Talk:Metalloprotein

A fact from Metalloprotein appeared on Wikipedia's Main Page in the Did you know column on 11 January 2009, and was viewed approximately 393 times (disclaimer) (check views). The text of the entry was as follows:

Did you know... that the presence of the metal ion in metalloprotein enzymes allows them to perform functions, such as catalyzing redox reactions, that other polypeptide enzymes cannot achieve?

A record of the entry may be seen at Wikipedia:Recent additions/2009/January.

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Molecular Biology: MCB

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This article is or was the subject of a Wiki Education Foundation-supported course assignment. Further details are available on the course page. Student editor(s): Mdavydova. Peer reviewers: Mdavydova.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 03:57, 17 January 2022 (UTC)[reply]

A request[edit]

Being that all known enzymes are proteins this would seem to be the correct page for metalloenzymes & metal activated enzymes. I'm not sure I'm enough of an authority on this subject. Could someone add more info? Thanks. Gregogil 19:14, 6 February 2007 (UTC)[reply]

external link[edit]

Metalloprotein at eMedicine Dictionary does not work. Petergans (talk) 13:20, 4 January 2009 (UTC)[reply]

Is this break-down not odd?[edit]

This seems like an odd breakdown of metalloproteins. I had only heard of them being categorized as Gregogil refers to above: metalloenzymes and metal activated enzymes. For example, I have always heard of cytochrome c as being referred to as a metalloenzyme, but it does not have an empty coordination site (the tetrapyrrole, a His, and a Met). But cyt c is not categorized under metalloenzymes here, and if it were, it would directly contradict the statement in this article: Metalloenzymes all have one feature in common, namely, that the metal ion is bound to the protein with one coordination site free. On the other hand, cyt c catalysis does not take place on the metal center. Does this article need a rework or have the classifications changed? BobertWABC (talk) 17:54, 2 March 2009 (UTC)[reply]

I don't think I'd classify cytochrome C as an enzyme. All it does is transfer electrons between proteins, so I'd call it a redox intermediate, like thioredoxin. Tim Vickers (talk) 22:15, 2 March 2009 (UTC)[reply]

Further issues with quote from above[edit]

Actually, the statement "Metalloenzymes all have one feature in common, namely, that the metal ion is bound to the protein with one coordination site free," should probably be completely omitted. For example, resting catalase-peroxidase is hexacoordinate, with the sixth ligand being water. The water is displaced for catalysis. If we do not consider the water to be an occupied coordination site, there are numerous examples of coordination spheres with multiple solvent ligands. In that case, the statement is still incorrect as there are more than one open coordination sites (non-protein ligands), even if the substrate interacts with only one specifically. BobertWABC (talk) 17:59, 2 March 2009 (UTC)[reply]

To clarify my position: I expanded this article from an existing kernel, so I did not create the article originally. My justification for bringing these examples together lies in the chemistry of the metal centre, which is of interest to (bio-)inorganic chemists. Maybe "labile" would be a better word than "vacant". Petergans (talk) 19:27, 2 March 2009 (UTC)[reply]

I suppose if we're including hemoproteins, then here none of the metal coordination sites are bound directly to the protein. The protein binds to the porphyrin ring, which in turn binds the metal. Tim Vickers (talk) 22:18, 2 March 2009 (UTC)[reply]

Sorry, Tim, but I will have to disagree with you. All hemoproteins that I can think of have at least one metal coordination site occupied by an amino acid. Histidine, cystine, methionine, aspartate, and tyrosine are heme ligands that come to mind immediately. And, as mentioned with cyt c, a few where the chemistry takes place at the heme edge have two amino acid ligands. And some hemes are bis-his coordinated and inactive, until binding of another metal like calcium which results in the "propping up" of one of the histidines to allow substrate access to the heme iron (class II peroxidases). To Petergans, I would accept labile, but again, only if there is consensus that this class does not include proteins like cyt c. Like I said, I've never seen this sort of breakdown of metalloproteins before; but with the wiki just trying to give some basic info about the topic I don't think it's important that everything align with the most strict classification. Anybody that needs more in depth information shouldn't be here anyway =P. BobertWABC (talk) 03:38, 3 March 2009 (UTC)[reply]

Organizational challenges, 2011[edit]

Since somewhere between 1/4 and 1/2 of all proteins contain metal ions, the scope of metalloproteins is vast. So we need to think about what goes into this article and in what order. Although we could organize by function (e transfer, element storage and transport, oxidases etc), such lists end up being somewhat arbitrary or, worse, decided by people who just like "their protein" and want to promote it. So we should think of a weighting system that involves something like:

most pervasive metalloproteins (must be a list somewhere)
most important (meaning of "important")
most instructive (perhaps best understood, like carboxypeptidase, myoglobin)

We also need to decide on the following:

do we include Mg²⁺, Na⁺, etc (many proteins carry these things as structural components, some as functional components also.

Overall, I am suggesting that we figure out (achieve consensus) on the right questions to ask about scope, and then build that consensus into the article sectioning. Otherwise, the very inclusion of various topics is a form of original research, it seems.--Smokefoot (talk) 07:34, 10 December 2011 (UTC)[reply]

"DNA enzymes" etc.[edit]

First, no "DNA-enzymes" have been "discovered", as written in the article: They are all man-made! I have changed this accordingly.

Second, they are not called "DNA-enzymes", but "DNAzymes". Also, there are no "RNA-enzymes", only "Ribozymes". The word "enzyme" is reserved for proteins (this is btw implicitly written so in the Wikipedia article an enzymes). I left the term "metalloenzyme" though, even though I don't really see the need to phrase it this way.

Third, RNAzymes developed by e.g. SELEX execute many more functions than natural RNAzymes and I could not find sources that state that DNAzymes are able to execute significantly more and/or different functions than ribozymes. I leave it up to the author to phrase that part differently, however. --Felix Tritschler (talk) 10:04, 21 February 2018 (UTC)[reply]

General term for non-metal, "non-organic" containing proteins (selenoprotein, etc?)[edit]

"Metalloprotein" describes proteins that contain a metal. Is there a general term for proteins that contain other "non-organic-element" atoms? Selenium, iodine, and boron come to mind. Are there others? Jimw338 (talk) 18:25, 4 January 2023 (UTC)[reply]