Target+-+Protein+Tyrosine+Phosphatase+Putative+(Leishmania+major)


 * Target (protein/gene name):** Putative Protein Tyrosine Phosphatase

Gene symbol: LMJF_05_0280 Gene ID: 5648889
 * NCBI Gene # or RefSeq#:**

[|TriTrypDB / LmjF04.0560] [|GeneDB / LmjF04.0560]
 * Protein ID (NP or XP #) or Wolbachia#:**


 * Organism (including strain):** //Leishmania major strain Friedlin//


 * Etiologic Risk Group (see link below):** Risk group 2 (RG2) - parasitic agents

//Leishmania major// is a protozoan species associated with the disease zoonotic cutaneous leishmaniasis (the most common form of leishmaniasis). The intracellular pathogen affects hosts' immune systems by infecting dendritic cells and macrophages. //L. major// is largely endemic to the Eastern hemisphere, specifically the Middle East, and the northern regions of Africa, China, and India. However, leishmaniasis is also found in the Americas, and has even recently spread to North Texas. There are approximately 1-1.5 million worldwide cases of cutaneous leishmaniasis a year. The disease is transmitted by the bite of female sandflies (spread by vectors). Clinical presentations of cutaneous leishmaniasis include acute infection and lesions at the bite site. Nodules that ulcerate may form. Sores may remain for a few months to a year. The patient's immune system is usually naturally restored within 3-6 months after infection. A current antiprotozoal oral drug administered to treat cutaneous leishmaniasis is miltefosine, proven to be efficacious in clinical trials. Preventive measures include avoiding sandfly bites and applying insecticides in areas prone to //L. major.//
 * Background/Disease Information (sort of like the Intro to your Mini Research Write up):**

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106324/ //Trypanosoma brucei:// protozoan and order = trypanosomatida //Leishmania major:// protozoan and order = trypanosomatida
 * Essentiality of this protein:** essential after 6 days
 * Gene/Ortholog:** Tb09.v1.0350 (OG4_15067); **Phenotype:** significant loss of fitness in bloodstream forms (6 days); **Source study:** alsford
 * alsford:** High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome. Genome Res 2011, 21:915-924


 * Complex of proteins?:** No


 * Druggable Target:** Druggability index (range: 0 to 1): 0.2


 * *EC#: ** 3.1.3.48


 * Link to BRENDA EC# page:** http://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.1.3.48&Suchword=&organism%5B%5D=Leishmania+major+Friedlin+V9&show_tm=0
 * --** Show screenshot of BRENDA enzyme mechanism schematic:

http://www.sigmaaldrich.com/etc/medialib/docs/Sigma/Bulletin/ptp101bul.Par.0001.File.tmp/ptp101bul.pdf http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3097125/ 10 µl pNP. (5 mg tablets - $32.60, Sigma Aldrich) 250 mM 1× phosphatase buffer ($89.30, Sigma Aldrich) 1N NaOH ($18.50, Sigma Aldrich) 40 µl immunoprecipitated protein ($162.50, Sigma Aldrich)
 * Enzyme Assay information (spectrophotometric, coupled assay?, reagents):** type of enzyme assay: spectrophotometric
 * -- link to Sigma (or other company) page for assay or assay reagents (substrates):**
 * -- link (or citation) to paper that contains assay information:**
 * -- List cost and quantity of substrate reagents and supplier:**

-- PDB #: 3S4O
 * Structure Available (PDB or Homology model)**

alendronate galectin-1 (for CD45) 4-Isoavenaciolide tetronic acid derivative RK-682
 * Current Inhibitors:**

Expressed in //E. coli//
 * Expression Information (has it been expressed in bacterial cells):**

Chromatographic separation on fast flow Q-Sepharose, heparin-agarose, l-histidyldiazobenzylphosphonic acid agarose, and hydroxylapatite
 * Purification Method:**


 * Image of protein (PyMol with features delineated and shown separately):**



MGIKDMYLLAYNAGMCVGWGTILVKIIVHLAEGRDPASVYPDIARLLCVAQTGAVAEIFHAAFGIVRSPV GTTFLQVLSRLIVLYGAVRIGDTDSTKSLVFVQMLVAWCLSEIIRYSFYGANLLRVNVASLTWLRYSAFM VLYPVGITGEIGCLYKALPYIKKHKPWTVELPNKLNFTFSWYNAVWFILLGIYPYGSYVMYSYMLAQRRK TFAKAAPERSKKSA
 * Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):**


 * length of your protein in Amino Acids:** 224 Amino Acids


 * Molecular Weight of your protein in kiloDaltons using the [|Expasy ProtParam]website:** 25166.8 kDa

Ext. coefficient 57090 Abs 0.1% (=1 g/l) 2.268, assuming all pairs of Cys residues form cystines Ext. coefficient 56840 Abs 0.1% (=1 g/l) 2.259, assuming all Cys residues are reduced
 * 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.

ATGGAGGTGAACGCTACGCTGATCGACTGCTGCGACCCGCAGAAGCCGTCGAGGGTGCTCTTTCACTTTC TCATCCTCGACGCGCCGTCCCCCAGCAACCTCCCGACATACATCAAGGAGCTGCAGCACCGCGGCGTGCG GCACTTGGTGCGGGTATGCGGCCCGACCTACGACGCCACCCTTGTCAAGAGCAGGGGCATTGATGTCCAC AGCTGGCCATTCGACGACGGCGCGCCTCCGACGCGTGCGGTGCTTGACAGCTGGCTGAAGCTGCTCGACA CGGAGCTTGCGCGTCAGCAGGAGGATCCCTCCGTGCCTCCGCCAACCATCGGCGTGCACTGCGTGGCGGG CCTGGGCCGCGCACCAATCTTGGTGGCGCTGGCGCTGGTGGAGTACGGCAACGTATCTGCACTAGACGCT ATCGCACTGATCCGCGAGAAGCGCAAGGGTGCAATTAATCAGACACAGATGCACTGGATCACCAAGTACA AGCGTCGCCACCAGGGTGCGGGCTGCGTGATCATGTAG
 * CDS Gene Sequence (paste as text only):**


 * GC% Content for gene:** 33.9%

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.
 * CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):**
 * GC% Content for gene (codon optimized):**
 * 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):**

http://www.metalife.com/PDB/3S4O_76577 http://biocyc.org/LEISH/NEW-IMAGE?type=REACTION&object=PROTEIN-TYROSINE-PHOSPHATASE-RXN http://tdrtargets.org/targets/view?gene_id=26652 http://www.sigmaaldrich.com/catalog/search?interface=All&term=protein%20tyrosine%20phosphatase%20&lang=en®ion=US&focus=product&N=0+220003048+219853269+219853286 http://www.rcsb.org/pdb/explore/explore.do?structureId=3S4O http://www.genomicsplace.com/gc_calc.html http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&primary_key=LmjF16.0230 http://onlinelibrary.wiley.com/doi/10.1002/anie.200461517/full http://www.ncbi.nlm.nih.gov/pubmed/12112018 http://www.ncbi.nlm.nih.gov/gene/5648889
 * References:**