[madscientist]

Hi all,  Im a bit stuck on what would be considered a domain in Phosphofructokinase-1 pictured below.  I know there is four subunits, substrate binding sites, binding sites for allosteric regulator,alpha helices, beta sheets.... but cant seem to figure out where (if there is one) the domain is and what it consists of.  to me it seems that each subunit is a domain???

any help would be much appreciated,

[Yggdrasil]

Protein domains are evolutionarily-conserved, independently-folded structural unit of one polypeptide chain that performs a certain function.  Protein domains are generally continuous in the primary sequence and can sometimes be identified by looking at the primary sequence and comparing to other proteins containing such a domain.  Often, protein domains are identified by limited proteolysis, which cleaves the flexible structural regions joining domains, but will not cleave within the more tightly folded structure of the protein domains.

I would look at the literature on PFK, as others have probably identified the domains of the protein already.  IIRC, the protein has a kinase domain (containing the active site), and an allosteric domain which regulates the activity of the kinase domain.

[madscientist]

Thanks Yggdrasil, its hard (for me) to tell the difference between a domain and a subunit.  Is it just that a subunit consists of a different chain within a protein and a domain is a separately folded part of the same chain?

[Yggdrasil]

Yes.  A protein can be composed of multiple subunits.  These subunits consist of single polypeptide chains.  Protein domains are small sections of the polypeptide chains.  So, in terms of a size hierarchy:

protein > subunit > domain

[refid]

what about motifs? I can never distiguish those from domains.

[Equi]

A motif can occur within a domain (e.g. certain super-secondary structures) or might even constitute a whole domain. I doubt there is a clear definition for this term.

[Yggdrasil]

I agree with equi.  I would say that a motif is smaller than a domain.  Here's how I would distinguish between domains and motifs, although this is not a rigorous/official definition by any means:

A domain is a functional unit of a protein.  For example, when you express a domain in isolation from the rest of a protein it can perform a certain function (i.e. interaction with another protein, catalytic ability, binding of a small molecule, etc.).  A motif is not necessarily a functional unit, it is merely a conserved structural unit (such as a super-secondary structure).

If you really want to go into more classification of protein structure, smaller than domains and motifs, you have folds, which are smaller, conserved structural "motifs" (for lack of a better word).  These are more rigorously defined, for example, the  SCOP database (structural classification of proteins) has a list of folds.

[madscientist]

Thanks for all the help peoples! much appreciated.