Transaminase - PMP

PDB file 1AMS

This file depicts Transaminase (Aspartate Aminotransferase), with prosthetic group pyridoxamine-5'-phosphate (PMP), and bound glutarate, an analog of a-ketoglutarate lacking the reactive keto group on C2. This structure was solved by I. Miyahara, K. Hirotsu, H. Hayashi, & H. Kagamiyama (1994).

Suggested display options:

Start with protein in wireframe, and color chain.
Select
hetero-ligand, color CPK and display as ball & sticks or sticks.
Identify the pyridoxamine phosphate (PMP) and the substrate analog glutarate.

Note the proximity of C#2 of glutarate to the amine N of pyridoxamine.


Use the command line to select
lys258, color CPK and display as ball & sticks.
Note the position of the lysine side-chain amino group that forms a Schiff base linkage when the prosthetic group is in the form of pyridoxal phosphate.
View also in
spacefill display to better judge distances.

Try to identify the following:
(1) The conserved aspartate whose side-chain carboxyl forms a salt bridge to the positively charged N of the PMP ring.
(2) The positively charged amino acid side chain that forms part of the binding site for the phosphate moiety of PMP.


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