NADH-dependent+fumaratae+reductase+(Trypanosome+brucei

 ***NCBI Gene # or RefSeq#:**  ***Protein ID (NP or XP #) or Wolbachia#:** 11602
 * *Target (protein/gene name): **NADH-dependent fumarate reductase

 ***Organism (including strain):** // Trypanosoma brucei //

 **Etiologic Risk Group (see link below):** Appendix B-II-C. Risk Group 2 – Parasitic Agenthttp://www.utexas.edu/research/rsc/ibc/agent_class.html#_Toc7238334

 ***Background/Disease Information (sort of like the Intro to your Mini Research Write up):**

 **Essentiality of this protein:** [|**http://jb.asm.org/content/190/21/7170.long**] The protein NADH-dependent fumarate reductase is essential to the functioning of the cellular redox balance. Without this protein the cell wouldn’t be able to reduce its target compound possibly compromising the integrity of the tricarboxylic acid cycle in respiration.

 **Complex of proteins?:** The protein fumarate reductase works with other proteins in a complex to accomplish the tasks of the tricarboxylic acid cycle. After forming the succinate in the reaction another enzyme then comes in and uses the product formed in the next step of the process.

 **Druggable Target:** fumarate + NADH + H+ []


 * *EC#: 1.3.1.6 **

 **Link to BRENDA EC# page:** []

 **--** <span style="color: #000000; font-family: 'Times New Roman','serif'; font-size: 16px;">Show screenshot of BRENDA enzyme mechanism schematic <span style="color: #000000; 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):** <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">Information regarding the spectrophotometric boundaries, and running the assay are in the following two links.

<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;"> **-- link (or citation) to paper that contains assay information** <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">[]

<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;">Catalog #: 47910-5G, Price: $33.60, Supplier: Sigma-Aldrich

<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;"> -- 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 Query 394 LSAAIEAAGCGAQVVLMEKEAKLGGNSAKATSGINGWGTRAQAKASIVDGGKYFERDTYK 453 SAAI A GA+V+L+EKE +GGN+ A G+N T Q I D + DT KSbjct 139 FSAAISATDSGAKVILIEKEPVIGGNAKLAAGGMNAAWTDQQKAKKITDSPELMFEDTMK 198 Query 454 SGIGGNTDPALVKTLSMKSADAIGWLTSLGVPLTVLSQLGGHSRKRTHRAPDKKDGTPLP 513 G N DPALVK LS S D++ W+T++G LT + +GG S R HR P G Sbjct 199 GGQNIN-DPALVKVLSSHSKDSVDWMTAMGADLTDVGMMGGASVNRAHR-PTGGAG 252 Query 514 IGFTIMKTLEDH-VRGNLSGRITIMENCSVTSLLSETKERPDGTKQIRVTGVEFTQAGSG 572 +G +++ L D+ V+ N+ R+ T + K+ K I V G+ GSbjct 253 VGAHVVQVLYDNAVKRNIDLRMN---TRGIEVLKDDKGTVKGILVKGMY-KG 300 Query 573 KTTILADAVILATGGFSNDKTADSLLREHAPHLVNFPTTNGPWATGDGVKLAQRLGAQLV 632 + ADAVILATGGF+ + + L P L F +TN P A GDG+ +A+ G L Sbjct 301 YYWVKADAVILATGGFAKNNERVAKLD---PSLKGFISTNQPGAVGDGLDVAENAGGALK 357 Query 633 DMDKVQLHPTGLINPKDPANPTKFLGPEALRGSGGVLLNKQGKRFVNELDLRSVVSKAIM 692 DM +Q HPT + + EA+RG+G +L+N++GKRFVNE+ + S AI+Sbjct 358 DMQYIQAHPTLSVK---GGVMVTEAVRGNGAILVNREGKRFVNEITTKDKASAAIL 410 Query 693 EQGAEYPGSGGSMFAYCVLNAAAQKLFGVSSHEFYWKKMGLFVKADTMRDLAALIGCPVE 752 Q +G S AY + + + +K S + +G+ AD++ L + G +Sbjct 411 AQ--TGKS--AYLIFDDSVRKSL---SKIDKYIGLGVAPTADSLVKLGKMEGIDGK 459 Query 753 SVQQTLEEYERLSTSQRSCPITRKSVYPCVLGTKGPYYVAFVTPSIHYTMGGCLI 807 ++ +T+ Y L +S + R ++ P L +G YY VTP +H+TMGG +ISbjct 460 ALTETVARYNSLVSSGKDTDFERPNL-PRAL-NEGNYYAIEVTPGVHHTMGGVMI 512 <span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> Query Coverage: 37%

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> Max % Identities:55%

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> % Positives: 50%

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> Chain used for homology: 1JRY

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> **Current Inhibitors:**

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> **Expression Information (has it been expressed in bacterial cells): N/A**

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> **Purification Method: Partial release from subcellular compartment by treatment with digitonin.**

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> **Image of protein (PyMol with features delineated and shown separately): (This is an image of the protein that is being compared, __NOT__ the original protein as it could not be found on the PDB website.** <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> ***Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):** MVDGRSSASIVAVDPERAARERDAAARALLQDSPLHTTMQYATSGLELTVPYALKVVASA
 * My protein sequence:**

DTFDRAKEVADEVLRCAWQLADTVLNSFNPNSEVSLVGRLPVGQKHQMSAPLKRVMACCQ

RVYNSSAGCFDPSTAPVAKALREIALGKERNNACLEALTQACTLPNSFVIDFEAGTISRK

HEHASLDLGGVSKGYIVDYVIDNINAAGFQNVFFDWGGDCRASGMNARNTPWVVGITRPP

SLDMLRNPPKEASYISVISLDNEALATSGDYENLIYTADDKPLTCTYDWKAKELMKPSQS

NIAQVSVKCYSAMYADALATACFIKRDPAKVRQLLDGWRYVRDTVRDYRVYVRENERVAK

MFEIATEDAEMRKRRISNTLPARVIVVGGGLAGLSAAIEAAGCGAQVVLMEKEAKLGGNS

AKATSGINGWGTRAQAKASIVDGGKYFERDTYKSGIGGNTDPALVKTLSMKSADAIGWLT

SLGVPLTVLSQLGGHSRKRTHRAPDKKDGTPLPIGFTIMKTLEDHVRGNLSGRITIMENC

SVTSLLSETKERPDGTKQIRVTGVEFTQAGSGKTTILADAVILATGGFSNDKTADSLLRE

HAPHLVNFPTTNGPWATGDGVKLAQRLGAQLVDMDKVQLHPTGLINPKDPANPTKFLGPE

ALRGSGGVLLNKQGKRFVNELDLRSVVSKAIMEQGAEYPGSGGSMFAYCVLNAAAQKLFG

VSSHEFYWKKMGLFVKADTMRDLAALIGCPVESVQQTLEEYERLSTSQRSCPITRKSVYP

CVLGTKGPYYVAFVTPSIHYTMGGCLISPSAEIQMKNTSSRAPLSHSNPILGLFGAGEVT

GGVHGGNRLGGNSLLECVVFGRIAGDRASTILQRKSSALSFKVWTTVVLREVREGGVYGA

GSRVLRFNLPGALQRSGLSLGQFIAIRGDWDGQQLIGYYSPITLPDDLGMIDILARSDKG

TLREWISALEPGDAVEMKACGGLVIERRLSDKHFVFMGHIINKLCLIAGGTGVAPMLQII

KAAFMKPFIDTLESVHLIYAAEDVTELTYREVLEERRRESRGKFKKTFVLNRPPPLWTDG

VGFIDRGILTNHVQPPSDNLLVAICGPPVMQRIVKATLKTLGYNMNLVRTVDETEPSGSS

KI ADNLAEFHVQNQECDSCHTPDGELSNDSLTYENTQCVSCHGTLAEVAETTKHEHYNAHASHFPGEVACTS CHSAHEKSMVYCDSCHSFDFNMPYAKKWLRDEPTIAELAKDKSERQAALASAPHDTVDVVVVGSGGAGFS AAISATDSGAKVILIEKEPVIGGNAKLAAGGMNAAWTDQQKAKKITDSPELMFEDTMKGGQNINDPALVK VLSSHSKDSVDWMTAMGADLTDVGMMGGASVNRAHRPTGGAGVGAHVVQVLYDNAVKRNIDLRMNTRGIE VLKDDKGTVKGILVKGMYKGYYWVKADAVILATGGFAKNNERVAKLDPSLKGFISTNQPGAVGDGLDVAE NAGGALKDMQYIQAHPTLSVKGGVMVTEAVRGNGAILVNREGKRFVNEITTKDKASAAILAQTGKSAYLI FDDSVRKSLSKIDKYIGLGVAPTADSLVKLGKMEGIDGKALTETVARYNSLVSSGKDTDFERPNLPRALN EGNYYAIEVTPGVHHTMGGVMI
 * Homology model protein sequence:**

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> ***length of your protein in Amino Acids: 1142aa**

<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: **<span style="font-family: 'Times New Roman','serif'; font-size: 16px;">123689.8 kiloDaltons

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> **Molar Extinction coefficient of your protein at 280 nm wavelength: 117450**

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> ** TMpred graph Image ** ( <span style="color: #0000ff; font-family: 'Times New Roman','serif'; font-size: 16px;">@http://www.ch.embnet.org/software/TMPRED_form.html <span style="font-family: 'Times New Roman','serif'; font-size: 16px;">). 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):** ATGGTAGACGGGCGATCTTCTGCATCAATTGTTGCCGTTGATCCCGAAAGGGCTGCGCGT

GAGCGCGACGCAGCAGCGCGTGCCCTTCTTCAAGACAGTCCGCTACACACGACCATGCAA

TATGCAACGTCTGGTCTTGAGCTTACCGTTCCCTACGCACTTAAGGTGGTTGCCAGTGCT

GACACCTTCGATCGCGCTAAGGAGGTTGCCGATGAGGTGCTACGCTGCGCATGGCAACTC

GCCGACACCGTGTTGAACAGTTTCAACCCGAACAGTGAGGTTTCACTCGTGGGTCGCCTG

CCTGTGGGGCAGAAGCACCAAATGTCTGCTCCACTCAAGCGTGTGATGGCATGCTGCCAG

CGTGTGTATAACTCATCGGCTGGATGTTTTGATCCCTCCACAGCACCCGTCGCAAAGGCG

CTGCGTGAGATTGCACTGGGGAAGGAGCGGAACAATGCTTGTCTGGAGGCACTTACTCAA

GCGTGTACGCTTCCCAACAGTTTTGTGATCGATTTCGAAGCTGGAACTATCAGCCGTAAG

CACGAGCATGCGTCTCTGGACCTAGGTGGGGTTAGCAAAGGTTATATCGTTGATTATGTC

ATTGATAATATCAATGCTGCTGGATTTCAAAACGTTTTTTTTGACTGGGGTGGAGACTGC

CGTGCGAGTGGTATGAACGCGCGCAATACCCCGTGGGTTGTTGGTATAACTCGCCCTCCG

TCCCTTGATATGCTCCGCAACCCGCCAAAGGAAGCGTCGTATATCAGCGTTATCTCTCTC

GACAACGAGGCCCTTGCCACGAGTGGCGATTATGAAAACTTAATATACACCGCTGATGAT

AAACCCCTTACCTGCACTTATGACTGGAAGGCGAAGGAACTGATGAAACCTTCTCAGTCC

AATATCGCGCAGGTATCGGTTAAATGTTATAGCGCCATGTACGCTGACGCGCTTGCGACT

GCGTGTTTCATAAAGCGGGATCCCGCGAAGGTTCGACAGCTGCTGGACGGTTGGCGTTAC

GTGCGTGATACAGTGAGAGATTACAGGGTCTACGTTCGTGAAAATGAGCGAGTAGCGAAG

ATGTTTGAAATCGCCACAGAGGATGCGGAAATGAGGAAGAGGCGGATCAGCAACACACTT

CCCGCTCGTGTCATTGTGGTGGGCGGTGGTCTCGCGGGTTTGTCCGCGGCCATCGAAGCT

GCAGGATGCGGTGCTCAGGTTGTGCTTATGGAGAAGGAGGCGAAGCTCGGAGGCAACAGC

GCCAAGGCGACATCTGGTATCAACGGATGGGGCACACGTGCTCAGGCGAAGGCAAGCATT

GTGGATGGTGGGAAATACTTCGAGCGTGACACATACAAGTCTGGTATCGGGGGTAACACC

GATCCTGCCCTTGTGAAGACACTTTCTATGAAAAGTGCTGACGCTATTGGGTGGCTGACC

TCGTTGGGTGTACCGCTGACGGTATTGTCACAGCTTGGGGGTCACAGCCGCAAGCGCACA

CATCGGGCACCGGATAAGAAAGATGGTACACCTCTACCTATCGGATTTACAATCATGAAA

ACCCTCGAGGATCACGTGCGTGGTAACCTTTCTGGCCGCATCACCATAATGGAAAACTGC

AGTGTAACGTCGTTGCTCAGTGAGACGAAGGAACGGCCAGATGGCACTAAACAGATACGA

GTTACTGGTGTGGAGTTCACGCAGGCTGGCAGTGGGAAGACGACCATACTTGCAGATGCT

GTCATCCTTGCCACTGGTGGATTTTCTAACGACAAAACTGCAGACTCCCTGCTTCGTGAG

CACGCCCCGCACTTGGTCAACTTCCCTACGACGAATGGCCCGTGGGCGACAGGTGATGGC

GTGAAACTTGCACAGCGACTTGGCGCTCAACTGGTGGATATGGACAAGGTCCAGTTGCAT

CCGACAGGCCTCATCAACCCGAAGGATCCAGCGAACCCTACAAAGTTCCTTGGACCTGAG

GCGCTACGTGGATCCGGTGGCGTTTTGTTAAACAAGCAAGGCAAGCGCTTCGTTAATGAA

CTTGACCTCCGTTCTGTGGTATCGAAAGCCATCATGGAACAGGGTGCGGAATATCCTGGA

TCGGGTGGTAGCATGTTCGCCTACTGTGTGTTGAATGCTGCGGCGCAGAAGCTCTTTGGT

GTCAGCTCACACGAGTTCTACTGGAAGAAGATGGGTCTCTTCGTGAAGGCTGACACCATG

AGGGACCTCGCTGCACTCATTGGGTGCCCAGTGGAATCTGTGCAGCAGACGCTGGAGGAG

TACGAGCGGCTCTCCACATCACAGCGTTCCTGCCCCATCACGCGCAAGAGCGTCTATCCG

TGCGTGCTCGGCACTAAGGGCCCCTACTACGTCGCCTTCGTGACACCTTCGATTCACTAC

ACAATGGGTGGATGTCTCATCTCGCCTTCTGCTGAAATACAAATGAAGAACACATCATCA

CGCGCTCCACTGAGTCACAGCAACCCAATCCTCGGGTTATTTGGTGCCGGTGAGGTAACG

GGTGGTGTGCACGGTGGGAACCGGTTGGGCGGCAATTCGCTGCTTGAGTGCGTCGTGTTT

GGGAGAATTGCGGGTGATCGGGCCTCGACCATCCTTCAGAGGAAGTCCTCAGCACTTTCC

TTCAAGGTGTGGACGACCGTGGTGCTGCGTGAAGTACGCGAAGGTGGTGTGTACGGTGCT

GGGTCCCGCGTGCTTCGCTTTAATTTACCCGGGGCGCTGCAACGGTCTGGTCTGAGCCTC

GGCCAATTTATCGCAATTCGTGGTGATTGGGACGGTCAGCAGTTGATCGGTTATTACAGT

CCCATCACGCTGCCAGATGATCTTGGCATGATCGATATACTCGCCCGCAGTGATAAGGGG

ACGCTGAGGGAGTGGATTTCCGCTCTGGAGCCGGGTGACGCTGTGGAGATGAAGGCATGC

GGTGGTCTGGTGATTGAGCGCCGCTTAAGCGATAAGCACTTTGTGTTCATGGGACACATT

ATCAACAAGCTTTGTCTAATTGCTGGTGGAACGGGTGTGGCACCGATGCTGCAAATAATC

AAAGCAGCCTTTATGAAACCCTTCATTGACACATTGGAGAGCGTTCATCTCATCTATGCC

GCGGAGGACGTAACGGAGTTGACGTATCGCGAGGTGCTGGAGGAGCGCCGTCGTGAGTCA

CGTGGAAAGTTCAAGAAAACGTTTGTCCTCAACCGGCCCCCGCCCCTATGGACTGATGGT

GTTGGCTTCATCGACCGGGGCATCCTCACAAATCATGTGCAGCCGCCATCTGACAACCTG

CTGGTGGCCATATGCGGACCACCGGTAATGCAGCGCATTGTAAAGGCGACCCTGAAGACT

TTGGGCTACAACATGAACCTTGTGAGGACTGTGGATGAAACGGAGCCGAGCGGCTCATCC

AAAATTTGA

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;">
 * Sequence Length: 3429 bp **

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;"> ***GC% Content for gene: 54%**

<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;">Websites used: (others are listed under specific sections)

<span style="font-family: 'Times New Roman','serif'; font-size: 16px;">**RESOURCE PAGES:** [] http://www.utexas.edu/research/rsc/ibc/agent_class.html#_Toc7238334 @http://www.niaid.nih.gov/Pages/default.aspx @http://eupathdb.org/eupathdb/ @https://patricbrc.vbi.vt.edu/portal/portal/patric/Home @http://tdrtargets.org/

@http://www.ncbi.nlm.nih.gov/gene @http://blast.ncbi.nlm.nih.gov/