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Is this another name for the active site of an enzyme? What does the structure of the catalytic domain of an enzyme look like?

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    $\begingroup$ Quick answers: yes, and it varies tremendously. Enzymes catalyze a huge variety of reactions, from cutting DNA to adding amino acids to a growing polypeptide chain, to breaking down complex sugars, and many more besides. Catalytic domains vary from enzyme family to family, and even between enzymes in a single family. There really is no generalization you can make about structure or function, as it is so different from one to another. $\endgroup$ – MattDMo Sep 25 '14 at 20:36
  • $\begingroup$ AFAIK MattDMo is correct. The catalytic site is the active site where the reaction takes place that triggers the conformation change. He is also correct about there being nearly infinite potential catalytic site designs. $\endgroup$ – MCM Sep 25 '14 at 21:38
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    $\begingroup$ I would say that catalytic domains are a little different from active sites. The active site is the location where the substrates bind and the reaction occurs, the catalytic domain is the portion of the enzyme that contains the active site. Many proteins have multiple domains. $\endgroup$ – user137 Sep 25 '14 at 22:13
  • $\begingroup$ I agree with @user137. The catalytic domain is a subdomain of active site (which also contains binding domains). $\endgroup$ – WYSIWYG Sep 26 '14 at 14:40
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Both parts overlap. Proteins are a chain of linked amino acids. This chain can be grouped into functional units which are called protein domains. Usually all parts of a domain are closely located in the protein and they form functional domains in the 3D structure of the protein. Proteins usually contain more than one domain (these are manifold but for example can be dimerization, activation or binding domains).

The catalytic domain is the part of the protein chain which contains the region where the catalyzed chemical reaction takes place. The 3D structure of the catalytic domain forms the active site, so the enzyme requires proper folding to be active. If you denature the enzyme, the catalytic domain will still be present (as this is a function of the protein sequence) but the active site will be gone.

As there are really many enzymes for all kinds of reactions it is hard to define a general form for the active site. A motif which is present in a lot of enzymes is the the form of a catalytic pocket or groove to which only the correct substrate of the enzyme has access. Additionally the binding of the substrate to the enzyme often induces a conformational change in the protein which closes this pocket. When the reaction is finished and the substrate is not bound anymore by the enzyme, the conformation changes again and releases the products of the reaction. See the image for a schematically drawing of this principle (image from here):

enter image description here

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