Problem Set 5 Key

Problem Set 5 Key

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Unformatted text preview: e GnT I, water molecules (hydroxyl group of incoming acceptor for GnT I) are positioned for the nucleophilic attack at the donor sugar C1. 3. Protein Glycosylation (30 points): 5 a. Lizak, C., et al. (2011, Nature, 474, 350- 356) published the crystal structure of the well- characterized bacterial oligosaccharyltransferase (OST), PglB, encoded in the protein glycosylation locus (pgl) of the gram- negative bacteria, Campylobacter lari. i. Prepare a figure of the interaction site showing PglB in complex with the acceptor peptide DQNATF (PDB ID: 3RCE). Be sure to show the residues on PglB that are involved in acceptor binding and metal ion coordination. (10 points) ii. How does the structure explain the requirement for a Thr or Ser at the +2 position of the acceptor peptide? Why are sequences containing a Thr in the +2 position glycosylated 40- fold more efficiently than sequences containing a Ser in the position? (5 points) The side- chain hydroxyl group on the +2 Thr makes hydrogen bonds with all three residues within the “WWD” motif. In addition, the side- chain methyl group on the +2 Thr contacts the side- chain methyl group within Ile572 on PglB (van der Waals). This contact is lost if Ser is present at the +2 position, explaining the enzyme’s preference for Thr. iii. The PglB structure identifies novel residues that are involved in acceptor binding. Identify the residues and their functions. How does their presence provide an explanation for how glycosylation is specific for Asn residues? (5 points) The novel residues are D56 and E319...
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This note was uploaded on 01/09/2014 for the course CH 170A taught by Professor Clemens during the Fall '13 term at Caltech.

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