*Target (protein/gene name): 6-phosphogluconate dehydrogenase decarboxylating, putative
*NCBI Gene # or RefSeq#: 12980488
*Protein ID (NP or XP #) or Wolbachia#: XP_003722728 (link!)
*Organism (including strain): Leishmania Major
Etiologic Risk Group (see link below): Risk Group 2 (link!)
*/Disease Information(sort of like the Intro to your MiniResearch Writeup):
Leishmaniasis is a metazoonosis disease caused by the gensus Leishmania found from a bite of a phlebotomine female sand fly of the genera Phlebotomus and Lutzomyia [1]. When a parasitic female sand fly bites into a human host, the parasite undergoes the intracellular stage where it takes on a promastigote form. Then the parasite reproduces and multiplies within the macrophages until it lyses, and then the cycle continues, affecting even “lymph nodes, spleen, liver and the bone marrow” [1]. This disease is primarily found in the tropics and “primarily in poor and underserved populations” [2]. There are 3 majors severity levels of Leishmaniasis that are visceral (kala-azar), cutaneous, and mucocutaneous. Visceral is the most severe due to the fact that the “vector-borne infection has clinical spectrums that ranges” depending successful the immune system inhibits the proliferation of the parasite [3]. Since the parasite invades the host cell by impairing cell functions by “altering the maturation process of the phagolysosome, cytokine, and chemokine production,” it is extremely difficult to diagnosis the disease [3]. Due to the fact that Leishmaniasis is a silent killer, where symptoms do not become apparent until the disease has progressed, it is the “most deadly parasitic disease after malaria” [3]. Current treatments against leishmaniasis are expensive due to its large scope of resistance against several clinical treatments. Even though there are many medical tests, for instance the Indirect Fluorescent Antibody (IFA) test, that detects the early stages of the injection, but not after six to nine months, there is a need for new treatments against Leishmaniasis [1].

Link to TDR Targets page (if present): (**link!)**
Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.)
Essentiality of this protein:
It is essential the pathway of the pentose phosphate pathway (PPP) and the NADP-dependent reaction where NADPH is formed. 6PGDdp plays a crucial role of the host-parasite relationship by providing the parasite the need to generate a defense against oxidative stress [6]. Inhibiting this reaction mechanism with PPP is crucial in reducing the biosynthesis pathways and the cellular redox exchange as well as reducing the synthesis of nucleotides for nucleotide and nucleic acid production

Is it a monomer or multimer as biological unit? (make prediction at http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html):Dimer
Complex of proteins?: Dimer
Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism): 0.8 (TDR Target)
*EC#: 1.1.1.44
Link to BRENDA EC# page: (link!)
-- Show screenshot of BRENDA enzyme mechanism schematic

rxnbreanda-lmaj.png

Figure 1: Reaction Mechanism of 6-phosphogluconate dehydrogenase (E.C. 1.1.1.44) obtained from BRENDA [4].

Enzyme Assayinformation (spectrophotometric, coupled assay ?, reagents):
http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Enzyme_Assay/6phosphoglucdehydro74.pdf
http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Bulletin/1/mak038bul.pdf
-- links to assay reagents (substrates) pages:
http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Enzyme_Assay/6phosphoglucdehydro74.pdf
--- List cost and quantity of substrate reagents, supplier, and catalog #
http://www.sigmaaldrich.com/catalog/product/sigma/mak038?lang=en®ion=US

Structure (PDB or Homology model)
-- PDB # or closest PDB entry if using homology model:Homology 1PGJ
-- For Homology Model option:
---- Show pairwise alignment of your BLASTP search in NCBI against the PDB
---- Query Coverage:97%
---- Max % Identities:339/465% (73%)
---- % Positives: 388/465 (83%)
---- Chain used for homology: Chain A
homology-lmaj.png
Figure 2: Homology Model Pair Alignment with 1PGJ (T. Brucei) with Query Coverage 97%, Maximum % of Identities 73%, and Positive % 83% for Chain A.

Current Inhibitors: 4a) 4-phospho-D-erythronate, 4b) 2-Deoxy-6-phosphogluconate, and 4c) 5-phospho-d-rinbonate.
ligand-lmaj.png
Figure 3: PYMOL representation of the 3 inhibitors shown as purple sticks of 6PGD used with the active site shown as purple of the homology model PDB 1PGJ surface transperancy of 0.5 with carbon colored as green . The ligans are as labeled 4a) 4-phospho-D-erythronate, 4b) 2-Deoxy-6-phosphogluconate, and 4c) 5-phospho-d-rinbonate.

Expression Information (has it been expressed in bacterial cells): E.Coli pNIC-Bsa4
Purification Method: Metal Affinity Chromatography (NIckle-NTA)
Image of protein (PyMol with features delineated and shown separately):
PDBPymol-Lmaj.png
Figure 4: PYMOL representation of homology model of PDB 1PGJ of target protein shown as surface transperency 0.5 and overall with green carbons. Active region shown as cyan.

*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
MSNDLGIIGLGVMGANLALNIAEKGFKVAVFNRTYAKTTSFLKEHESEKFAANLNGYETM
KEFAASLKKPRRAFILVQAGAATDSTIEQLKEVFENGDIIIDTGNANFKDQDKRAAQLES
QGLRFLGMGISGGEEGARKGPAFFPGGTPSVWEEVRPIVEAAAAKAEDGRPCVTFNGKGG
AGSCVKMYHNAGEYAVLQIWGEAYSALLAFGFDNDQIADVFESWKADGFLKSYMLDISIA
ACRAREATGNYLSEKVKDRIGSKGTGLWSAQEALEIGVPAPSLNMAVISRQMTMYKGERI
ANCKAFPNFPRGPSEEATDKSPNSPEAKKLYHAVSLCIIASYAQMFQCLRELDKVYGFGL
NLPATIATFRAGCILQGYLLGPMTKAFEENPNLPNLMDAFTKEIAAGLDDCRQILAKLTV
NTAVSLPVMMASLSYINAMYTETLPYGQLVSLQRDVFGRHGYERTDKDGRESFEWPALQX
*length of your protein in Amino Acids: 430 aa
Molecular Weightof your protein in kiloDaltons using theExpasy ProtParamwebsite: 52314.88 g/mol
MolarExtinction coefficientof your protein at 280 nm wavelength: 51840 Lmol-1cm-1
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
tmed6PGDDP-lmaj.png
*CDSGene Sequence(paste as text only):
ATGTCTAACGACCTGGGCATCATTGGCCTGGGTGTTATGGGTGCGAACCTGGCGCTGAAC
ATCGCAGAAAAAGGTTTCAAAGTAGCGGTTTTTAACCGCACCTACGCCAAGACCACCTCT
TTCCTGAAGGAACATGAATCTGAGAAATTCGCCGCTAATCTGAACGGTTACGAAACCATG
AAAGAATTCGCTGCTTCTCTCAAGAAGCCGCGTCGTGCTTTCATCCTCGTTCAGGCAGGT
GCAGCGACTGACTCTACTATCGAGCAACTCAAGGAAGTGTTCGAAAATGGTGACATCATT
ATTGACACGGGTAATGCGAACTTCAAAGACCAGGACAAGCGTGCCGCGCAACTGGAATCT
CAGGGTCTCCGTTTCCTGGGTATGGGTATCTCTGGTGGTGAAGAAGGCGCACGTAAGGGT
CCAGCGTTCTTTCCGGGTGGTACCCCGTCTGTTTGGGAAGAGGTTCGTCCGATCGTAGAA
GCGGCTGCGGCAAAAGCTGAGGACGGTCGTCCATGCGTTACCTTTAACGGCAAGGGCGGT
GCGGGTAGCTGCGTTAAAATGTACCATAACGCGGGTGAGTATGCTGTGCTCCAAATCTGG
GGTGAGGCGTACTCTGCGCTGCTGGCATTCGGCTTTGACAATGACCAGATCGCCGACGTT
TTTGAGTCTTGGAAGGCGGACGGTTTTCTCAAATCTTATATGCTCGACATCTCTATCGCT
GCGTGTCGCGCACGCGAAGCAACCGGTAACTACCTGTCTGAAAAAGTTAAAGACCGTATC
GGTTCTAAGGGTACCGGCCTGTGGAGCGCGCAGGAAGCGCTGGAAATCGGTGTTCCGGCA
CCGAGCCTCAACATGGCTGTTATCTCTCGTCAGATGACCATGTATAAGGGCGAGCGTATC
GCGAACTGCAAAGCATTCCCGAACTTTCCTCGTGGTCCGTCTGAAGAGGCAACGGACAAA
TCTCCGAACTCTCCGGAAGCAAAGAAGCTGTATCACGCGGTCTCCCTGTGCATTATCGCG
TCTTACGCGCAGATGTTCCAGTGCCTGCGTGAACTGGACAAAGTTTACGGCTTCGGTCTG
AACCTGCCAGCCACGATCGCCACTTTCCGCGCTGGCTGCATCCTGCAAGGCTATCTGCTG
GGCCCTATGACCAAGGCATTTGAGGAAAATCCGAATCTGCCAAACCTGATGGACGCGTTC
ACCAAAGAAATTGCTGCGGGCCTGGATGACTGCCGCCAGATCCTGGCGAAACTGACGGTT
AACACCGCAGTTTCTCTGCCTGTGATGATGGCCTCTCTGTCTTACATCAACGCGATGTAT
ACGGAAACGCTCCCGTATGGTCAGCTGGTGTCTCTGCAACGTGACGTATTCGGCCGTCAC
GGTTATGAACGTACCGATAAAGATGGCCGTGAATCTTTTGAATGGCCGGCTCTCCAGTAA


*GC% Content for gene:53.125%
*CDS Gene Sequence (codon optimized) - copy fromoutputofPrimer DesignProtocol (paste as text only):
ATGTCTAACGACCTGGGCATCA
GATGTTCAGCGCCAGGTTCGCACCCATAACACCCAGGCCAATGATGCCCAGGTCGTTAGA
AACCTGGCGCTGAACATCGCAGAAAAAGGTTTCAAAGTAGCGGTTTTTAACCGCACCTAC
TCTCAGATTCATGTTCCTTCAGGAAAGAGGTGGTCTTGGCGTAGGTGCGGTTAAAAACCG
CCTGAAGGAACATGAATCTGAGAAATTCGCCGCTAATCTGAACGGTTACGAAACCATGAA
AAAGCACGACGCGGCTTCTTGAGAGAAGCAGCGAATTCTTTCATGGTTTCGTAACCGTTC
AGCCGCGTCGTGCTTTCATCCTCGTTCAGGCAGGTGCAGCGACTGACTCTACTATCGAGC
CAATAATGATGTCACCATTTTCGAACACTTCCTTGAGTTGCTCGATAGTAGAGTCAGTCG
TTCGAAAATGGTGACATCATTATTGACACGGGTAATGCGAACTTCAAAGACCAGGACAAG
AGGAAACGGAGACCCTGAGATTCCAGTTGCGCGGCACGCTTGTCCTGGTCTTTGAAGTTC
CTCAGGGTCTCCGTTTCCTGGGTATGGGTATCTCTGGTGGTGAAGAAGGCGCACGTAAGG
CTTCCCAAACAGACGGGGTACCACCCGGAAAGAACGCTGGACCCTTACGTGCGCCTTCTT
CCCCGTCTGTTTGGGAAGAGGTTCGTCCGATCGTAGAAGCGGCTGCGGCAAAAGCTGAGG
CCCGCACCGCCCTTGCCGTTAAAGGTAACGCATGGACGACCGTCCTCAGCTTTTGCCGCA
AAGGGCGGTGCGGGTAGCTGCGTTAAAATGTACCATAACGCGGGTGAGTATGCTGTGCTC
CCGAATGCCAGCAGCGCAGAGTACGCCTCACCCCAGATTTGGAGCACAGCATACTCACCC
CGCTGCTGGCATTCGGCTTTGACAATGACCAGATCGCCGACGTTTTTGAGTCTTGGAAGG
AGAGATGTCGAGCATATAAGATTTGAGAAAACCGTCCGCCTTCCAAGACTCAAAAACGTC
CAAATCTTATATGCTCGACATCTCTATCGCTGCGTGTCGCGCACGCGAAGCAACCGGTAA
ACCCTTAGAACCGATACGGTCTTTAACTTTTTCAGACAGGTAGTTACCGGTTGCTTCGCG
ACCGTATCGGTTCTAAGGGTACCGGCCTGTGGAGCGCGCAGGAAGCGCTGGAAATCGGTG
TCTGACGAGAGATAACAGCCATGTTGAGGCTCGGTGCCGGAACACCGATTTCCAGCGCTT
TGGCTGTTATCTCTCGTCAGATGACCATGTATAAGGGCGAGCGTATCGCGAACTGCAAAG
CGTTGCCTCTTCAGACGGACCACGAGGAAAGTTCGGGAATGCTTTGCAGTTCGCGATACG
CCGTCTGAAGAGGCAACGGACAAATCTCCGAACTCTCCGGAAGCAAAGAAGCTGTATCAC
ATCTGCGCGTAAGACGCGATAATGCACAGGGAGACCGCGTGATACAGCTTCTTTGCTTCC
GCGTCTTACGCGCAGATGTTCCAGTGCCTGCGTGAACTGGACAAAGTTTACGGCTTCGGT
AGCCAGCGCGGAAAGTGGCGATCGTGGCTGGCAGGTTCAGACCGAAGCCGTAAACTTTGT
ACTTTCCGCGCTGGCTGCATCCTGCAAGGCTATCTGCTGGGCCCTATGACCAAGGCATTT
TGAACGCGTCCATCAGGTTTGGCAGATTCGGATTTTCCTCAAATGCCTTGGTCATAGGGC
ACCTGATGGACGCGTTCACCAAAGAAATTGCTGCGGGCCTGGATGACTGCCGCCAGATCC
ATCACAGGCAGAGAAACTGCGGTGTTAACCGTCAGTTTCGCCAGGATCTGGCGGCAGTCA
GCAGTTTCTCTGCCTGTGATGATGGCCTCTCTGTCTTACATCAACGCGATGTATACGGAA
GTCACGTTGCAGAGACACCAGCTGACCATACGGGAGCGTTTCCGTATACATCGCGTTGAT
GGTGTCTCTGCAACGTGACGTATTCGGCCGTCACGGTTATGAACGTACCGATAAAGATGG
TTACTGGAGAGCCGGCCATTCAAAAGATTCACGGCCATCTTTATCGGTACGTTCATAA

*GC% Content for gene (codon optimized): 52.688679%
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 outputtext 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.
TACTTCCAATCCATGTCTAACGACCTGGGCATCATTGGCCTGGGTGTTATGGGTGCGAACCTGGCGCTGAACATCGCAGAAAAAGGTTTCAAAGTAGCGGTTTTTAACCGCACCTACGCC
AAGACCACCTCTTTCCTGAAGGAACATGAATCTGAGAAATTCGCCGCTAATCTGAACGGTTACGAAACCATGAAAGAATTCGCTGCTTCTCTCAAGAAGCCGCGTCGTGCTTTCATCCTC
GTTCAGGCAGGTGCAGCGACTGACTCTACTATCGAGCAACTCAAGGAAGTGTTCGAAAATGGTGACATCATTATTGACACGGGTAATGCGAACTTCAAAGACCAGGACAAGCGTGCCGC
GCAACTGGAATCTCAGGGTCTCCGTTTCCTGGGTATGGGTATCTCTGGTGGTGAAGAAGGCGCACGTAAGGGTCCAGCGTTCTTTCCGGGTGGTACCCCGTCTGTTTGGGAAGAGGTTCG
TCCGATCGTAGAAGCGGCTGCGGCAAAAGCTGAGGACGGTCGTCCATGCGTTACCTTTAACGGCAAGGGCGGTGCGGGTAGCTGCGTTAAAATGTACCATAACGCGGGTGAGTATGCTGT
GCTCCAAATCTGGGGTGAGGCGTACTCTGCGCTGCTGGCATTCGGCTTTGACAATGACCAGATCGCCGACGTTTTTGAGTCTTGGAAGGCGGACGGTTTTCTCAAATCTTATATGCTCGAC
ATCTCTATCGCTGCGTGTCGCGCACGCGAAGCAACCGGTAACTACCTGTCTGAAAAAGTTAAAGACCGTATCGGTTCTAAGGGTACCGGCCTGTGGAGCGCGCAGGAAGCGCTGGAAAT
CGGTGTTCCGGCACCGAGCCTCAACATGGCTGTTATCTCTCGTCAGATGACCATGTATAAGGGCGAGCGTATCGCGAACTGCAAAGCATTCCCGAACTTTCCTCGTGGTCCGTCTGAAGAG
GCAACGGACAAATCTCCGAACTCTCCGGAAGCAAAGAAGCTGTATCACGCGGTCTCCCTGTGCATTATCGCGTCTTACGCGCAGATGTTCCAGTGCCTGCGTGAACTGGACAAAGTTTAC
GGCTTCGGTCTGAACCTGCCAGCCACGATCGCCACTTTCCGCGCTGGCTGCATCCTGCAAGGCTATCTGCTGGGCCCTATGACCAAGGCATTTGAGGAAAATCCGAATCTGCCAAACCTG
ATGGACGCGTTCACCAAAGAAATTGCTGCGGGCCTGGATGACTGCCGCCAGATCCTGGCGAAACTGACGGTTAACACCGCAGTTTCTCTGCCTGTGATGATGGCCTCTCTGTCTTACATC
AACGCGATGTATACGGAAACGCTCCCGTATGGTCAGCTGGTGTCTCTGCAACGTGACGTATTCGGCCGTCACGGTTATGAACGTACCGATAAAGATGGCCGTGAATCTTTTGAATGGCCGG
CTCTCCAGTAACAGTAAAGGTGGATA

Primer design results for 'tail' primers (this is just 2 sequences):
Forward Primer: 5’ TACTTCCAATCCATGTCTAACGACCTGGGCATCATTGG 3’ 38 bp
Reverse Primer: 5’ TATCCACCTTTACTGTTACTGGAGAGCCGGCCATTC 3’ 36 b

References:
(1) Dawit, G. J. Bacteriol. Parasitol. 2013, 4, 2–7.
(2) Miranda, A.; Saldaña, A.; González, K.; Paz, H.; Santamaría, G.; Samudio, F.; Calzada, J. E. Trans. R. Soc. Trop. Med. Hyg. 2012, 106 (9), 544–548.
(3) Savoia, D. J. Infect. Dev. Ctries. 2015, 9 (6), 588–596.