Target+-+6-phosphogluconate+dehydrogenase,+decarboxylating,+putative+(P.+falciparum+3D7)

Saul: ** *Target (protein/gene name): **6-phosphogluconate dehydrogenase, decarboxylating, putative Saul: ** *NCBI Gene # or RefSeq#: **PF14_0520 Saul: ** *Protein ID (NP or XP #) or Wolbachia#: ** XP_001348694.1 Saul: ** *Organism (including strain): ** p. falciparum 3D7 Saul: ** Etiologic Risk Group (see link below): ** http://www.who.int/ith/diseases/malaria/en/ Saul: ** */ Disease Information (sort of like the Intro to your Mini __Research Write__ up): ** Malaria is caused by the protozoan parasite Plasmodium. Human malaria is caused by four different species of Plasmodium: P. falciparum, P. malariae, P. ovale and P. vivax. Humans occasionally become infected with Plasmodium species that normally infect animals, such as P. knowlesi. As yet, there are no reports of human-mosquitohuman transmission of such “zoonotic” forms of malaria. The malaria parasite is transmitted by female Anopheles mosquitoes, which bite mainly between dusk and dawn. Saul: ** Link to TDR Targets page (if present): **http://tdrtargets.org/targets/view?gene_id=2850 Saul: ** Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.) ** http://www.ncbi.nlm.nih.gov/gene/812102 Saul: ** Essentiality of this protein: ** biding, catalytic activity, coenzyme biding, NADP biding, oxidoreductase binding Is it a monomer or multimer as biological unit ** ? (make prediction at ** @http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html): Saul: ** Complex of proteins?: none ** Saul: ** Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism): ** yes https://www.ebi.ac.uk/chembldb/index.php/target/inspect/11938 3 papers http://tdrtargets.org/targets/papers/?tid=11938 Saul: ** *EC#: ** [|1.1.1.44] Saul: ** Link to BRENDA EC# page: **http://www.brenda-enzymes.org/enzyme.php?ecno=1.1.1.44 Saul: ** -- ** Show screenshot of BRENDA enzyme mechanism schematic
 * Target Team: **Saul H, Lauren M, Carlos Gio O.

Gio: ** Enzyme Assay information (spectrophotometric, coupled assay ?, reagents): **mixture of 66.7mMtris-HC1 (pH 7.8), 0.334mM 6-phosphogluconate, 0.134mM NADP+, and 1.7 m~MgSO4 in a 1-ml volume Gio: ** -- link to Sigma (or other company ) page for assay (see Sigma links below) ** http://www.sigmaaldrich.com/catalog/product/sigma/b2517?lang=en®ion=US Gio: ** -- -or link (or citation) to paper that contains assay information ** http://download.springer.com/static/pdf/728/art%253A10.1007%252FBF00504362.pdf?auth66=1412571262_3d630219b69007a0c2da0e8c8be777c5&ext=.pdf Gio: ** -- links to assay reagents (substrates) pages. ** Gio: ** --- List cost and quantity of substrate reagents, supplier, and catalog # ** Sigma $106.00 for 100MG Gio: ** Structure (PDB or Homology model) ** Gio: -- PDB # or closest PDB entry if using homology model: __4GWG__ Gio: -- For Homology Model option: no need for homology model Gio: Show pairwise alignment of your BLASTP search in NCBI against the PDB Gio: Query Coverage: Gio: Max % Identities: Gio: % Positives Gio: Chain used for homology:

Lauren: ** Current Inhibitors: ** N/A(Cofactor: SO4) Lauren: ** Expression Information (has it been expressed in bacterial cells): ** Lauren: ** Purification Method : ** Lauren: ** Image of protein (PyMol with features delineated and shown separately): ** Lauren: ** *Amino Acid Sequence (paste as text only - not as screenshot or as 'code'): ** MCDIGLIGLAVMGQNLSLNISSKGFKIGVYNRTYERTEETMKRAKEENLVVYGYKTVEELINNLKKPRKV ILLIKAGPAVDENISNILKHFEKGDIIIDGGNEWYINSERRIKLCKEKDVEYLAMGVSGGEAGARYGCSF MPGGSKYAYDCVKEILEKCSAQVGNSPCVTYIGPGSSGNYVKMVHNGIEYGDMQLISESYVIMKHILKYD NQKLSEVFNKWNEGILNSYLIEITANILAKKDDLTNNYLVDMILDIAGAKGTGKWTMLEATERGIPCPTM CAALDARNISVFKELRTKAESNFNKDNILIDPNEDLNDFENDLLNALYCCKIISYTQGLFLLKQVSEEMN WKLNLGEIARIWRGGCIIRAVFLDRIANAYKNNEKLELLFLDNEFSDDIKNKLPSLRKIVLMATKYSIPI PAFSASLAYFQMVTSQNLPLNLVQAQRDYFGSHTYRRTDREGNYHTLW Lauren: ** *length of your protein in Amino Acids: ** 468 Lauren: ** Molecular Weight of your protein in kiloDaltons using the [|Expasy ProtParam] website: **52994.0 Lauren: ** Molar Extinction coefficient of your protein at 280 nm wavelength: ** 69385 Lauren: ** TMpred graph Image ** (@http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.



Lauren: ** *CDS Gene Sequence (paste as text only): **

ATGTGTGATATTGGTTTGATAGGTTTGGCTGTCATGGGCCAGAATTTAAGTTTGAATATTTCAAGCAAAGGTTTTA AAATTGGTGTTTATAATAGGACATATGAAAGAACAGAAGAAACAATGAAAAGAGCAAAAGAAGAGAATTTGGTTG TTTATGGTTATAAAACAGTAGAAGAATTAATAAATAATTTGAAAAAACCAAGGAAAGTTATTTTATTAATCAAAGCAG GTCCAGCTGTAGATGAGAATATTAGTAATATATTAAAACATTTTGAAAAAGGAGATATAATAATTGATGGTGGGAAT GAATGGTATATTAATTCAGAAAGAAGAATAAAATTATGTAAAGAAAAAGATGTAGAATATTTAGCTATGGGTGTGAG TGGAGGTGAAGCAGGTGCAAGATATGGTTGTTCATTTATGCCTGGTGGTTCTAAATATGCATATGATTGTGTGAA AGAAATATTAGAAAAATGTTCAGCTCAAGTTGGAAATTCTCCTTGTGTTACTTATATAGGTCCAGGTTCCTCAGGG AATTATGTAAAAATGGTACATAATGGAATAGAATATGGAGATATGCAATTAATATCAGAAAGTTATGTAATTATGAAAC ATATATTAAAATATGATAATCAGAAATTATCAGAAGTTTTTAATAAATGGAATGAAGGTATATTAAATTCTTACTTAATT GAAATTACTGCAAATATTCTTGCAAAAAAAGATGACTTAACAAATAATTATTTAGTTGATATGATATTAGATATTGCTG GAGCAAAAGGTACAGGGAAATGGACTATGCTTGAAGCTACCGAAAGAGGTATCCCTTGTCCAACTATGTGTGCT GCTTTAGATGCACGTAATATAAGTGTTTTTAAAGAATTAAGAACTAAAGCAGAATCTAATTTTAATAAAGATAATATTC TTATTGACCCAAATGAAGATTTAAATGATTTTGAAAATGATTTATTAAATGCTCTTTATTGTTGTAAAATTATTTCATAT ACTCAAGGTCTTTTCCTTTTAAAACAAGTTTCTGAAGAAATGAACTGGAAATTAAATTTGGGAGAAATTGCTAGAA TATGGAGAGGTGGTTGTATTATAAGAGCTGTTTTCTTAGATCGTATAGCAAATGCTTATAAAAATAATGAAAAATTAG AATTATTATTCCTAGATAATGAATTCTCAGATGATATTAAAAATAAATTACCTTCCTTAAGAAAAATTGTTCTTATGGCT ACAAAATATTCCATACCAATTCCTGCCTTCTCAGCTAGTTTAGCATATTTTCAAATGGTAACCTCACAAAATTTACCT CTTAATTTAGTGCAAGCCCAAAGGGATTATTTTGGATCACACACATATAGGAGAACAGATCGTGAAGGAAATTATC ACACCTTGTGGTGA Lauren: ** *GC% Content for gene: ** 28.6% Lauren: ** *CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only): ** 1 ATGTGCGACATTGGTCTGATTGGCCTGGCGGTTATGGGTCAGAATCTGTCTCTGAATATC

61 TCCTCTAAGGGTTTCAAAATCGGTGTTTACAACCGTACCTACGAACGTACGGAAGAAACC

121 ATGAAACGTGCGAAAGAAGAGAACCTCGTGGTCTACGGTTACAAAACCGTTGAGGAACTG

181 ATCAATAATCTGAAAAAACCACGTAAGGTTATCCTCCTCATCAAGGCGGGTCCGGCGGTT

241 GACGAAAACATTTCTAATATTCTGAAACACTTCGAGAAAGGTGACATTATCATCGACGGT

301 GGTAACGAATGGTACATCAACTCTGAACGTCGTATCAAACTGTGCAAGGAAAAAGACGTT

361 GAATACCTGGCGATGGGTGTTTCTGGTGGTGAAGCCGGTGCGCGTTACGGCTGTTCTTTC

421 ATGCCAGGTGGCTCTAAATATGCGTACGACTGCGTTAAGGAAATCCTGGAAAAGTGCTCT

481 GCTCAGGTGGGTAACTCTCCATGTGTCACTTACATCGGTCCGGGTAGCTCTGGTAACTAC

541 GTTAAAATGGTTCACAACGGTATCGAATACGGCGACATGCAGCTGATCTCCGAATCTTAC

601 GTCATCATGAAGCACATCCTCAAATACGACAACCAGAAGCTGTCTGAAGTCTTCAACAAG

661 TGGAACGAAGGTATCCTGAATAGCTACCTGATTGAAATCACCGCGAACATCCTGGCAAAG

721 AAAGACGATCTGACCAACAACTACCTGGTTGACATGATTCTCGACATCGCGGGTGCTAAA

781 GGTACCGGCAAATGGACCATGCTGGAAGCGACCGAACGTGGTATCCCGTGCCCGACTATG

841 TGTGCGGCGCTGGATGCCCGCAATATTTCTGTTTTCAAAGAACTCCGTACCAAAGCGGAA

901 TCTAACTTCAATAAAGACAACATTCTCATTGACCCTAACGAAGACCTGAACGACTTCGAA

961 AACGACCTGCTCAACGCGCTCTACTGCTGCAAAATCATCTCTTACACCCAAGGTCTCTTT

1021 CTGCTGAAGCAAGTTTCTGAAGAAATGAACTGGAAACTCAACCTGGGTGAGATCGCGCGT

1081 ATCTGGCGTGGTGGTTGCATCATCCGTGCGGTTTTCCTGGACCGTATTGCGAATGCCTAT

1141 AAGAATAACGAAAAGCTGGAGCTGCTGTTCCTCGACAATGAATTTTCTGACGACATCAAA

1201 AACAAACTGCCGTCTCTGCGCAAAATTGTTCTGATGGCGACCAAATACTCTATCCCGATC

1261 CCGGCGTTCTCTGCTTCTCTCGCGTACTTCCAGATGGTTACCTCTCAGAACCTGCCGCTC

1321 AATCTGGTTCAGGCGCAGCGTGACTACTTCGGTTCTCACACGTATCGTCGTACTGATCGT

1381 GAGGGCAACTATCATACCCTGTGGTAA Lauren: ** *GC% Content for gene (codon optimized): ** 47.8%

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)

__** Saul Huerta: **__ Forward Primer: 5’ TACTTCCAATCCATGTGCGACATTGGTCTGATCGG 3’ 35 bp Reverse primer: 5’ TATCCACCTTTACTGTTACCACAGGGTGTGGTAGT 3’ 35 bp __** Lauren McGregor: **__
 * Primer design results for 'tail' primers (this is just 2 sequences): **
 * Forward Primer:**

TACTTCCAATCCATGTGCGACATTGGTCTGAT ACTATCATACCCTGTGGTAACAGTAAAGGTGGATA
 * Reverse Primer:**