Databases Of Enzymes Composed By Multiple Units?

Question

[Giovanni M Dall'Olio]

I wonder why I can't find any database for enzymes composed by multiple proteins as separate entities.

I'll explain better: the OST complex is a multiple-units enzyme composed by 6-7 proteins, like OST4, STT3A or STT3B, RPN1, DAD1, etc... If I look for any of these proteins in Uniprot, I get a nice entry for each: for example, if you look at STT3A you get a lot of informations, including a description that explains that this protein partecipates to the OST complex.

However, if you look for 'OST complex' in uniprot, there is not a separate entity for this multiple-units enzyme... I wonder if you know of a database where complex enzymes are described, or if you have faced this problem before.

[Giovanni M Dall'Olio]

well, many multi-protein complexes are well characterized, at least to a level when it is worth annotating them. Think of other complexes that have been characterized in the literature: the ATP synthase, the nucleosomes, etc.. On the OST complex there are ~20 years of literature, including many reviews. In any case, I am not looking at a database that annotates the exact composition of each enzyme, but it will be sufficient to have one that summarizes all the possible hypothesis and experimental evidences on it.

[Phis]

A database would definitely be a Good Thing, agreed.

[Phis]

Maybe because of lack of good quality and comparable data? Although there are some experimental approaches, studying molecular interactions isn't exactly an easy thing. And except maybe for a few special cases, probably also not straightforward to predict.

[Phis]

Maybe because of lack of good quality and comparable data? Although there are some experimental approaches, studying molecular interactions isn't exactly an easy thing. And except maybe for a few special cases, probably also not straightforward to predict. (For example: How do you know that OST contains exactly those proteins, maybe you're missing some, maybe some of those listed are artefactual or only present under certain circumstances?)

[Phis]

Yes. But the relatively well characterised ones are not so many. As they grow in number, you'd expect some database to emerge finally. Maybe we're just not quite there yet.

[Giovanni M Dall'Olio]

I don't think so... the majority of the enzymes are composed by multiple proteins, and there is already enough literature to make a database, if someone has the resources.

Answer 1

[Neilfws]

Does this one help? CORUM – the Comprehensive Resource of Mammalian protein complexes.

Just tried a quick search using "DAD1" and it seemed to return useful results.

[Giovanni M Dall'Olio]

seems very good, thanks.. it has been updated recently and they have references for every entry. I'll wait for other answer and then accept yours, ok? cheers

Answer 2

[Michael Kuhn]

KEGG has some of the information. E.g. here is a pathway that at least contains the information that your enzyme is composed of STT and OST subunits.

If two boxes are right next to each other in KEGG, then this means that you have a multi-subunit complex. When you click on OST in this case, you get different subunits, but it looks like the subunit composition is not conserved, hence they didn't add the subunits as separate boxes.

[Giovanni M Dall'Olio]

thanks... but I have been using Kegg for a while, and unfortunately I can tell you that they don't use always the same convention in those figures. For example, the three DPM1, DPM2, DPM3 genes act in a complex called DPM synthase, which is not represented; and if you click on 'MAN1', you get a list of genes that catalyze chained reactions, but are not in a complex. The fact that two enzymes are represented in the same node in a kegg pathway doesn't mean that they form a complex enzyme.

[Michael Kuhn]

sure, I was only pointing out that separate, adjacent boxes mean that you have different subunits

Answer 3

[Khader Shameer]

3D Complex is a database of multi-protein complexes with structural data. Provides a hierarchical schema for protein complexes with structural data.

Ref.

• http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020155
• http://www.ncbi.nlm.nih.gov/pubmed/17997962