Target+-+1-deoxy-D-xylulose-5-phosphate+reductoisomerase+(P.+falciparum)

**NCBI Gene # or RefSeq#:** 812223 [|__https://www.ncbi.nlm.nih.gov/gene/812223__] **"PF14_0641** has essentiality data **Gene/Ortholog:** mtu2917 (OG4_13658); **Phenotype:** non-essential; **Source study:** nmpdr  **Gene/Ortholog:** eco174 (OG4_13658); **Phenotype:** undefined; **Source study:** blattner  **Gene/Ortholog:** eco174 (OG4_13658); **Phenotype:** essential; **Source study:** gerdes  **Gene/Ortholog:** eco174 (OG4_13658); **Phenotype:** essential; **Source study:** keio  **Gene/Ortholog:** eco174 (OG4_13658); **Phenotype:** essential; **Source study:** shigen" __[]__
 * Target (protein/gene name):** 1-deoxy-D-xylulose 5-phosphate
 * Protein ID (NP or XP #) or Wolbachia#:** [|__**XP_001348815.1**__]
 * Organism:** Plasmodium falciparum 3D7
 * Etiologic Risk Group (see link below):**
 * Background/Disease Information:**
 * Essentiality of this protein:**

“Most significantly, the DOXP pathway has become attractive as a target for a new class of antimalarial agents since malaria parasites are efficiently killed //in vitro// and in the murine model by fosmidomycin and FR900098, both specific inhibitors of the DOXP reductoisomerase (Kuzuyama //et al.// 1998; Zeidler //et al.// 1998; Jomaa //et al.// 1999).” Source: Plasmodium falciparum: Detection of the Deoxyxylulose 5-Phosphate Reductoisomerase Activity

**EC#: 1.1.1.26 Source:** [|__http://tdrtargets.org/targets/view?gene_id=2971__] **Link to BRENDA EC# page:** []
 * Complex of enzymes: N/A**

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 * Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):**

**List cost and quantity of reagents and supplier (new item)** Supplied by Sigma-Aldrich
 * **Reagent** || **Cost** || **Quantity** || **Product No.** ||
 * Tris-HCl || $47.80 || 100g || T5941 ||
 * MnCl2 || $42.90 || 10g || 244589 ||
 * NADPH || $97.90 || 25mg || N5130 ||

__[]__ __[]__ __[]__ 0.6 Source: http://tdrtargets.org/targets/view?gene_id=2971
 * Structure Available (PDB or Homology model)**
 * Druggable Target (see Databases for this):**

“To date, several DXR inhibitors have been identified [19-23], fosmi- domycin and its analogue FR900098 have been shown to be the most potent...exhibit reduced pharmacological properties and their potential to become drugs is considered poor [24].” Source: [|__http://benthamscience.com/ppl/sample/ppl17-1/0015E.pdf__]
 * Current Inhibitors:**

“...However, malarial recrudescence is a common problem because it is difficult to completely eradicate malaria parasites from the human body. Therefore, the refinement of the anti-malarial performance of fosmidomycin alone or in combination with another compound is expected to lead to more effective anti-malarial drugs.” Source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3216497/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2833050/?tool=pubmed
 * Expression Information (has it been expressed in bacterial cells):**

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2833050/?tool=pubmed
 * Purification Method:**


 * Image of protein (PyMol or etc):**

Source: http://www.pdb.org/pdb/explore/explore.do?structureId=3AU8 1 mkkyiyiyff fititindlv inntskcvsi errknnayin ygigyngpdn kitksrrckr 61 iklckkdlid igaikkpinv aifgstgsig tnalniirec nkienvfnvk alyvnksvne 121 lyeqareflp eylcihdksv yeelkelvkn ikdykpiilc gdegmkeics snsidkivig 181 idsfqglyst myaimnnkiv alankesivs agfflkklln ihknakiipv dsehsaifqc 241 ldnnkvlktk clqdnfskin ninkiflcss ggpfqnltmd elknvtsena lkhpkwkmgk 301 kitidsatmm nkglevieth flfdvdyndi evivhkecii hscvefidks visqmyypdm 361 qipilysltw pdriktnlkp ldlaqvstlt fhkpslehfp ciklayqagi kgnfyptvln 421 asneiannlf lnnkikyfdi ssiisqvles fnsqkvsens edlmkqilqi hswakdkatd 481 iynkhnss Source: https://www.ncbi.nlm.nih.gov/protein/XP_001348815.1
 * Amino Acid Sequence:**

488 aa Source: https://www.ncbi.nlm.nih.gov/protein/XP_001348815.1
 * length of your protein in Amino Acids:**

55756.7 Source: Expasy ProtParam 55757 DA Source: http://tdrtargets.org/targets/view?gene_id=2971
 * Molecular Weight of your protein in kiloDaltons using the** [|__**Expasy ProtParam**__] **website**

Ext. coefficient 48540 Abs 0.1% (=1 g/l) 0.871, assuming all pairs of Cys residues form cystines Ext. coefficient 47790 Abs 0.1% (=1 g/l) 0.857, assuming all Cys residues are reduced
 * Molar Extinction coefficient of your protein at 280 nm wavelength:**

Source: Expasy ProtParam

ORIGIN 1 atgaagaaat atatttatat atattttttc ttcatcacaa taactattaa tgatttagta 61 ataaataata catcaaaatg tgtttccatt gaaagaagaa aaaataacgc atatataaat 121 tatggtatag gatataatgg accagataat aaaataacaa agagtagaag atgtaaaaga 181 ataaagttat gcaaaaagga tttaatagat attggtgcaa taaagaaacc aattaatgta 241 gcaatttttg gaagtactgg tagtataggt acgaatgctt taaatataat aagggagtgt 301 aataaaattg aaaatgtttt taatgttaaa gcattgtatg tgaataagag tgtgaatgaa 361 ttatatgaac aagctagaga atttttacca gaatatttgt gtatacatga taaaagtgta 421 tatgaagaat taaaagaatt ggtaaaaaat ataaaagatt ataaacctat aatattgtgt 481 ggtgatgaag ggatgaaaga aatatgtagt agtaatagta tagataaaat agttattggt 541 attgattctt ttcaaggatt atattctact atgtatgcaa ttatgaataa taaaatagtt 601 gcgttagcta ataaagaatc cattgtctct gctggtttct ttttaaagaa attattaaat 661 attcataaaa atgcaaagat aatacctgtt gattcagaac atagtgctat atttcaatgt 721 ttagataata ataaggtatt aaaaacaaaa tgtttacaag acaatttttc taaaattaac 781 aatataaata aaatattttt atgttcatct ggaggtccat ttcaaaattt aactatggac 841 gaattaaaaa atgtaacatc agaaaatgct ttaaagcatc ctaaatggaa aatgggtaag 901 aaaataacta tagattctgc aactatgatg aataaaggtt tagaggttat agaaacccat 961 tttttatttg atgtagatta taatgatata gaagttatag tacataaaga atgcattata 1021 cattcttgtg ttgaatttat agacaaatca gtaataagtc aaatgtatta tccagatatg 1081 caaataccca tattatattc tttaacatgg cctgatagaa taaaaacaaa tttaaaacct 1141 ttagatttgg ctcaggtttc aactcttaca tttcataaac cttctttaga acatttcccg 1201 tgtattaaat tagcttatca agcaggtata aaaggaaact tttatccaac tgtactaaat 1261 gcgtcaaatg aaatagctaa caacttattt ttgaataata aaattaaata ttttgatatt 1321 tcctctataa tatcgcaagt tcttgaatct ttcaattctc aaaaggtttc ggaaaatagt 1381 gaagatttaa tgaagcaaat tctacaaata cattcctggg ccaaagataa agctaccgat 1441 atatacaaca aacataattc ttcatag //
 * CDS Gene Sequence:**

Source: https://www.ncbi.nlm.nih.gov/nuccore/XM_001348779.1

Source: http://bioinformatics.org/sms2/dna_stats.html 1 ATGAAAAAGTATATCTACATCTACTTCTTCTTTATCACTATCACGATTAACGACCTGGTC 61 ATTAACAACACGTCTAAATGCGTTTCTATTGAACGTCGTAAGAACAACGCTTACATCAAC 121 TACGGTATCGGTTACAACGGTCCAGATAATAAGATCACCAAGTCTCGTCGTTGCAAACGT 181 ATTAAACTGTGCAAAAAAGACCTCATCGATATTGGCGCGATCAAAAAGCCTATCAACGTA 241 GCGATCTTCGGTTCTACGGGCTCTATCGGTACCAACGCGCTCAACATCATTCGTGAATGT 301 AACAAAATTGAAAACGTCTTCAACGTGAAAGCGCTGTATGTAAATAAGTCTGTTAACGAG 361 CTGTACGAACAAGCCCGTGAGTTCCTGCCGGAATACCTGTGCATCCACGACAAAAGCGTT 421 TACGAAGAGCTGAAAGAACTGGTTAAAAACATCAAGGATTACAAGCCGATTATCCTGTGC 481 GGTGATGAAGGCATGAAGGAAATCTGCTCTTCTAATAGCATTGACAAGATCGTCATCGGT 541 ATTGACAGCTTCCAGGGTCTGTACTCTACCATGTACGCAATTATGAACAATAAGATTGTG 601 GCGCTGGCAAACAAAGAATCTATCGTTTCTGCGGGTTTTTTCCTCAAAAAACTGCTCAAT 661 ATCCACAAGAATGCCAAAATCATCCCGGTCGACTCTGAGCACTCTGCAATCTTCCAATGC 721 CTGGACAACAACAAGGTTCTCAAAACCAAGTGCCTCCAGGACAACTTCTCTAAAATCAAC 781 AATATCAATAAAATCTTTCTCTGCTCCTCTGGCGGTCCGTTCCAGAACCTGACCATGGAT 841 GAACTCAAGAACGTTACCTCTGAAAATGCCCTCAAGCACCCGAAGTGGAAAATGGGTAAG 901 AAGATTACTATCGATTCTGCGACCATGATGAATAAAGGTCTGGAAGTTATCGAAACCCAC 961 TTCCTGTTCGACGTTGACTACAATGACATTGAAGTAATCGTTCACAAAGAGTGCATTATC 1021 CACTCTTGCGTTGAATTTATCGACAAATCTGTTATTTCTCAGATGTACTACCCGGACATG 1081 CAGATCCCGATCCTGTATTCTCTGACCTGGCCGGACCGTATCAAGACCAATCTGAAACCG 1141 CTCGACCTCGCGCAGGTTTCTACGCTGACCTTCCACAAACCGTCTCTCGAACACTTCCCG 1201 TGCATCAAGCTGGCGTACCAGGCGGGTATTAAGGGTAACTTCTACCCGACCGTACTCAAC 1261 GCGTCCAACGAAATCGCGAATAACCTGTTTCTGAATAACAAGATTAAGTATTTCGACATC 1321 TCCTCTATCATCTCTCAGGTACTGGAGAGCTTCAACTCCCAGAAGGTTAGCGAGAATTCC 1381 GAAGACCTGATGAAACAAATCCTCCAGATTCACTCCTGGGCGAAAGACAAAGCGACTGAT 1441 ATCTATAACAAACACAACTCTTCTTGA
 * GC% Content for gene:** 24.88%
 * CDS Gene Sequence (codon optimized) - after having done Primer Design:**


 * GC% Content for gene (codon optimized):** 43.83%

1 ATGAAAAAGTATATCTACATCTACTTCTTCTTTATCACTATCACGATTAACGACCTG 57 2 CGTTCAATAGAAACGCATTTAGACGTGTTGTTAATGACCAGGTCGTTAATCGTGATAGTG 60 3 GTCTAAATGCGTTTCTATTGAACGTCGTAAGAACAACGCTTACATCAACTACGGTATCGG 60 4 GACGAGACTTGGTGATCTTATTATCTGGACCGTTGTAACCGATACCGTAGTTGATGTAAG 60 5 GATAATAAGATCACCAAGTCTCGTCGTTGCAAACGTATTAAACTGTGCAAAAAAGACCTC 60 6 ACGTTGATAGGCTTTTTGATCGCGCCAATATCGATGAGGTCTTTTTTGCACAGTTTAATA 60 7 CGATCAAAAAGCCTATCAACGTAGCGATCTTCGGTTCTACGGGCTCTATCGGTACCAACG 60 8 GACGTTTTCAATTTTGTTACATTCACGAATGATGTTGAGCGCGTTGGTACCGATAGAGCC 60 9 GTGAATGTAACAAAATTGAAAACGTCTTCAACGTGAAAGCGCTGTATGTAAATAAGTCTG 60 10 GCAGGAACTCACGGGCTTGTTCGTACAGCTCGTTAACAGACTTATTTACATACAGCGCTT 60 11 AGCCCGTGAGTTCCTGCCGGAATACCTGTGCATCCACGACAAAAGCGTTTACGAAGAGCT 60 12 ATCGGCTTGTAATCCTTGATGTTTTTAACCAGTTCTTTCAGCTCTTCGTAAACGCTTTTG 60 13 ACATCAAGGATTACAAGCCGATTATCCTGTGCGGTGATGAAGGCATGAAGGAAATCTGCT 60 14 TGTCAATACCGATGACGATCTTGTCAATGCTATTAGAAGAGCAGATTTCCTTCATGCCTT 60 15 AGATCGTCATCGGTATTGACAGCTTCCAGGGTCTGTACTCTACCATGTACGCAATTATGA 60 16 ATAGATTCTTTGTTTGCCAGCGCCACAATCTTATTGTTCATAATTGCGTACATGGTAGAG 60 17 CGCTGGCAAACAAAGAATCTATCGTTTCTGCGGGTTTTTTCCTCAAAAAACTGCTCAATA 60 18 AGAGTCGACCGGGATGATTTTGGCATTCTTGTGGATATTGAGCAGTTTTTTGAGGAAAAA 60 19 AATCATCCCGGTCGACTCTGAGCACTCTGCAATCTTCCAATGCCTGGACAACAACAAGGT 60 20 TGATTTTAGAGAAGTTGTCCTGGAGGCACTTGGTTTTGAGAACCTTGTTGTTGTCCAGGC 60 21 TCCAGGACAACTTCTCTAAAATCAACAATATCAATAAAATCTTTCTCTGCTCCTCTGGCG 60 22 GTAACGTTCTTGAGTTCATCCATGGTCAGGTTCTGGAACGGACCGCCAGAGGAGCAGAGA 60 23 ATGGATGAACTCAAGAACGTTACCTCTGAAAATGCCCTCAAGCACCCGAAGTGGAAAATG 60 24 TTATTCATCATGGTCGCAGAATCGATAGTAATCTTCTTACCCATTTTCCACTTCGGGTGC 60 25 GATTCTGCGACCATGATGAATAAAGGTCTGGAAGTTATCGAAACCCACTTCCTGTTCGAC 60 26 ACTCTTTGTGAACGATTACTTCAATGTCATTGTAGTCAACGTCGAACAGGAAGTGGGTTT 60 27 ATTGAAGTAATCGTTCACAAAGAGTGCATTATCCACTCTTGCGTTGAATTTATCGACAAA 60 28 TCTGCATGTCCGGGTAGTACATCTGAGAAATAACAGATTTGTCGATAAATTCAACGCAAG 60 29 TACTACCCGGACATGCAGATCCCGATCCTGTATTCTCTGACCTGGCCGGACCGTATCAAG 60 30 CAGCGTAGAAACCTGCGCGAGGTCGAGCGGTTTCAGATTGGTCTTGATACGGTCCGGCCA 60 31 GCGCAGGTTTCTACGCTGACCTTCCACAAACCGTCTCTCGAACACTTCCCGTGCATCAAG 60 32 GTCGGGTAGAAGTTACCCTTAATACCCGCCTGGTACGCCAGCTTGATGCACGGGAAGTGT 60 33 ATTAAGGGTAACTTCTACCCGACCGTACTCAACGCGTCCAACGAAATCGCGAATAACCTG 60 34 AGAGGAGATGTCGAAATACTTAATCTTGTTATTCAGAAACAGGTTATTCGCGATTTCGTT 60 35 GATTAAGTATTTCGACATCTCCTCTATCATCTCTCAGGTACTGGAGAGCTTCAACTCCCA 60 36 GGATTTGTTTCATCAGGTCTTCGGAATTCTCGCTAACCTTCTGGGAGTTGAAGCTCTCCA 60 37 CGAAGACCTGATGAAACAAATCCTCCAGATTCACTCCTGGGCGAAAGACAAAGCGACTGA 60 38 TCAAGAAGAGTTGTGTTTGTTATAGATATCAGTCGCTTTGTCTTTCGC 48
 * Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):**

Source: [|LOGFILE.txt]


 * Primer design results for 'tail' primers (this is just 2 sequences):**

We designed a forward and reverse primer that will allow us to PCR the P.fal. gene and insert it into an expression vector (pNIC-Bsa4).

__ Forward Primer: __ 5’ TACTTCCAATCCATGAAAAAGTATATCTACATCTAC 3’ 36 bp GC Content 30.6% 0 mM Mg2+ Tm 56.7 oC 1.5 mM Mg2+ Tm 64.9 oC 2 mM Mg2+ Tm 65.4 oC 4 mM Mg2+ Tm 66.5 oC 6 mM Mg2+ Tm 67.1 oC

__ Reverse Primer __ : 5’ AAACACAACTCTTCTTGA 3’ ** Reverse complement it: ** 5’ TATCCACCTTTACTGTCAAGAAGAGTTGTGTTT3’ 33 bp GC Content 36.4% 0 mM Mg2+ Tm 59.7 oC 1.5 mM Mg2+ Tm 67.6 oC 2 mM Mg2+ Tm 68.1 oC 4 mM Mg2+ Tm 69.2 oC 6 mM Mg2+ Tm 69.7 oC

Source: [] Source: [] Source: [] Source: []
 * Transmembrane Protein Prediction (several algorithms):**

Source: [] Source: []

@http://www.sigmaaldrich.com/etc/medialib/docs/Sigma/Product_Information_Sheet/2/n6505pis.Par.0001.File.tmp/n6505pis.pdf b -NADPH is soluble in 0.01 M sodium hydroxide (50 mg/ml), yielding a clear, light yellow solution. It is recommended to store Products N1630, N7505, and N6505 desiccated at –20 ° C protected from light. Product N9910 can be stored at room temperature. The normal impurities and/or decomposition products are b -NADP and monophosphoadenosine 5 ¢ - diphosphoribose. It is recommended to prepare solutions fresh and use promptly, unless you are sure this is an unnecessary precaution for your work. However, __it has been__ __reported that a 0.5 mM solution in 0.02 M NaOH __ __(pH 12.3) showed no loss of purity in a week at 4 ° <span style="font-family: Arial,sans-serif; font-size: 13.3333px;">C or __ __ - <span style="font-family: Arial,sans-serif; font-size: 13.3333px;">85 ° <span style="font-family: Arial,sans-serif; font-size: 13.3333px;">C, but a 13% loss at –20 ° <span style="font-family: Arial,sans-serif; font-size: 13.3333px;">C. <span style="font-family: Arial,sans-serif; font-size: 9.33333px;">3 __
 * NADPH** - sigma N6505
 * <span style="font-family: Arial,sans-serif; font-size: 13.3333px;">Preparation Instructions **
 * <span style="font-family: Arial,sans-serif; font-size: 13.3333px;">Storage/Stability **

Sigma 13368 solubility: 50 mg/ml in H2O storage life and conditions: ? Sigma Tech Support suggests aliquoting and storing in -80degC
 * 1-Deoxy-D-xylulose-5-phosphate sodium salt (DXP)**

Source: [] http://www.sciencedirect.com/science/article/pii/S0014489400945661 http://eprints.ru.ac.za/2712/1/TANNER-MSC-TR04-143.pdf http://benthamscience.com/ppl/sample/ppl17-1/0015E.pdf http://www.pdb.org/pdb/explore/explore.do?structureId=3AUA http://www.nature.com/srep/2011/110614/srep00009/full/srep00009.html?WT.ec_id=SREP-631-20110701 http://www.sigmaaldrich.com/etc/medialib/docs/Sigma/General_Information/glyoxylate_reductase.Par.0001.File.tmp/glyoxylate_reductase.pdf http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0019334 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2833050/?tool=pubmed
 * Sources:**