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Part 2: Analyzing mutations - obtaining data

Active- and Binding-sites

AIM: To find the active site and binding site residues using SwissProt

You are now going to look at three of the mutations in the context of the structure using PyMol to view the structure of G6PD. Your task is to identify which of the three mutations is close to (within 10A of) the active site or binding sites - i.e. you will see whether the mutations have a clear reason for affecting the protein function.

First you will use the UniprotKB/SwissProt entry to identify the active site and binding site residues. Proceed as follows:

Go to the UniProt entry for G6PD http://www.uniprot.org/uniprot/P11413 and click the Function option in the menu on the left of the page. Scroll down to the section header Features.

By looking at the Features section, make a list of all the amino acid positions that are involved in the active site and interactions with substrate. For these purposes, do not include the Nucleotide binding regions (i.e. residues binding to NADP⁺.

Obtaining mutation data

AIM: To identify a subset of mutations in G6PD using OMIM

You will now identify three of the mutations seen in G6PD by using their OMIM reference numbers. Proceed as follows:

Go to the OMIM entry for G6PD and scroll down to the 'ALLELIC VARIANTS' section: http://www.omim.org/entry/305900

Identify and record the mutations corresponding to variants:

.0030
.0044
.0047

Remember that the mutation appears on the line immediately after the variant identifier in the form 'PRO353SER' (indicating a native proline at position 353 is mutated to serine).

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