Tuesday, August 18, 2009


I always thought that ferrochelatase (EC has an absurd systematic name: “protoheme ferro-lyase (protoporphyrin-forming)”. Why? According to Enzyme Nomenclature,

Lyases are enzymes cleaving C—C, C—O, C—N and other bonds <in other words, any bond> by other means than by hydrolysis or oxidation.
“Protoheme ferro-lyase” implies that the reaction goes in the direction:

protoheme + 2 H+ → protoporphyrin + Fe2+(a)

while ferrochelatase, in fact, catalyses the reverse reaction:

protoporphyrin + Fe2+ → protoheme + 2 H+(b)

Usually, to release iron from protoheme, you have to break it. Heme oxygenase (EC does it by sequential oxidation of heme into the linear tetrapyrrole, biliverdin.

However, this paper demonstrates that there could be another way to do it.

Until today, all known enzymes performing iron extraction from heme did so through the rupture of the tetrapyrrol skeleton. Here, we identified 2 Escherichia coli paralogs, YfeX and EfeB, without any previously known physiological functions. YfeX and EfeB promote iron extraction from heme preserving the tetrapyrrol ring intact. This novel enzymatic reaction corresponds to the deferrochelation of the heme. YfeX and EfeB are the sole proteins able to provide iron from exogenous heme sources to E. coli.
Thus, deferrochelatase catalyses the reaction (a) and, indeed, can be named “protoheme ferro-lyase (protoporphyrin-forming)”.

Thursday, August 13, 2009

What is a correct InChI for chromate?

During the IUPAC International Chemical Identifier (InChI) Subcommittee meeting in Glasgow last month, we touched upon the issue of normalisation of metal complexes. I did not realise before that even simple entity such as chromate(2−), drawn in different ways (a)(c), will give different InChIs. (And different standard InChIs as well; and InChIKeys too.) This is, I am told, because the current InChI algorithm involves “disconnection” of metals before “normalisation”, while it really should do normalisation first. Bother.