity enhancement by a K354E mutation in tomato acidic leucine aminopeptidase.

Non-coding RNAs (ncRNAs) can be divided into circular non-coding RNAs (circRNAs) and linear ncRNAs. ncRNAs exist in different cell types, including normal cells, tumor cells and immunocytes. Linear ncRNAs, such as long ncRNAs and microRNAs, have been found to play important roles in the regulation of tumor immunity and immunotherapy; however, the functions of circRNAs in tumor immunity and immunotherapy are less known. Here, we review the current status of ncRNAs in the regulation of tumor immunity and immunotherapy and emphatically discuss the potential roles of circRNAs as tumor antigens in the regulation of tumor immunity and immunotherapy.

The Potential Role of circRNA in Tumor Immunity Regulation and Immunotherapy.

Backbone assignments for the isolated α-subunit of Salmonella typhimurium tryptophan synthase (TS) are reported based on triple resonance solution-state NMR experiments on a uniformly H,C,N-labeled sample. From the backbone chemical shifts, secondary structure and random coil index order parameters (RCI-S) are predicted. Titration with the 3-indole-D-glycerol 3'-phosphate analog, N-(4'-trifluoromethoxybenzenesulfonyl)-2-aminoethyl phosphate (F9), leads to chemical shift perturbations indicative of conformational changes from which an estimate of the dissociation constant is obtained. Comparisons of the backbone chemical-shifts, RCI-S values, and site-specific relaxation times with and without F9 reveal allosteric changes including modulation in secondary structures and loop rigidity induced upon ligand binding. A comparison is made to the X-ray crystal structure of the α-subunit in the full TS αββα bi-enzyme complex and to two new X-ray crystal structures of the isolated TS α-subunit reported in this work.

Backbone assignments and conformational dynamics in the S. typhimurium tryptophan synthase α-subunit from solution-state NMR.

The genus Xanthomonas comprises several cosmopolitan plant-pathogenic bacteria that affect more than 400 plant species, most of which are of economic interest. Citrus canker is a bacterial disease that affects citrus species, reducing fruit yield and quality, and is caused by the bacterium Xanthomonas citri subsp. citri (Xac). The Xac3819 gene, which has previously been reported to be important for citrus canker infection, encodes an uncharacterized glutathione S-transferase (GST) of 207 amino-acid residues in length (XacGST). Bacterial GSTs are implicated in a variety of metabolic processes such as protection against chemical and oxidative stresses. XacGST shares high sequence identity (45%) with the GstB dehalogenase from Escherichia coli O6:H1 strain CFT073 (EcGstB). Here, XacGST is reported to be able to conjugate glutathione (GSH) with bromoacetate with a K of 6.67 ± 0.77 mM, a k of 42.69 ± 0.32 s and a k/K of 6.40 ± 0.72 mM s under a saturated GSH concentration (3.6 mM). These values are comparable to those previously reported for EcGstB. In addition, crystal structures of XacGST were determined in the apo form (PDB entry 6nxv) and in a GSH-bound complex (PDB entry 6nv6). XacGST has a canonical GST-like fold with a conserved serine residue (Ser12) at the GSH-binding site near the N-terminus, indicating XacGST to be a serine-type GST that probably belongs to the theta-class GSTs. GSH binding stabilizes a loop of about 20 residues containing a helix that is disordered in the apo XacGST structure.

Article	Year
The structure of a Xanthomonas general stress protein involved in citrus canker reveals its flavin-binding property. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 22751670	2012
Structure of tomato wound-induced leucine aminopeptidase sheds light on substrate specificity. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 24914976	2014
Structural insights into chaperone-activity enhancement by a K354E mutation in tomato acidic leucine aminopeptidase. Acta crystallographica. Section D, Structural biology\| PubMed ID: 27139632	2016
The Potential Role of circRNA in Tumor Immunity Regulation and Immunotherapy. Frontiers in immunology\| PubMed ID: 29403493	2018
Backbone assignments and conformational dynamics in the S. typhimurium tryptophan synthase α-subunit from solution-state NMR. Journal of biomolecular NMR\| PubMed ID: 32415580	2020
Structural and biochemical characterization of a glutathione transferase from the citrus canker pathogen Xanthomonas. Acta crystallographica. Section D, Structural biology\| PubMed ID: 32744260	2020

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