Target+-+protein-tyrosine-phosphotase+ywlE+(Bacillus+subtilis)

Format for Individual Target pages (copy this list to new Target page and then fill in for your target):
//Bacillus subtilis// is a rod-shaped bacteria commonly found in soil. It was discovered in 1835 by Christian Gottfriend Ehrenberg, where he originally named it "//Vibrio subtilis". B. subtilis// is a bacteria that forms an endospore that can withstand extreme temperatures and dry environments. Because it is resistant to extreme temperatures, the bacteria can stand high cooking temperatures. //B. subtilis// is present everywhere: the air, soil, and in plant compost. The bacteria spends most of its time in the inactive spore form, however when it is active it produces many enzymes. //B. subtilis// can be found in the human body in mostly the skin or in the intestinal tract. Along with the enzymes the bacteria makes, it also produces a toxin called subtilisin. Subtilisin can cause allergic reactions if there is exp osure to high concentrations of it over and over again. Subtilisin is also found in laundry detergent, where it can cause allergic reactions after using the detergent.[1] The bacteria is also responsible for causing food poisoning in people with relatively low immune systems. //B. subtilis// can also be responsible for causing infections that include: a case of endocarditis in a drug abuse patient; fatal pneumonia and bacteremia in three leukemic patients; septicemia in a patient with breast cancer; and infection of a necrotic axillary tumor in another breast cancer patient.[2] //B. subtilis// was once used as a broad spectrum antibiotic. [1]
 * *Target (protein/gene name): **ywlE low molecular weight protein-tyrosine-phosphatase
 * *NCBI Gene # or RefSeq#: **937021
 * *Protein ID (NP or XP #) or Wolbachia#: ( ** None on PDB page)
 * *Organism (including strain): **//Bacillus substilis// strain substilis 168
 * Etiologic Risk Group (see link below): **RG2
 * *Background/Disease Information (sort of like the Intro to your Mini Research Write up): **


 * 1. [] **
 * 2. [] **

[] [] [|https://cansar.icr.ac.uk/cansar/molecular-targets/target_report_drugs/P39155/#main_tab_holder:target_report_tab:target_report_druggability] "Studies indicated that YwlE shows similar activity towards the substrate p-nitrophenylphosphate (pNPP), but a lower activity on the protein substrate of YwqE. A recent genetic and biochemical study suggested that YwlE plays roles in B. subtilis stress resistance.Unlike Arg18 in BPTP, Arg13 may not be directly involved in initial phosphate binding in YwlE. However, the sequence conservation and its possible stabilization by Asp115 suggest its importance in forming a phosphate-binding pocket." []
 * Link to TDR Targets page (if present): **There isn't a TDR target page present.
 * Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.) **
 * Essentiality of this protein: **
 * Complex of proteins?: **YwlE consists of a twisted central four-stranded parallel β-sheetwith seven α-helices packing on both sides.
 * Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism): **



[|https://cansar.icr.ac.uk/cansar/molecular-targets/target_report_drugs/P39155/#main_tab_holder:target_report_tab:target_report_druggability]


 * *EC#: 3.1.3.48 **
 * Link to BRENDA EC# page: **
 * [] **


 * Enzyme Assay information (spectrophotometric, coupled assay ?, reagents): **
 * " **Activity assays for tyrosine phosphatases are based on the hydrolysis of a arylphosphate moiety from a synthetic substrate yielding a spectroscopically active product. Many different substrates can be used for these assays with p-nitrophenyl phosphate (pNPP), fluorescein diphosphate (FDP), and 6,8-difluoro-4-methylumbellyferyl phosphate (DiFMUP) being the most efficient and versatile."

The link below is a journal article that lists different types of enzymatic assays that can be used for protein tyrosine phosphatase. []
 * []**

Cost: $8**4.50** []
 * -- links to assay reagents (substrates) pages. **
 * [] **
 * []**
 * --- List cost and quantity of substrate reagents, supplier, and catalog # **
 * Supplier: ** Sigma
 * Catalog #: **P4744-1G

-- PDB # or closest PDB entry if using homology model: The PubMed ID is not available for the protein target, however there is still a PDB page for the target. The molecule can be found using the search 4ETN. -- For Homology Model option: Did not need to use the homology model because there is a PDB page for the Xray crystal structure. Show pairwise alignment of your BLASTP search in NCBI against the PDB Query Coverage: Max % Identities: % Positives Chain used for homology:
 * Structure Available (PDB or Homology model) **

Range 1: 139 to 147 Graphics Alignment statistics for match #1||~ Score Query 79 LKEPPQGAH 87 LKE G+H Sbjct 139 LKEYVTGSH 147
 * Similarity to Humans:**
 * ~ Expect ||~ Method ||~ Identities ||~ Positives ||~ Gaps ||
 * 13.5 bits(23) || 2.8 || Compositional matrix adjust. || 5/9(56%) || 6/9(66%) || 0/9(0%) ||

Range 2: 139 to 162 Graphics [|First Match] Alignment statistics for match #2||~ Score Query 131 LKLFVTRIMQDFESDTFFPEIDLEK 155 LK +VT D D F ID+ K Sbjct 139 LKEYVTGSHGDV-LDPFGGSIDIYK 162
 * ~ Expect ||~ Method ||~ Identities ||~ Positives ||~ Gaps ||
 * 13.1 bits(22) || 3.3 || Compositional matrix adjust. || 10/25(40%) || 12/25(48%) || 1/25(4%) ||

There is about 504 number of compounds for the protein tyrosine phosphatase target. This target looks like it has been overstudied, however for some of the more specific targets it hasn't.
 * Current Inhibitors: **

Expression Information (has it been expressed in bacterial cells): The gene ywlE has been expressed in bacterial cells during the dephosphorylation process of the substrate pNPP. The target, however, isn't expressed at high levels and is only expressed at certain times. Also, the target ywlE becomes inhibited with high concentrations of the substrate. [][]

Purification Method: O verexpressing //Escherichia coli// strains.

Image of protein:

*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'): code format="sequence" MDIIFVCTGN TCRSPMAEAL FKSIAEREGL NVNVRSAGVF ASPNGKATPH AVEALFEKHI

7__0__        8__0__         9__0__        10__0__        11__0__        12__0__ ALNHVSSPLT EELMESADLV LAMTHQHKQI IASQFGRYRD KVFTLKEYVT GSHGDVLDPF

13__0__       14__0__        15__0__ GGSIDIYKQT RDELEELLRQ LAKQLKKDRR code

*length of your protein in Amino Acids: 150 Molecular Weight of your protein in kiloDaltons using the [|Expasy ProtParam] website: 16785.1 Molar Extinction coefficient of your protein at 280 nm wavelength: code Ext. coefficient: 4595, assuming all pairs of Cys residues [|form] cystines

Ext. coefficient: 4470, assuming all Cys residues are reduced code 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): AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG**
 * Starts = ---M---MMMMM---M**
 * Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG**
 * Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG**
 * Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG**


 * *GC% Content for gene: 29.48 % **
 * *CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only): **


 * *GC% Content for gene (codon optimized): 42.3% **


 * Do Not Need this info for Spring (but still copy these lines to your Target page for now) **
 * 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) **
 * -- 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 'tail' primers (this is just 2 sequences): **