Target_Serine_threonine_protein_phosphatase5_(Trypanosoma+brucei)


 * Target (protein/gene names):**

__Serine/Threonine Protein Phosphatase 5 (Trypanosoma brucei)__ PDB: 1S95


 * NCBI Gene # or RefSeq#:**

3657550


 * Protein ID (NP or XP #) or Wolbachia#:**

Tb927.10.13670


 * Organism:**

T. brucei


 * Etiologic Risk Group (see link below):**

Risk 2

Trypanosoma brucei causes the parasitic disease African trypanomiasis. This disease can infect both humans and animals, and is characterized by fever and headaches, until the lymphatic and circulatory systems become affected. The disease then progresses rapidly and has a variety of manifestations including severely disrupted sleep cycles due to the parasite passing through the blood brain barrier, anemia, endocrine malfunctions, cardiac problems and kidney dysfunctions.
 * Background/Disease Information:**

The disease begins in the midgut of the fly where it eventually makes its way to the salivary glands of the fly. The fly will then bite a mammalian host (Human, monkey, etc.) and spread the disease.


 * Link to TDR Targets page (if present):**

[]


 * Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.)**
 * Essentiality of this protein:**


 * *EC#: **

3.1.3.16

[][]=Trypanosoma+brucei&show_tm=0
 * Link to BRENDA EC# page:**


 * Complex of proteins?:**

[]
 * Druggable Target:** A similar target has been used in successful runs by the study alsford, and the TDR gives it a druggability index of 0.5. It displays some similarity to a human, but not an exact match with 49% similarity on a 98% query coverage.




 * --** Show screenshot of BRENDA enzyme mechanism schematic


 * Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):**


 * -- 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 #**

Alkaline Phosphatase Yellow (pNPP) Liquid Substrate System for ELISA: $74.20

http://www.sigmaaldrich.com/catalog/product/sigma/p7998?lang=en®ion=US

-- PDB # or closest PDB entry if using homology model: -- For Homology Model option: Show pairwise alignment of your BLASTP search in NCBI against the PDB Query Coverage: 99% Max % Identities: 49% % Positives 68 Chain used for homology:
 * Structure Available (PDB or Homology model)**




 * Current Inhibitors:**

Only 5 hits were found in the binding database, the top hit being CHEMBL318778. Expression Information: The protein is usually expressed via its natural protozoa, but has been cloned and characterized from e.coli before. []


 * Expression Information (has it been expressed in bacterial cells):**


 * Purification Method:**

microcystin-Sepharose bead chromatography []


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


 * Image of protein:**
 * [[image:http://www.rcsb.org/pdb/images/1wao_bio_r_500.jpg caption="http://www.rcsb.org/pdb/images/1wao_bio_r_500.jpg"]] ||
 * http://www.rcsb.org/pdb/images/1wao_bio_r_500.jpg ||

Cartoon image of 1WAO, the closest protein resembling the chosen target. [] []


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

MAGVEEADKLKQLGNAAFSERKWHLAIDMYTKAIELTKTPTLFCNRALAELRAELPGAAL ADADAALGIEPTFAKAYYHKASAYLSLGKHKQALTNYKKVVDLAPQNSDAQAKVEFCKKE IRRINFENAIMTPDEAPLSQTIKLGSVRADYDGPRIENETVTVEFVEAMKEHFRLEKLID RHDVIFILLEVQKILKKCPNFVSINVPVGEEITVCGDTHGQYYDLLNIFKLNGNPLETNR YLFNGDFVDRGSYSFENIMTLFAYKVLYPDHFFLSRGNHEGVSMNRMYGFEGEVTQKYNS EMFRLFTEVFNSLPIGHIINNEVFVVHGGLYSSDKVTLDDLQHPNRFRDIPESGLICESL WSDPQPMPGRAPSKRGVSCLSFGPDVTETFLNNNNLKLLVRSHEVKDEGYEIEHGGKCIT VFSAPNYCDQMGNKGAFIRFTGGDMKPRFTTFTHVPHPGKRPMHYATGFGLF


 * length of your protein in Amino Acids**

code format="genbank" 1 magveeadkl kqlgnaafse rkwhlaidmy tkaieltktp tlfcnralae lraelpgaal 61 adadaalgie ptfakayyhk asaylslgkh kqaltnykkv vdlapqntda qakvefckke 121 irrinfenai ttpdeaplsq tiklgsvrad ydgprienet vtvelveamk ehfrleklid 181 rhdvifille vqkilkkcpn fvsinvpvge ditvcgdthg qyydllnifk lngnpletnr 241 ylfngdfvdr gsysfgnimt lfaykvlypd hfflsrgnqe gvsmnrmygf egevtqkyns 301 emfrlftevf nsppighinn nevfvlhggl yssdkvtldd lqqpnrfrdi pesglicesl 361 wsdpqpmpgr apskrgvscl sfgpdvtetf lnnnnlkllv rshevkdegy eiehggkcit 421 vfsapnycdq mgnkgafirf tggdmkprft tfthvphpgk rpmhyatgfg lf code

472

http://blast.ncbi.nlm.nih.gov/Blast.cgi#146083777


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

53312.7


 * Molar Extinction coefficient of your protein at 280 nm wavelength:**

38320


 * 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):**

code format="genbank" 1 tattaaaaga acagtttctg tactatattg cattggctgg aaggtcgtgt tgcg atggcc 61 <span class="feat_h">ggggtagagg aagcagacaa gctgaagcag ctgggaaacg cagcctttag tgagcgcaag 121 <span class="feat_h">tggcaccttg ccattgacat gtatacgaag gctatcgaac tgacaaaaac gccaacattg 181 <span class="feat_h">ttttgcaacc gtgcacttgc agagcttaga gctgagcttc ccggtgcggc gcttgctgac 241 <span class="feat_h">gctgatgcgg cgttagggat agagccaacc ttcgcaaagg cctattacca caaggcatcc 301 <span class="feat_h">gcgtatctga gccttggaaa acacaagcag gcgctgacaa actacaagaa agttgtagat 361 <span class="feat_h">ttggcaccac aaaataccga tgcgcaggcg aaggtggagt tttgtaagaa ggaaatacgc 421 <span class="feat_h">agaatcaact ttgaaaatgc cattacgact ccagacgagg caccgctgtc gcagacaatt 481 <span class="feat_h">aaactgggca gtgtgcgtgc tgattacgat gggcctcgta tcgaaaatga aaccgtcacc 541 <span class="feat_h">gtagaactcg tggaagcgat gaaggagcat ttcaggttag agaaactcat tgaccggcac 601 <span class="feat_h">gacgttatat ttattctgtt ggaggtgcag aagattctga aaaaatgccc caactttgtg 661 <span class="feat_h">tccatcaacg tgccagttgg tgaagacata acagtatgtg gtgacactca cgggcagtat 721 <span class="feat_h">tacgatctcc tcaatatatt caagttgaac gggaatccct tggaaacgaa ccggtacctt 781 <span class="feat_h">ttcaacggtg actttgtgga ccgcggttcg tactcatttg gaaatatcat gactctgttt 841 <span class="feat_h">gcgtataaag tactttaccc ggatcacttt ttcttatctc gtgggaacca agagggtgtt 901 <span class="feat_h">tccatgaacc gaatgtatgg gtttgaaggg gaagtaaccc aaaagtacaa cagcgaaatg 961 <span class="feat_h">tttcgcctct tcacggaggt attcaacagt cctccaatcg gtcacattaa taacaacgag 1021 <span class="feat_h">gtgtttgtac tgcacggcgg tctttactcc tcggataagg tgacattgga tgacctgcaa 1081 <span class="feat_h">caacctaacc gattccgtga tatacctgag agcggtctaa tctgcgaaag cctgtggtcc 1141 <span class="feat_h">gatccacagc cgatgcctgg gcgagcccca agtaagcgtg gggtgagctg cctgtctttc 1201 <span class="feat_h">gggccggacg taaccgagac gttcctaaac aataacaacc ttaaactgct cgtacgctct 1261 <span class="feat_h">catgaggtaa aggacgaggg gtacgagata gaacacggtg gcaaatgcat tacagtcttc 1321 <span class="feat_h">agcgcaccaa actattgtga ccaaatgggc aacaagggag cattcatccg ttttaccggc 1381 <span class="feat_h">ggtgacatga aaccaagatt cacaacattc acgcacgtgc cgcatcctgg gaaacggcca 1441 <span class="feat_h">atgcattacg ccacaggatt tggcctgttt tga <span class="ff_line">ggaagag taaaaaggaa tggagggaaa 1501 <span class="ff_line">gcgagacatc gcaggggaga gctgtgacca aagccaatgc acccgtgaca aggggcggcg 1561 <span class="ff_line">ggggaaatat cattgggaaa tatattagtt aggatgcgta tatgcatgtg tatttgtgta 1621 <span class="ff_line">tatatgcatg tgtgtaagca tcgttgaaat atgccttctc ttcctgcgca ggtatcgttc 1681 <span class="ff_line">cttcgttgga gcctctgttc ttcagacatc ttccgtgcgc aggaggtgcg ttctgcaact 1741 <span class="ff_line">attaggtcaa gtgcactact tgaagtggga tgggggaaaa aaataacatc accactaaca 1801 <span class="ff_line">ggggttgtat ttcactctcg tgcttgttct tcttttccta ttcttatagt ttgttggctc 1861 <span class="ff_line">acctgtgcct aatcaatgtc taagtggctc gcagccgttt gtatctcccc tattcgattt 1921 <span class="ff_line">ctccatcgga cggctgtagg ggctggttta tggggacctg tttcgtgcat ttttcacact 1981 <span class="ff_line">attgtccata tgaaatgcac ataccacctg aagctactcc tttctcaatc tccagttgcc 2041 <span class="ff_line">gctgtcttcg ttgtgtgttt gtcctttgtc agattgcaat atatatatat atatatatat 2101 <span class="ff_line">gccatttatt attttaccgt gaattgtttc ttctacagat ttttgttttt tctattcttg 2161 <span class="ff_line">tttatcattt cactgtgtgt gtggcgccca tcctaatcca cttggagaaa atgcagtgat 2221 <span class="ff_line">atctaagtaa ctaaaaagtg agtaatgagg aagaagaaaa ttaattaaag ggcaagaggg 2281 <span class="ff_line">gagggggcga aaggattgaa tgaagaaacg taagcagatg aggacatgca tctaatcgta 2341 <span class="ff_line">tttgcgcaaa ggttcttggg agagggaagg aaaggagttg aaagcgtctg gtagtggtgg 2401 <span class="ff_line">tggtaattac cacctgttac ggcatcagtg ctggcaccgc atgactgatt ggcgggtgac 2461 <span class="ff_line">ggcccgtccc ccccttccat atttattttc gcggtgtaaa taatcaggtg ctgttttcaa 2521 <span class="ff_line">aaaaaaaaaa aaaaaaaaaa aa // code


 * GC% Content for gene:**


 * CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):**


 * GC% Content for gene (codon optimized):**

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):**

Resources:
See **ProtocolTargetDiscoveryVDS.docx** for more Etiologic Risk Group Categories (for pathogens): http://www.utexas.edu/research/rsc/ibc/agent_class.html#_Toc7238334

Enzyme Explorer @http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer.html
 * SIGMA-ALDRICH RESOURCES**

Enzyme Classification Index (EC number) @http://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=14573088

@http://www.niaid.nih.gov/Pages/default.aspx @http://eupathdb.org/eupathdb/ @https://patricbrc.vbi.vt.edu/portal/portal/patric/Home @http://www.nmpdr.org/FIG/wiki/view.cgi/Main/EssentialGenes @http://tubic.tju.edu.cn/deg/ @http://csgid.org/csgid/cake/pages/community_request_gateway @http://tdrtargets.org/ @http://gsc.jcvi.org/status.shtml
 * Databases of genes/organisms:**

@http://wwwnc.cdc.gov/eid/pages/scientific-nomenclature.htm
 * Scientific Nomenclature page from Center for Disease Control (gene, protein names and abbreviations)**

NCBI GENE Page: @http://www.ncbi.nlm.nih.gov/gene BLAST Page: @http://blast.ncbi.nlm.nih.gov/
 * Gene Information:**

NCBI Protein Page: @http://www.ncbi.nlm.nih.gov/protein Protein Expression Website Protein Expression Paper:
 * Protein Information:**


 * Primer Overlap PCR Articles**


 * Is my target good for Virtual Screening programs?**