Target+-+dihydroorotate+dehydrogenase+(malaria)

[]  ***Protein ID (NP or XP #) or Wolbachia#:** XP_966023.1  ***Organism (including strain):** //Plasmodium falciparum 3D7//  **Etiologic Risk Group (see link below):** Appendix B-II-C. Risk Group 2 (RG2) - Parasitic Agents Plasmodium falciparum is a protozoan parasite that can cause malaria in humans. Female mosquitos transmit it. Malaria can be transmitted by other organisms, but ¾ of the cases are caused by plasmodium falciparum. This is also the most deadly of all malaria.  **Essentiality of this protein:** Phenotype: significant loss of fitness in bloodstream forms (6 days); Source study: alsford; http://www.tdrtargets.org/targets/view?gene_id=4387 "Analysis of bloodstream and insect life-cycle stages and differentiated libraries revealed genome-scale knockdown profiles of growth and development, linking thousands of previously uncharacterized and "hypothetical" genes to essential functions. Genes underlying prominent features of trypanosome biology are highlighted, including the constitutive emphasis on post-transcriptional gene expression control, the importance of flagellar motility and glycolysis in the bloodstream, and of carboxylic acid metabolism and phosphorylation during differentiation from the bloodstream to the insect stage." http://www.ncbi.nlm.nih.gov/pubmed/21363968 "Pyrimidine biosynthesis presents an attractive drug target in malaria parasites due to the absence of a pyrimidine salvage pathway. A set of compounds designed to inhibit the Plasmodium falciparum pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (PfDHODH) was synthesized." http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=275413&loc=ea_ras#aDescription
 * TDR Targets ID: 4387 **
 * P. falciparum 3D7, dihydroorotate dehydrogenase, mitochondrial precursor **
 * *Target (protein/gene name): **dihydroorotate dehydrogenase
 *  *NCBI Gene # **3885966 **or RefSeq#:** NC_004327.2
 * *Background/Disease Information (sort of like the Intro to your Mini Research Write up): **

 **Complex of proteins?: no**  **Druggable Target:** yes  **Link to BRENDA EC# page:** http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.3.98.1
 * *EC#: 1.3.98.1 **

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> **--** <span style="color: #000000; font-family: 'Times New Roman','serif'; font-size: 16px;">Show screenshot of BRENDA enzyme mechanism schematic <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> **Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):** "Dihydroorotate oxidation was usually measured by following ferricyanide reduction (reaction 1, below) as previously described (15). Where indicated, 2, 6-dichlorophenolindolphenol 98 (DCI) (0.2 usmol) or cytochrome c (1 mg) was substituted for ferricyanide in the standard protocol. Reduction of the acceptor was followed spectrophotometrically at 600 nm for DCI and at 550 nm for cytochrome c as described previously." <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> **-- link to Sigma (or other company) page for assay or assay reagents (substrates)** <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">[] <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">[] <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">[] <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">[]
 * <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">-- link (or citation) to paper that contains assay information **
 * <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">-- List cost and quantity of substrate reagents and supplier **

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> **Structure Available (PDB or Homology model)** <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">[] <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">-- PDB # or closest PDB entry if using homology model: <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> -- For Homology Model option: <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> Show pairwise alignment of your <span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">BLASTP search in NCBI against the PDB <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> Query Coverage: <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> Max % Identities: <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> % Positives <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> Chain used for homology: <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> **Current Inhibitors:** <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">" Both teriflunomide and leflunomide are inhibitors of the mitochondrial enzyme dihydroorotate dehydrogenase, which is critically involved in pyrimidine synthesis." <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">[]

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> **Expression Information (has it been expressed in bacterial cells):** <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">From Brenda information, this organism has been expressed in <span style="color: #000000; font-family: 'Times New Roman','serif'; font-size: 16px; text-decoration: none;">Lactobacillus delbrueckii subsp. bulgaricus <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">, <span style="color: #000000; font-family: 'Times New Roman','serif'; font-size: 16px; text-decoration: none;">Crithidia fasciculata <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">, <span style="color: #000000; font-family: 'Times New Roman','serif'; font-size: 16px; text-decoration: none;">Escherichia coli <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">, <span style="color: #000000; font-family: 'Times New Roman','serif'; font-size: 16px; text-decoration: none;">Lactococcus lactis <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">, <span style="color: #000000; font-family: 'Times New Roman','serif'; font-size: 16px; text-decoration: none;">Homo sapiens <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">, <span style="color: #000000; font-family: 'Times New Roman','serif'; font-size: 16px; text-decoration: none;">Sulfolobus solfataricus <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">, and <span style="color: #000000; font-family: 'Times New Roman','serif'; font-size: 16px; text-decoration: none;">Trypanosoma cruzi

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> **Purification Method**: []
 * <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">Image of protein (PyMol with features delineated and shown separately): **

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> ***Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):** misklkpqfm flpkkhilsy crkdvlnlfe qkfyytskrk esnnmknesl lrlinynryy nkidsnnyyn ggkilsndrq yiysplceyk kkindissyv svpfkinirn lgtsnfvnnk kdvldndyiy enikkekskh kkiifllfvs lfglygffes ynpefflydi flkfclkyid geichdlfll lgkynilpyd tsndsiyact nikhldfinp fgvaagfdkn gvcidsilkl gfsfieigti tprgqtgnak prifrdvesr siinscgfnn mgcdkvtenl ilfrkrqeed kllskhivgv sigknkdtvn ivddlkycin kigryadyia invsspntpg lrdnqeagkl kniilsvkee idnleknnim ndestynedn kivekknnfn knnshmmkda kdnflwfntt kkkplvfvkl apdlnqeqkk eiadvlletn idgmiisntt tqindiksfe nkkggvsgak lkdistkfic emynytnkqi piiasggifs gldalekiea gasvcqlysc lvfngmksav qikrelnhll yqrgyynlke aigrkhsks <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> ***length of your protein in Amino Acids: 569** <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> **Molecular Weight of your protein in kiloDaltons using the** [|**Expasy ProtParam**]**<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> website: **65558.4 <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> **Molar Extinction coefficient of your protein at 280 nm wavelength:** 51690 <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> ** TMpred graph Image ** (@http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it. <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> ***CDS Gene Sequence (paste as text only):** ATGATCTCTAAATTGAAACCTCAATTTATGTTTTTACCAAAGAAACATATTTTAAGTTATTGTAGAAAGG ATGTTTTAAATTTGTTTGAACAGAAGTTTTATTATACTAGCAAACGGAAAGAAAGTAATAATATGAAGAATGAATCTTTATTAAGATTAATTAATTATAATAGATATTATAATAAGATAGATTCTAATAATTATTATAATGGTGGAAAAATATTAAGTAATGATAGGCAATATATATATTCACCATTATGTGAATATAAAAAGAAAATAAATGATATATCATCATATGTATCTGTACCTTTTAAGATTAATATAAGAAATTTAGGTACTTCCAATTTTGTAAATAATAAGAAGGATGTACTTGATAATGATTATATTTATGAAAATATTAAAAAAGAAAAATCTAAGCATAAAAAAATAATATTTTTATTATTTGTTTCATTATTTGGATTATATGGTTTTTTTGAATCTTATAATCCTGAATTTTTTTTATATGATATATTTTTAAAATTCTGTTTAAAATATATTGATGGTGAAATATGTCATGACCTTTTTTTATTACTAGGAAAATATAATATATTACCATATGATACTAGTAATGATAGTATATATGCATGTACAAATATTAAACATCTTGATTTTATAAATCCATTCGGTGTTGCTGCAGGATTTGATAAAAACGGTGTATGTATAGATAGCATATTAAAATTAGGGTTTTCGTTTATCGAAATTGGTACCATAACCCCAAGGGGCCAAACGGGTAATGCAAAACCACGTATTTTTAGAGACGTTGAATCTAGAAGTATTATAAATTCATGTGGCTTTAATAATATGGGTTGTGACAAAGTTACAGAAAATTTAATACTTTTTCGTAAAAGACAAGAAGAAGATAAATTGTTAAGTAAACATATTGTAGGTGTCAGTATAGGTAAGAATAAAGATACTGTTAATATTGTAGATGATCTAAAATATTGTATTAATAAAATAGGAAGATACGCTGATTATATAGCTATTAATGTAAGCTCCCCTAATACACCTGGGTTAAGAGATAATCAAGAAGCTGGGAAGTTAAAAAATATAATTTTAAGTGTAAAAGAAGAAATAGATAATTTAGAAAAGAATAATATTATGAATGATGAAAGTACTTATAATGAAGATAATAAAATAGTAGAAAAAAAAAATAATTTTAATAAAAATAATAGTCACATGATGAAAGATGCTAAGGATAACTTCTTATGGTTTAATACAACAAAAAAGAAGCCCTTGGTTTTTGTTAAGTTAGCTCCAGATCTTAATCAAGAACAGAAAAAAGAAATTGCTGATGTATTACTTGAAACTAATATAGATGGTATGATTATTTCTAATACTACGACACAAATAAATGACATAAAAAGTTTTGAAAATAAAAAAGGAGGTGTTAGCGGAGCAAAACTAAAAGATATATCTACAAAATTTATATGTGAAATGTATAATTATACAAATAAACAAATACCCATTATTGCATCAGGAGGGATATTTAGTGGATTGGATGCTTTAGAAAAAATTGAAGCAGGTGCTTCAGTTTGTCAATTATATTCTTGTTTGGTTTTTAATGGTATGAAATCAGCTGTACAAATAAAAAGAGAATTGAATCACTTGCTATATCAAAGAGGATATTACAATTTAAAGGAGGCCATTGGCCGAAAGCATAGCAAAAGTTAA <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> ***GC% Content for gene: 24.561403508772%** <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> ***CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):** <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> ***GC% Content for gene (codon optimized):**

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;">Do Not Need this info for Spring (but still copy these lines to your Target page for now) <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> **Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):** <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> **( link to DNA Works output text file - **that should be saved in your Google Docs folder after you did the primer design protocol) <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> -- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> **Primer design results for 'tail' primers (this is just 2 sequences):**

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 * <span style="font-family: 'Times New Roman','serif'; font-size: 24px;">Resources: **