Target+-+Serine+threonine+protein+phosphatase+(Plasmodium+falciparum)

determine best PDB to use for Homology Model - see Target Discovery protocol create a Homology model using ICM - see GoogleDocs/Protocols/VirtualScreening/HomologyModel/ Instructions ProMol Project Homology Models v6 = = =Serine/threonine protein phosphatase PP1 (Plasmodium falciparum)= []
 * Dr. B Notes (090513):**
 * Target (protein/gene name):** serine/threonine protein phosphatase PP1

@http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&primary_key=PF14_0142

PF3D7_1414400
 * NCBI Gene # or RefSeq#:**


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

Plasmodium falciparum 3D7
 * Organism (including strain):**

Agents that are associated with human disease which is rarely serious and for which preventive or therapeutic interventions are //often// available
 * Etiologic Risk Group (see link below):** Risk Group 2 (RG2) - Parasitic Agents

//Plasmodium falciparum// is a parasite that is one of the most common causes of malaria. In 2002, it was estimated that 2.2 billion people were exposed to malaria, resulting in approximately 515 million clinical attacks of this disease. The majority (~70%) of incidence of this disease in 2002 occurred in Africa, with a substantial incidence rate (~25%) in Southeast Asia [1]. A global map depicting the endemicity of malaria in 2007 showed high endemicity in Africa, low endemicity with pockets of mid to high endemicity in Central/Southeast Asia, and uniformly low endemicity in the Americas [2].
 * Background/Disease Information (sort of like the Intro to your Mini Research Write up):**

Because malaria is generally concentrated in lower income countries, the ideal treatment option for malaria would be cheap, single-dose and have minimal side effects. However, the current treatment options fall short of meeting this criteria. For decades, choroquine (CQ) was the main treatment option for malaria; however, as years passed, CQ-resistant malaria developed. Today, CQ is no longer a viable treatment option for most instances of malaria. Other drugs used in malaria treatment have serious side effects. As such, there is a pronounced need for novel anti-malarial drugs [3].

Serine and threonine have similar side-chain compositions and thus can be phosphorylated by a single enzyme called serine/threonine protein kinase. The addition of the phosphate group can be reversed by an enzyme called serine/threonine phosphatase. The removal of the phosphate group helps to regulate many cellular pathways involved in cell proliferation, programmed cell death (apoptosis), embryonic development, and cell differentiation.
 * Essentiality of this protein:**

Gene/Ortholog: Tb927.10.13670 (OG4_11778); Phenotype: no significant loss or gain of fitness in bloodstream forms (3 days); Source study: alsford Gene/Ortholog: Tb927.10.13670 (OG4_11778); Phenotype: significant loss of fitness in bloodstream forms (6 days); Source study: alsford Gene/Ortholog: Tb927.10.13670 (OG4_11778); Phenotype: significant loss of fitness in procyclic forms; Source study: alsford Gene/Ortholog: Tb927.10.13670 (OG4_11778); Phenotype: significant loss of fitness in differentiation of procyclic to bloodstream forms; Source study: alsford

no
 * Complex of proteins?:**

0.6 (yes)
 * Druggable Target:**


 * *EC#: **3.1.3.16


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

__Assay:__ 4-nitrophenyl phosphate (PNPP) []
 * Assay:** Assay for Calcineurin (3.1.3.16 ); **Source:** [|Sigma-Aldrich]

__Reagent:__ MAL13P1.274; __Type:__ cloned gene; __Source:__ BRENDA __Notes:__ A gene with this EC number or name or sequence has been cloned from Plasmodium falciparum ( [|1] );
 * Reagent availability:**

__Reagent:__ MAL13P1.274; __Type:__ purified protein; __Source:__ BRENDA __Notes:__ A protein with this EC number or name or sequence has been purified from Plasmodium falciparum ( [|1] );


 * -- List cost and quantity of substrate reagents and supplier**

@http://www.ncbi.nlm.nih.gov/protein/410562615?report=genbank&log$=prottop&blast_rank=3&RID=8JUAP21S01R
 * Structure Available (PDB or Homology model)**

@http://www.rcsb.org/pdb/explore/explore.do?pdbId=3v4y

Newest Blastp homology result (Sept. 4, 2013):

-- For Homology Model option:

Show pairwise alignment of your BLASTP search in NCBI against the PDB



Query Coverage: Max % Identities: 85% % Positives: 95% Chain used for homology: 3v4y_G


 * Current Inhibitors:**


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


 * Purification Method:**


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

MALEIDIDNVISKLIEVRGTRPGKNVNLTENEIKILCLSSREIFLNQPILLELEAPIKIC GDIHGQFYDLLRLFEYGGFPPDANYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLR GNHECASINRIYGFYDECKRRYSVKLWKTFIDCFNCLPVAAIIDEKIFCMHGGLSPELNN MEQIRKITRPTDVPDNGLLCDLLWSDPEKEINGWGENDRGVSFTFGQDVVHNFLRKHELD LICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPVEKK KAAN
 * Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):**


 * length of your protein in Amino Acids:** 304 aa


 * Molecular Weight of your protein in kiloDaltons using the [|Expasy ProtParam] website:** 76889


 * 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:** 50%

1 ATGGCGCTGGAAATCGACATCGACAACGTGATCTCCAAACTGATCGAAGTTCGTGGTACC 61 CGTCCAGGCAAGAACGTTAACCTGACCGAGAATGAGATCAAAATTCTGTGCCTGTCTTCT 121 CGTGAAATCTTTCTCAATCAGCCGATCCTGCTCGAACTGGAAGCGCCGATTAAGATCTGC 181 GGTGATATCCATGGTCAGTTCTACGACCTGCTCCGTCTGTTCGAATATGGTGGTTTCCCA 241 CCGGACGCGAATTATCTGTTCCTGGGTGACTACGTTGACCGCGGCAAACAGTCTCTGGAG 301 ACCATCTGTCTGCTCCTGGCGTACAAAATCAAATATCCGGAAAATTTCTTCCTGCTGCGT 361 GGTAACCATGAATGCGCGTCTATCAACCGTATCTACGGTTTCTATGACGAATGCAAACGT 421 CGTTACTCTGTTAAACTGTGGAAGACCTTCATCGACTGCTTCAACTGCCTCCCGGTTGCG 481 GCGATTATCGACGAAAAAATCTTCTGTATGCACGGTGGTCTCTCTCCGGAACTGAACAAC 541 ATGGAACAAATCCGTAAAATCACCCGCCCAACGGACGTTCCTGACAACGGTCTGCTGTGC 601 GACCTCCTGTGGTCTGACCCTGAAAAAGAAATCAACGGTTGGGGTGAAAACGACCGTGGT 661 GTTTCTTTCACCTTCGGTCAAGACGTCGTGCACAATTTTCTGCGTAAACATGAACTCGAC 721 CTGATCTGCCGTGCGCATCAGGTTGTTGAAGACGGTTACGAATTCTTCGCTAAGCGTCAG 781 CTCGTTACCCTGTTCTCTGCGCCGAACTACTGTGGTGAGTTCGATAACGCGGGTGCGATG 841 ATGTCTGTTGACGAAACCCTGATGTGCTCTTTCCAGATTCTGAAGCCGGTTGAAAAGAAG 901 AAGGCGGCGAACTAA
 * CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):**


 * GC% Content for gene (codon optimized):** 50%

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):**


 * References**

[1] Snow, R.W.; Guerra, C.A.; Noor, A.M.; Myint, H.Y.; Hay, S.I., The global distribution of clinical episodes of plasmodium falciparum malaria. //Nature// **2005**, 434, (7030), 214-217.

[2] Hay, S.I.; Guerra, C.A.; Gething, P.W.; Patil, A.P.; Tatem, A.J.; Noor, A.M.; Kabaria, A.M.; Manh, B.H.; Elyazar, I.R.F.; Brooker, S.; Smith, D.L.; Moyeed, R.A.; Snow, R.W., A world malaria map: Plasmodium falciparum endemicity in 2007. //PLoS Med// **2009,** 6, (3).

[3] Bell, D.J.; Molyneux, M.E., Treatment of childhood plasmodium falciparum malaria: Current challenges. //Expert Review of Anti-Infective Therapy// **2007**, 5, (1), 141.