Talk:Catalytic triad

LBHB

the existance of a low barrier hydrogen bond in serine proteases is controversial at best; and it has been directly ruled out by high-res x-ray for alpha-LP: (http://pubs.acs.org/cgi-bin/abstract.cgi/jacsat/2006/128/i28/abs/ja057721o.html). i propose we revert that portion to something more like the previous version. Xcomradex 05:03, 19 February 2007 (UTC)

2013 overhaul

For such a fundamental enzymology page, this article has been in need of attention for a while. I've tried to keep what I could from the previous version.

Changes made

• Removed entirely the previous sections:
  • Example - The introduction sentences were sadly incorrect and misleading.
  • Amino acid sequence, histidine 57 - which simply looked at similarities between three S01 serine proteases
  • Four atom characterize different ASP-HIS-SER enzyme families - very specific point based on a single paper. I had hoped to integrate some the information elsewhere, however the original paper was too poorly written.
• Added non-protease examples
• Attempted to represent the range of different triads whilst emphasising their similarities
• Introduced sections on convergent and divergent evolution
• Added images to help clarify

To be done

• My background is in proteases. Examples from non-proteases would help to balance this article
• I aim to add a few images to illustrate the convergence and divergence (Complete 31 October 2013)
• Make sure that other relevant enzymology pages link to this (Complete 21 November 2013)

Evolution and evolvability (talk) 15:41, 27 October 2013 (UTC)

Class A

The level of detail and information in this article compares well with other Class A articles. Hopefully it can make it up to Good Article status with a bit more work.

• A history section would be useful by someone who's been in the field long enough to have a good knowledge of the old literature.
• Examples from other enzymologists on the triads from non-proteases would help give a more general view of triads.
• Additionally, perhaps chemists may have some input as to why the use of a triad is so common an active site construction

Evolution and evolvability (talk) 11:41, 1 December 2013‎ (UTC)

A few comments

Ha, Evolution and evolvability, when I first got here I started to respond to your previous posts without realizing they were from 2013! Had been meaning to look at this article since you mentioned it at WT:MCB last week but got distracted by the outbreak of stupidity around here (which probably went unnoticed by anyone who doesn't hang around the Broad Street pump ANI).

• The beginning of the history section is confusing. The structure was solved in the 1930s? That can't be right. And the reference (#6 at the moment) goes to a paper about administering endothelin to rats. There must be some typos in here. I think you mean trypsin was purified and crystallized in the 30s (Kunitz?).

 Done Ha, originally I'd written 'crystallised', then evidently forgotten what I was doing and changed it to 'solved the structure'. No idea how the Norothrop & Kunitz ref went so wrong though.

• A minor nitpick, but I personally prefer to use "hydroxyl" rather than "alcohol" for the functional group; I think it creates less confusion.

 Done You're right, and the wikilink goes through to hydroxyl anyway. I just really dislike the matching 'sulfhydryl', but I suspect it won't matter mixing thiol and hydroxyl.

Ha, I do this all the time and hadn't really thought about the parallelism fail :) Opabinia regalis (talk) 06:02, 10 July 2015 (UTC)

• Most of the text in the acid subsection is about various circumstances in which there is no acid.

 Done I've added some more detail on why Glu and Asp are the most common residues for this, to balance out the 'exceptions to the rule' examples.

• "Possibly low-barrier hydrogen bond" - it would be interesting to see a bit more detail on this dispute (which I take it is not resolved)

 Started Every time I think I'm getting to grips with this, the controversy turns out to be deeper and more complicated! I'll try to write a couple of sentences of summary and maybe update the LBHB page.

Oh good, then I will just read your summary and consider myself up to speed because I have completely lost track of this issue ;) Better than a review article! Opabinia regalis (talk) 07:58, 27 July 2015 (UTC)

 Done Ok, I've put together 4 references for the history section since the consensus (largely driven by Arieh Warshel) seems to be pretty definitively against it since the new millenium. I may put a more detailed description in the LBHB article, since it's probably not useful here.

Cool, nice work! I figured Warshel would be involved :) Opabinia regalis (talk) 19:37, 10 August 2015 (UTC)

• Kind of a hard problem to solve, but the description of the mechanism in words under Ser-His-Asp is definitely going to be hard to follow without a mechanism drawing like what's currently in the comparison section below. But there's enough text in between that even on my ginormous monitor I can't look at them both at once without opening a new window.

 Started I'm fixing this in a couple of ways. Firstly, I've moved a lot of the mechanism details to a dedicated function/mechanism section. Secondly, I'll make a clearer mechanism diagram to go in that section.

 Done Finally done a mechanism diagram. It's as general as I can make it so that it's not specific to protease, or even hydrolase/transferase.

• Maybe highlight in a different color the relevant functional group for each example in the figure?
• "The chirality is reversed" - some confused premed is going to write on his exam that lipases have D-amino acids in them.

 Done Fixed to 'orientation of the triad members'

• You give the MEROPS classifications for proteases as you name them, but anyone who's decided to consult wikipedia about biochemistry has no idea what they mean and they're kind of obtrusive in short paragraphs (eg the cys-his-asp section). Maybe put them in endnotes?

 Done Definitely sensible. I've gone through and replaced with {{efn}} notes. I've also made {{MEROPS}} to link them out (e.g. {{MEROPS|clan=PA|fam=S1}} → MEROPS: clan PA, family S1.

• "Nucleophilic enzymes..." - are enzymes whose mechanisms involve nucleophiles described as "nucleophilic"?

 Done I think you already fixed this, but you're right, no one really says a "nucleophilic enzyme".

• "Here I concentrate on..." - this isn't a review paper :) This whole section reads as a bit too technical.

 Done I've split up this section so that its integrated into the simpler information in the rest of the article. I think I was just keeping it together since that's the way I'd originally written it.

• There's some repetition in the convergent evolution section.

 Done Fixed!

• There's a lot of references to the oxyanion hole but neither article has a picture of one the way it's usually depicted in textbooks; eg. this or this one.

 Done I've added one of the images you suggested into the oxyanion hole article, and largely rewritten it (though it's still a stub). I found some nice references at least.

• For interesting non-proteases, sinapoyltransferases/plant SCPLs come to mind. I don't know of a case where the catalytic triad occurs in a non-protease that doesn't have obvious protease ancestry.

 No action I've read up a bit on these guys. Since they're not yet on wikipedia, and their reactions are not trivial to describe, I'll leave them for now. I've added in a few other interesting non-protease examples though.

Opabinia regalis (talk) 00:54, 2 July 2015 (UTC)

@Opabinia regalis: Thank you for your detailed read-through, it's really helpful to have someone else cast their eye over the article. I'll tick off your points above as I go through correcting the article. T.Shafee(Evo﹠Evo)^talk 12:02, 2 July 2015 (UTC)

You know, I just noticed you'd already nominated it for GA. I should've just done an official review given the insane backlog over there. Sorry. But all those checkboxes and cutesy graphics give me a headache. Opabinia regalis (talk) 21:36, 2 July 2015 (UTC)

References

GA Review

This review is transcluded from Talk:Catalytic triad/GA1. The edit link for this section can be used to add comments to the review.

Reviewer: Stigmatella aurantiaca (talk · contribs) 22:40, 10 August 2015 (UTC)

Beginning review. I will be adding my comments over the next few days. Stigmatella aurantiaca (talk) 22:40, 10 August 2015 (UTC)

Passes copyvio test Earwig's Copyvio Detector Stigmatella aurantiaca (talk) 22:50, 10 August 2015 (UTC)

History

• "A serine in each of trypsin and chymotrypsin was identified as one the catalytic nucleophile (by diisopropyl fluorophosphate modification) in the 1950s." (Unclear phrase: "as one the catalytic nucleophile")
• "The structure of chymotrypsin was solved in the 1960s" (Using X-ray crystallography, of course.)
• "The MEROPS classification system in the 1990s and 2000s started to class proteases into structurally related enzyme superfamilies" ("Started to class"? They don't any longer? Why the past tense?)

 Done T.Shafee(Evo﹠Evo)^talk 10:53, 17 August 2015 (UTC)

Function

• "Enzymes that contain an catalytic triad use it for one of two reaction types: either to split a substrate (hydrolases) or transfer one portion of a substrate over to a second substrate (transferases)." (Defective sentence parallel structure. Should be "or to transfer")
• "They occur as an inter-dependent set of residues" (Unclear pronoun antecedent. Does the word "They" refer back to "Enzymes", "catalytic triad", "substrate" or what? Replace with "Catalytic triads".)
• "Catalysis occurs because the triad residues act together" (Verbose. Suggest "The triad residues act together")

 Done T.Shafee(Evo﹠Evo)^talk 10:57, 17 August 2015 (UTC)

Mechanism

• "In order to generate a nucleophilic enough residue for catalysis, the functional groups of the other triad members are used to increase its reactivity." (Reword in non-teleological terms. Avoid using words suggesting "purpose" or "design". For example, suggest "The reactivity of this nucleophilic residue is increased by the functional groups of the other triad members" or some other such wording.)
• "If this substrate is water then the result is hydrolysis, if it is an organic molecule then the result is transfer of that molecule" (Run-on sentence. Use a semicolon or period rather than a comma.)

Stigmatella aurantiaca (talk) 11:18, 11 August 2015 (UTC)

 Done Well spotted. I'd not noticed how teleological the writing sounded. T.Shafee(Evo﹠Evo)^talk 11:03, 17 August 2015 (UTC)

Noticed by the peer review tool

• Please make the spelling of English words consistent with either American or British spelling, depending upon the subject of the article. Examples include: honor (A) (British: honour), ization (A) (British: isation), isation (B) (American: ization), catalyse (B) (American: catalyze), hydrolyse (B) (American: hydrolyze), sulphur (B) (American: sulfur).
• Add a "British English" template to the Talk page if British English is your intention. There are some online spell checkers that you can use. It won't necessarily be possible to stamp out 100% of the mixed usages (eg. in quotes, wikilinks, references), but you should try.

Stigmatella aurantiaca (talk) 11:41, 11 August 2015 (UTC)

 Done I've added the template. T.Shafee(Evo﹠Evo)^talk 12:47, 17 August 2015 (UTC)

Nucleophile

• "The lone pair of electrons present on the oxygen or sulphur attack the electropositive carbonyl carbon." (Number agreement. "The lone pair...attacks" not "attack".)
• "Embedding the nucleophile in a triad is necessary to increase its reactivity for efficient catalysis." (Avoid teleological language. "Embedding the nucleophile in a triad increases its reactivity for efficient catalysis.")
• "Alternatively, threonine proteases use the secondary hydroxyl of threonine, however such proteases have to use their N-terminal amide as the base, rather than a separate amino acid, due to steric hindrance of the extra methyl group."

1. Telelogical language
2. Steric hindrance of which extra methyl group? I presume you mean that of threonine.

• "Serine is therefore more dependent on other residues to reduce its pKa for concerted deprotonation with catalysis by optimal orientation of the acid-base triad members" (Unclear run-on sentence. Do you mean that the constraints on orientation of the other triad members are more stringent than with other amino acids?)
• "Sterically, the sulphur of cysteine also has longer bonds and a bulkier Van der Waals radius to fit in the active site" (Do you mean that it is less able to fit in the active site?)
• "and a mutated nucleophile can be trapped in unproductive orientations" (I presume that you mean that experimental replacement of cysteine with other nucleophiles results in trapping of the mutated nucleophile in unproductive orientations. This is not clear.)

Stigmatella aurantiaca (talk) 22:20, 11 August 2015 (UTC)

 Done T.Shafee(Evo﹠Evo)^talk 10:21, 18 August 2015 (UTC)

Base

• "Since no natural amino acids are strongly nucleophilic, the base in a catalytic triad polarises and deprotonates the nucleophile to increase its reactivity." (Teleological language. Try something like "No natural amino acids are strongly nucleophilic. The base in a catalytic triad polarises and deprotonates the nucleophile, increasing its reactivity.")
• "It is most commonly histidine since its pKa allows for effective base catalysis as well as both hydrogen bonding to the acid residue and deprotonating the nucleophile residue." (Unclear pronoun antecedent. What is "It"? Sentence parallel structure is a bit messed up. Try something like "The base is most commonly histidine since its pKa allows for effective base catalysis, hydrogen bonding to the acid residue, and deprotonation of the nucleophile residue.")
• "In order to avoid steric clashes, threonine proteases use their N-terminal amide as the base, to increase the reactivity of the catalytic threonine residue." (Teleological language)

Stigmatella aurantiaca (talk) 22:32, 11 August 2015 (UTC)

 Done T.Shafee(Evo﹠Evo)^talk 10:32, 18 August 2015 (UTC)

Acid

• "Cytomegalovirus proteases uses a pair of histidines" (Number agreement. Proteases use, not uses.)

Stigmatella aurantiaca (talk) 22:41, 11 August 2015 (UTC)

 Done T.Shafee(Evo﹠Evo)^talk 11:33, 19 August 2015 (UTC)

Examples of triads

• "This allows the histidine to act as a powerful general base and activate the serine nucleophile." (Parallel structure. "and to activate".
• "It also has an oxanion hole consisting of several backbone amides for stabilising charge build-up on intermediates." (Teleological language. Try "which stabilises")
• "Removing the acid histidine only results in a 10-fold activity loss" ("results in only a 10-fold activity loss" rather than "only results in a 10-fold activity loss", which would imply that the activity loss is the only effect. Unless you really mean that that is the only outcome, of course.)
• "This triad has been interpreted as a possible way of generating a less active enzyme to control cleavage rate." (OK, I'll allow this. It isn't your teleological interpretation, but the interpretation of Ekici et al.)
• "The middle serine then forms two strong hydrogen bonds to he nucleophilic serine" ("to he" -> "to the" or "with the")
• "The triad is further unusual in that the lysine and cis-serine both act as the base in activating the catalytic serine but the same lysine also performs the role of the acid member as well as making key structural contacts." (Use a comma before the "but" since it separates two independent clauses. The rules on commas can be a bit complicated.)

Stigmatella aurantiaca (talk) 11:00, 12 August 2015 (UTC)

 Done T.Shafee(Evo﹠Evo)^talk 11:33, 19 August 2015 (UTC)

Divergent evolution

• "Additionally, an alternative transferase mechanism has been evolved by amidophosphoribosyltransferases in which the catalytic cysteine of one domain hydrolyses a glutamine substrate to release free ammonia, which diffuses though an internal tunnel in the enzyme to a second active site, where the ammonia is transferred to a second substrate." (Excessively long sentence)
• "Despite chemical differences between the possible triad nucleophiles, some protease superfamilies have evolved from one nucleophile to another through divergent evolution." (Initial clause seems superfluous. Try "Some protease superfamilies have evolved from one nucleophile to another through divergent evolution" or similar wording.)

 Done Split the first mega-sentence into three, and have also clarified significance 'Despite chemical differences' in separate sentence. T.Shafee(Evo﹠Evo)^talk 11:46, 19 August 2015 (UTC)

Convergent evolution

• "leading evolution to independently converge on equivalent solutions repeatedly." (Most modern English usage guides have dropped the objection to the split infinitive, but this is an especially bad example. Try "leading evolution repeatedly and independently to converge on equivalent solutions.")
• "Similarly, the same has occurred with cysteine proteases such as viral C3 protease and papain[c] superfamilies." (Try "Similar convergent evolution has occurred...")
• "Consequently, most threonine proteases use an N-terminal threonine in order to avoid such steric clashes" (Teleological phrasing)
• "Two evolutionarily independent enzyme superfamilies with different protein folds are known to use the N-terminal residue as a nucleophile; Superfamily PB (proteasomes using the Ntn fold) and Superfamily PE (acetyltransferases using the DOM fold)" (Use full colon instead of semicolon)

Stigmatella aurantiaca (talk) 03:54, 14 August 2015 (UTC)

 Done T.Shafee(Evo﹠Evo)^talk 12:00, 19 August 2015 (UTC)

Response

@Stigmatella aurantiaca: Thank you for a thorough read of the article. I've gone through an addressed the points you raised (almost always using your suggested wording). In particular, thank you for pointing out how teleological some of my writing has been. I'm going to take greater care in future to catch myself. T.Shafee(Evo﹠Evo)^talk 12:03, 19 August 2015 (UTC)

You're welcome! I really enjoyed this article. It's been twenty years since I last taught a biochemistry class, and it is always amazing to me to see the progress in this science! Stigmatella aurantiaca (talk) 16:10, 19 August 2015 (UTC)