PDB file 1REQ
This file depicts structure of a bacterial Methylmalonyl-CoA Mutase, solved by P. R. Evans & F. Mancia in 1996. The enzyme has been co-crystallized with desulfo-Coenzyme A (an analog lacking the reactive thiol). Glycerol, included in the medium during crystallization, is present, including in the active site. Deoxyadenosyl moiety is lacking in the crystal. The cobalt is concluded to be at oxidation state II.
Suggested display options:
First make the protein disappear by selecting hide.
Select ligand, display as ball & stick, & color CPK, to visualize coenzyme B12 and other ligands.
Select cobalt, & display as spacefill.
There are two copies of everything in this dimeric structure.
Abbreviations that you can use to select different "hetero" compounds:
DCA = desulfo-CoA, which does not display with the usual CPK colors.
GOL = glycerol. 800 = coenzyme B12.
Compare to the chemical structure of coenzyme B12.
Note the 4 N atoms of the corrin ring that serve as ligands to the cobalt.
The corrin ring is planar. Do its side chains lie in the plane?
Now select protein and display as
cartoons with color
Select protein-sheet and change color, e.g., to magenta.
Note the unusual arrangement in which CoA (which would be part of the substrate) extends right through an a,b-barrel to position the methylmalonyl moiety of the substrate adjacent to coenzyme B12 (position occupied here instead by glycerol).
Identify the N of
the dimethylbenzimidazole moiety that serves as an axial ligand to the cobalt in free
Identify and visualize with CPK color the enzyme histidine N that is an axial ligand to the cobalt, replacing the dimethylbenzimidazole N.