Heme nomenclature, Met Ligand chirality

Heme nomenclature conventions, Met Ligand chirality

heme conventions
Figure of hemin showing conventional numbering for the 8 substituents and two different conventions for numbering the 4 pyrrol rings.
heme conventions
Orientation and Chirality of the met ligand in cyt c1. Structures 1bcc, 1be3, and 1ezv were oriented to superimpose the hemes of cyt c1. Orienting the heme with propionates down and ring B on the left, Methionine is in front (towards the viewer) of the heme. The MET CG-SD bond is nearly horizontal from right to left. The S-CE slants down to the right in the chicken (1bcc) and yeast (1ezv) structures, putting CE over the heme NA atom. It slants up towards the right in the beef structure, putting CE over the NB atom of the heme. However note that the resolution of 1bcc and 1be3 is not high enough to acurately determine this, and it may be the authors used topology/param files from cyt c which constrained the chirality. heme conventions
In our new orthorhombic beef bc1 crystals, the resolutionis significantly higher, and we can see a clear bulge in the SD density where the CE protrudes. In this structure the chirality is the same as in the yeast enzyme.

The chirality can be accurately measured by a structural parameter called an "improper dihedral" angle. Like a conventional dihedral this involves the relation between four atoms, but they need not be sequentially connected, rather in this case three atoms are attached to a central one. If the four angles lie in a plane the improper has value 0 (or 180?), and deviation from planarity gives increasing postive or negative value depending on the chirality.

If the improper is defined as folows:
IMPRoper SD CG CE FE ! chirality or flatness improper -38.79
IMPRoper SR29 CR28 CR30 FER3 750.0 0 -35.000 ! Nobs = 1 ... Value = -38.786
Then R chrality corresponds to negative values and to the situation seen in 1BE3,
while S chirality corresponds to positive values and the situation seen in 1bcc and 1ezv.

Soluble cytochromes c and c2, as well as E. coli cyt b562, have R chirality.
bacterioferritin and now cytochrome c1 have S chirality.
heme	struct	improper
b562		-42, -38
cyt c	1ycc	-39*
Rcbfr	bfr	+19
Ecbfr	1bfr	+22	
Ecbfr	1bcf	+52
chbc1	1bcc
y bc1	1ezv
bfbc1	bfo