5.451 F2005 Problem Set 1. 1. (25 pts) Shown below is the structure of the cyclic peptide cystothiazole, a potent antibiotic, produced by the bacteria Cystobacter fuscus. Draw a reasonable biosynthetic pathwaythat includes chemical structures of intermediates and the names or abbreviation of the types of enzymes involved. N S S N 3 H3 3 O OCHCO OCHcystothiazole Professor Sarah O'Connor Massachusetts Institute of Technology5.451 F2005Problem Set 1.2. (25 pts) Predict the structure of the polyketide that is encoded by the following set ofenzymes.KS-Q AT-mm ACP KS AT-mm KR ACP KS AT-m DH KR ACPKS AT-mm ACP KS AT-mm DH ER KR ACPKS AT-mm KR ACP KS AT-mm ACP TEenzyme 1enzyme 2enzyme 3Professor Sarah O'ConnorMassachusetts Institute of Technology5.451 F2005 Problem Set 1. 3. (20 pts) Labeling studies have shown that the following molecule from Streptomycescoelicoloris made up of one unit of proline, one unit of serine, one unit of glycine andmultiple units of acetate (i.e. malonyl CoA). The biosynthetic pathway is convergent,with the two intermediates A and B condensing to form the final product. Proposebiosynthetic pathways for A and B and indicate the basic type of enzymes that would beused for the biosynthetic steps. acetate, glycine NH proline, serine, acetate, SAM (note: a PLP enzyme decarboxylates serine in this pathway) N H3N H3H O A B HN CO NH HN CO Professor Sarah O'Connor Massachusetts Institute of Technology5.451 F2005 Problem Set 1. 4. (20 pts) Draw the thioester-tethered linear polyketide intermediate for the followingcompound, and show the steps that convert the intermediate into the final product.(Enzymes not required to be mentioned in the answer). If the producing organism Streptomyces glaucescens) is cultured in the presence of [1,2-13C2]acetate, show the 13C labeling pattern expected to be observed in the final productusing a bold line between the desired two carbons. example O O OH HO OH OH Professor Sarah O'Connor Massachusetts Institute of Technology5.451 F2005 Problem Set 1. 5. (10 pts) Sequence homology- looking at the amino acid sequence similarity among proteins- is one modern method to predict the function of a new protein. How are homologogues picked out of a database?? You isolate a piece of genomic DNA that you think may be part of a natural product gene cluster. The DNA sequence of the fragment is attached as a text file on the 5.451 website (file “dnasequence”). Go to the website http://www.ncbi.nlm.nih.gov/On the left hand side of the screen click on Tools Click on “ORF Finder” (about 5 paragraphs down the page)Paste the DNA sequence into the box. Click on the button that says “orffind” The computer has now found all possibles ORFs (i.e. stop and start codons that are inframe) and highlighted them as turquiose boxes.Click on one of the turquiose boxes. The program will translate the DNA into peptide sequence. At the top of the page click the button that says “BLAST”. BLAST is one of the most common algorithms for finding homologous proteins. Click the botton that says “Format” on the screen that comes up. All homologous proteins will be listed, withthe most similar proteins showing up first, and the least similar showing up last.Find an ORF that encodes a gene involved in natural product biosynthesis. Question: The “unknown” DNA is most likely part of the biosynthetic pathway for what naturalproduct??? (Click on the links of the homologous proteins to read about their functionand thereby predict what natural product is encoded.) Professor Sarah O'Connor Massachusetts Institute of