Target-+PHOSPHOTYROSINE+PROTEIN+PHOSPHATASE+PTPB+(Mycobacterium+tuberculosis)

Primarily a pathogen of the mammalian respiratory system, MTB infects the lungs. The most frequently used diagnostic methods of TB are the tubercuin skin test, acid-fast stain, and chest radiographs. It was first discovered in 1882 by Robert Koch, M. by having him discover a staining technique that would enable him to see Mycobacterium tuberculosis. Tuberculosis has an unusual, waxy coating on its cell surface, which is primarily mycolic acid, which makes the cells impervious to Gram staining.
 * Target (protein/gene name):** PHOSPHOTYROSINE PROTEIN PHOSPHATASE PTPB
 * NCBI Gene # or RefSeq#:** 886842
 * Protein ID (NP or XP #) or Wolbachia#:** Rv0153c
 * Organism (including strain):** Mycobacterium tuberculosis
 * Etiologic Risk Group (see link below):** RG3
 * Background/Disease Information (sort of like the Intro to your Mini Research Write up):** Mycobacterium tuberculosis is a pathogentic bacterial species in the family Mycobacteriaceae and the causative agent of most cases of tuberculosis. It has been present in the human population since antiquity. Fragments of the spinal column from Egyptian mummies from 2400 BCE show definite signs of tuberculosis.
 * Link to TDR Targets page (if present):** [|http://www.tdrtargets.org/targets/view?gene_id=6950]
 * Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.):** []
 * Essentiality of this protein:** PtpA is essential for mycobacterial intracellular persistence, emerging as a promising target for therapeutic intervention.
 * Complex of proteins?:** N/a
 * Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism):** 0.2


 * *EC#: ** 3.1.3.48
 * Link to BRENDA EC# page:** []
 * --** Show screenshot of BRENDA enzyme mechanism schematic




 * Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):** The phosphatase activity was measured at 25 °C using p-nitrophenol phosphate (pNPP) as substrate keeping a fixed concentration of protein (1 μM) in a reaction mixture of Tris buffer containing 0.1 M Tris, 0.15 M NaCl and 1 mM EDTA of pH 7.5. Synthetic CPs were dissolved in methanol and the methanol concentration was adjusted so as not to exceed 3% (v/v) in the final reaction mixture. This ensured the phosphatase activity of the enzyme to remain unaffected. The release of p-nitrophenol at 405 nm was quantified both in case of control and in presence of the inhibitors. The effective inhibitor and substrate concentrations were usually varied from 10–50 μm to 100–300 μm, respectively. Each assay was repeated in triplicate.

[] [] $75.90 for 100ML, SIGMA-ALDRICH, N7660 -- PDB # or closest PDB entry if using homology model: 1YWF Show pairwise alignment of your BLASTP search in NCBI against the PDB Query Coverage: 100% Max % Identities: 100% % Positives: 100% Chain used for homology: Chain A
 * -- link to Sigma (or other company) page for assay (see Sigma links below)**
 * -- -or link (or citation) to paper that contains assay information:**
 * -- links to assay reagents (substrates) pages:**
 * --- List cost and quantity of substrate reagents, supplier, and catalog #**
 * Structure Available (PDB or Homology model)**

(2E)-1-(2',5'-dimethoxyphenyl)-3-(1-naphthyl)-2-propen-1-one (2E)-1-(2'-hydroxyphenyl)-3-(1-naphthyl)-2-propen-1-one (2E)-1-(2,4-dimethoxyphenyl)-3-(naphthalen-1-yl)prop-2-en-1-one (2E)-1-(2-hydroxy-4,6-dimethoxyphenyl)-3-(3-nitrophenyl)prop-2-en-1-one (2E)-1-(2-hydroxyphenyl)-3-(naphthalen-2-yl)prop-2-en-1-one Upregulation ranking: this gene ranks in the mid 40-60% group of genes. Shows this level of upregulation in: Dormant phase. MAVRELPGAWNFRDVADTATALRPGRLFRSSELSRLDDAGRATLRRLGITDVADLRSSRE VARRGPGRVPDGIDVHLLPFPDLADDDADDSAPHETAFKRLLTNDGSNGESGESSQSIND AATRYMTDEYRQFPTRNGAQRALHRVVTLLAAGRPVLTHCFAGKDRTGFVVALVLEAVGL DRDVIVADYLRSNDSVPQLRARISEMIQQRFDTELAPEVVTFTKARLSDGVLGVRAEYLA AARQTIDETYGSLGGYLRDAGISQATVNRMRGVLLG Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water. Ext. coefficient 14440 Abs 0.1% (=1 g/l) 0.479, assuming all pairs of Cys residues form cystines Ext. coefficient 14440 Abs 0.1% (=1 g/l) 0.479, assuming all Cys residues are reduced atggcggtgcgcgaactgccgggcgcgtggaactttcgcgatgtggcggataccgcgacc gcgctgcgcccgggccgcctgtttcgcagcagcgaactgagccgcctggatgatgcgggc cgcgcgaccctgcgccgcctgggcattaccgatgtggcggatctgcgcagcagccgcgaa gtggcgcgccgcggcccgggccgcgtgccggatggcattgatgtgcatctgctgccgttt ccggatctggcggatgatgatgcggatgatagcgcgccgcatgaaaccgcgtttaaacgc ctgctgaccaacgatggcagcaacggcgaaagcggcgaaagcagccagagcattaacgat gcggcgacccgctatatgaccgatgaatatcgccagtttccgacccgcaacggcgcgcag cgcgcgctgcatcgcgtggtgaccctgctggcggcgggccgcccggtgctgacccattgc tttgcgggcaaagatcgcaccggctttgtggtggcgctggtgctggaagcggtgggcctg gatcgcgatgtgattgtggcggattatctgcgcagcaacgatagcgtgccgcagctgcgc gcgcgcattagcgaaatgattcagcagcgctttgataccgaactggcgccggaagtggtg acctttaccaaagcgcgcctgagcgatggcgtgctgggcgtgcgcgcggaatatctggcg gcggcgcgccagaccattgatgaaacctatggcagcctgggcggctatctgcgcgatgcg ggcattagccaggcgaccgtgaaccgcatgcgcggcgtgctgctgggc
 * Current Inhibitors:**
 * Expression Information (has it been expressed in bacterial cells):**
 * Image of protein (PyMol with features delineated and shown separately):**
 * Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):**
 * length of your protein in Amino Acids** 276
 * Molecular Weight of your protein in kiloDaltons using the [|Expasy ProtParam] website:** 30153.8 (Da)
 * Molar Extinction coefficient of your protein at 280 nm wavelength:**
 * TMpred graph Image ** (@http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
 * CDS Gene Sequence (paste as text only):**


 * GC% Content for gene:** 65.82%

Do Not Need this info for Spring (but still copy these lines to your Target page for now) -- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
 * Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):**
 * ( link to DNA Works output text file - **that should be saved in your Google Docs folder after you did the primer design protocol)


 * Primer design results for 'tail' primers (this is just 2 sequences):**