PDB file 1NGS

This file depicts Transketolase with bound erythrose-4-phosphate, an acceptor of the 2-C fragment transferred by this enzyme. This structure was solved by Nilsson, Lindquist, & Schneider, 1997.

Suggested display options:

To distinguish the 2 copies of the protein, color chain.

hetero-ligand, display as sticks or ball & stick, and color CPK.
Identify the thiamine pyrophosphate (TPP) and the erythrose-4-phosphate substrate,

Locate the carbon atom in the thiazole ring of TPP, between N (blue) and S (yellow), that tends to dissociate a proton to become a reactive carbanion.
Note the conformation of TPP & the position of the amino N of the aminopyridine moiety that is thought to accept a proton from the acidic carbon in the thiazolium ring.

Find the glutamate residue, near the aminopyridine ring, which promotes the proton transfer.
Note the position of the reactive carbon on TPP relative to the aldehyde at carbon #1 of the substrate erythrose-4-P. 

Then select protein, display as spacefill with color chain.
Are TPP and erythrose-4-P buried or at the enzyme surface?
Does each copy of the enzyme in the dimer have its own active site independent of the other subunit? 

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