Target+-+NAD-dependent+glyceraldehyde-3-phosphate+dehydrogenase+(Helicobacter+pylori)

//Helicobacter pylori// is a gram-negative bacterium responsible for about 80% of stomach ulcers and 90% of ulcers in the duodenum. Part of its name is derived from its spiral shape which has been determined to help the bacteria penetrate the stomach's protective mucous lining. The bacteria produce substances that weaken the mucous lining. This causes the stomach to be more susceptible to gastric acids. Another way the bacteria damages the stomach is attaching to the cells of the stomach and stimulating the production of excess stomach acid. Recently, this bacteria has been a significant problem in the US. About 20% of people under 40 and about 50% of the adults over 60 years old are infected. These rates are higher in developing countries. However, being infected by the bacteria does not necessarily mean that one will develop ulcers or stomach cancer. It is still unclear why this happens.
 * Target (protein/gene name):** NAD-dependent glyceraldehyde-3-phosphate dehydrogenase
 * NCBI Gene # or RefSeq#:** **RefSeq** : hp2017_0904
 * Protein ID (NP or XP #) or Wolbachia#:** **RefSeq** : ADZ50007.1
 * Organism (including strain):** // Helicobacter pylori //
 * Etiologic Risk Group (see link below):** Group I—Pathogens Newly Recognized in the Past Two Decades
 * Background/Disease Information (sort of like the Intro to your Mini Research Write up):**

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 * Essentiality of this protein:** Glyceraldehyde-3-phosphate dehydrogenase is essential for evasion from neutrophils.
 * Complex of proteins?: Yes**
 * Druggable Target: No**

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 * EC#: 1.2.1.12**
 * Link to BRENDA EC# page:**

[] [] [] Triethanolamine Buffer-$31, 3-phosphoglyceric acid disodium salt - $13.80, L-cysteine hydrochloride - $22.40
 * Enzyme Assay information (spectrophotometric, coupled assay ?, reagents): **
 * -- link to Sigma (or other company) page for assay or assay reagents (substrates)**
 * -- link (or citation) to paper that contains assay information**
 * -- List cost and quantity of substrate reagents and supplier**

-- PDB # or closest PDB entry if using homology model: -- For Homology Model option: code Query 1    MKIFINGFGRIGRCVLRAILERNDTNPQLEVIGINDPANWEILAYLLEHDSVHGLLNKEA  60 +K+ INGFGRIGR V RA L+   NP +EV+ +ND      LA+LL++DSVHG L+ E Sbjct  2    VKVGINGFGRIGRNVFRAALKNPDIEVVAVNDTGGANTLAHLLKYDSVHGRLDAEV  57
 * Structure Available (PDB or Homology model)**

Query 61   RYSNGKLIIGSLEIPVFNSIKDLK---GVGVIIECSGKFLEPKTLENYLLLGAKKV  113 +  L++   EI +  + +D +       GV +++E +G+F + +    +L  GAKKV Sbjct 58   SVNGNNLVVNGKEI-IVKAERDPENLAWGEIGVDIVVESTGRFTKREDAAKHLEAGAKKV  116

Query 114  LLSAPFMGEYDEKQYPTLVYGVNHFLYQNQA--IVSNASCTTNAIAPICAILDKAFSIKE  171 ++SAP  E       T+V GVN   Y  +A  ++SNASCTTN +AP   +L + F I Sbjct  117  IISAPAKNED-ITIVMGVNQDKYDPKAHHVISNASCTTNCLAPFAKVLHEQFGIVR  171

Query 172  GMLTTIHSYTSDQKLIDLAHPLDKRRSRAAASNIIPTTTKAALALHKVLPNLKNKMHGHS  231 GM+TT+HSYT+DQ+++D +H D RR+RAAA +IIPTTT AA A+  VLP LK K++G + Sbjct 172  GMMTTVHSYTNDQRILDASHK-DLRRARAAAESIIPTTTGAAKAVALVLPELKGKLNGMA  230

Query 232  VRVPSLDVSMIDLSLFLEKKALKESINDLLITASKGTLKGVLEIDLKERVSSDFISNPNS  291 +RVP+ +VS++DL  LEK+   E +N  L  A++G LKG+L    +  VS D+  +  S Sbjct  231  MRVPTPNVSVVDLVAELEKEVTVEEVNAALKAAAEGELKGILAYSEEPLVSRDYNGSTVS  290

Query 292  VIIASDLTFTLEN-MVKIMGWYDNEWGYSNRLVDMAQFM  329 I + T  ++  MVK++ WYDNE GYS+R+VD+A ++ Sbjct 291  STIDALSTMVIDGKMVKVVSWYDNETGYSHRVVDLAAYI  329 code Show pairwise alignment of your BLASTP search in NCBI against the PDB Query Coverage: 99% Max % Identities:43% % Positives 63% Chain used for homology: O

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 * Current Inhibitors:** Tetrose diphosphate []
 * Expression Information (has it been expressed in bacterial cells):** The protein was expressed in E. Coli cells

The protein was purified from E.coli by conventional ammonium sulfate fractionation, anion-exchange chromatography, hydrophobic chromatography and hydroxyapatite chromatography. [] code MKIFINGFGRIGRCVLRAILERNDTNPQLEVIGINDPANWEILAYLLEHDSVHGLLNKEA RYSNGKLIIGSLEIPVFNSIKDLKGVGVIIECSGKFLEPKTLENYLLLGAKKVLLSAPFM GEYDEKQYPTLVYGVNHFLYQNQAIVSNASCTTNAIAPICAILDKAFSIKEGMLTTIHSY TSDQKLIDLAHPLDKRRSRAAASNIIPTTTKAALALHKVLPNLKNKMHGHSVRVPSLDVS MIDLSLFLEKKALKESINDLLITASKGTLKGVLEIDLKERVSSDFISNPNSVIIASDLTF TLENMVKIMGWYDNEWGYSNRLVDMAQFMYHY code
 * Purification Method:**
 * Image of protein (PyMol with features delineated and shown separately):**
 * Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):**
 * length of your protein in Amino Acids**
 * 332**
 * Molecular Weight of your protein in kiloDaltons using the [|Expasy ProtParam] website**
 * 37.072**
 * Molar Extinction coefficient of your protein at 280 nm wavelength: 34630**
 * TMpred graph Image** (@http://www.ch.embnet.org/software/TMPRED_form.html).

code ATGAAAATTTTTATCAATGGATTTGGCCGCATTGGGAGATGCGTTTTAAGAGCGATTTTAGAGCGCAATG ATACAAACCCTCAACTAGAAGTGATAGGCATCAATGACCCCGCTAATTGGGAAATTCTCGCTTATCTTTT AGAGCATGACAGCGTACATGGATTGCTCAATAAGGAGGCGCGTTACTCTAATGGTAAGCTCATTATCGGC TCGTTAGAAATCCCTGTTTTTAATAGCATCAAAGACTTGAAGGGCGTGGGTGTTATCATAGAGTGTTCAG GGAAGTTTTTAGAGCCTAAAACGCTAGAAAATTACCTTTTGCTTGGGGCTAAAAAGGTGTTGTTATCCGC TCCTTTTATGGGCGAATACGATGAAAAACAATACCCTACTTTGGTGTATGGGGTCAATCATTTTCTCTAT CAAAACCAAGCCATTGTTTCTAACGCCTCTTGCACGACTAACGCTATTGCGCCCATTTGCGCGATTTTAG ATAAAGCTTTTAGCATTAAAGAGGGCATGCTAACGACCATTCATAGCTACACGAGCGATCAAAAGCTCAT TGATTTGGCCCACCCTTTGGATAAACGGCGCTCCAGAGCGGCTGCGAGCAACATTATCCCCACCACCACT AAAGCCGCCCTAGCCTTGCATAAAGTTTTACCCAATCTCAAAAACAAAATGCATGGGCATAGCGTTAGGG TGCCTAGCCTTGATGTGTCCATGATAGATTTGAGTTTGTTTTTAGAAAAAAAGGCTCTCAAAGAGTCGAT CAACGATTTATTGATTACAGCTTCTAAAGGGACTTTAAAAGGCGTGTTAGAGATAGATTTAAAAGAAAGG GTGAGTTCTGATTTCATTTCTAACCCTAATAGCGTTATCATCGCGTCTGATTTGACTTTCACGCTAGAGA ATATGGTCAAAATCATGGGGTGGTATGATAACGAATGGGGGTATTCTAATCGTTTGGTGGATATGGCGCA ATTCATGTATCATTATTAA code
 * CDS Gene Sequence (paste as text only):**
 * GC% Content for gene: 51%**
 * CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):**
 * GC% Content for gene (codon optimized):**

-- 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)


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

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 * References:**