Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?

Question

[O.rka]

https://www.genome.jp/dbget-bin/www_bget?K00004

I'm looking into Enzyme Commission (EC) numbers and I've noticed many annotations have the following scenarios:

• Multiple ECs
• An EC without only 3 levels

According to Expasy (https://enzyme.expasy.org/EC/1.1.1.-):

1.-.-.-: Oxidoreductases 
1.1.-.-: Acting on the CH-OH group of donors 
1.1.1.-: With NAD(+) or NADP(+) as acceptor

I have the following questions:

• Does this mean K00004 can function as both 1.1.1.4 and 1.1.1.303?
• Does this mean K00004 can function as all the enzymes within 1.1.1 level?
• If there is a pathway that requires 1.1.1.2 would a protein annotated as 1.1.1.- be sufficient?

Answer 1

[Mensur Dlakic]

They say that we remember better things we figured out on our own, rather than things we were taught. You were literally two clicks away from figuring this out, so I will try to help you that way rather than answering directly.

It says here that this enzyme is a (R,R)-butanediol dehydrogenase / meso-butanediol dehydrogenase / diacetyl reductase. To refresh your chemistry, this means it can do a dehydrogenase reaction on two different substrates (removes hydrogens) and a reductase reaction (adds hydrogens) on another substrate. Had you clicked on these two links:

• https://enzyme.expasy.org/EC/1.1.1.4
• https://enzyme.expasy.org/EC/1.1.1.303

to see what these enzymes are doing, the answer hopefully would have been obvious.

[O.rka]

Thank you. This answers my question. The reason I am asking is because I’m trying to do set enrichment analysis with BRENDA pathways using a hypergeometric test. In some pathways, there is a level 3 enzyme like 1.1.1.- and I’m wondering if I can use, for example, a 1.1.1.3 enzyme to fulfill that in my set enrichment? Also vice versa, If there was a 1.1.1.3 in the pathway and the protein was annotate as a 1.1.1.- enzyme. If the answer to either of those is true, then could I just remove the last level on all enzymes when I’m doing pathway enrichment?

[Mensur Dlakic]

Enzymes under the umbrella of 1.1.1.- work with NAD(+) or NADP(+) as acceptor. That only tells you about their cofactors, but not about their substrates.

Again, you'll do better by figuring this out on your own. Click randomly on a dozen or so 1.1.1.- enzymes and see if their functions (meaning substrates) are equivalent. If they are, then you can ignore the fourth number.