Talk:Ligase

Difference from Transferases

The reaction presented:

Ab + C → A–C + b

Seems not much different from the one corresponding to transferase

A–X + B → A + B–X

especially if rename the participants:

B–A + C → B + C–A

The distinction between the two classes likely should be highlighted, given the similarity in the presented mechanisms. I can somewhat get the impression that the difference between the two classes is the size/importance of the transferred group, but from the current phrasing I wouldn't be sure of it. Nor would I know at what size group would a ligase become a transferase, nor if the group size is the only difference between the two groups of enzymes. -- 140.142.20.229 (talk) 19:41, 22 November 2010 (UTC)

According to IUBMB Commission on enzyme nomenclature, EC 6 Ligase constitutes the following:

"EC6 Ligases: Ligases are enzymes that catalyse the joining of two molecules with concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. 'Ligase' is commonly used for the common name, but, in a few cases, 'synthase' or 'carboxylase' is used. 'Synthetase' may be used in place of 'synthase' for enzymes in this class."

Synthases that do not require ATP hydrolysis catalyse the reverse of the lyase reaction, and belong in EC 4 and are not ligases. At one time this was clearly distinguished by the difference in name 'synthase' and 'synthetase', but too many exceptions have crept in to the literature.

"EC 4. Lyases

Lyases are enzymes cleaving C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring. The systematic name is formed according to 'substrate group-lyase'. In common names, expressions like decarboxylase, aldolase, etc. are used. 'Dehydratase' is used for those enzymes eliminating water. In cases where the reverse reaction is the more important, or the only one to be demonstrated, 'synthase' may be used in the name."

In general, ligase reactions are reversed hydrolysis reactions. Since hydrolysis is almost invariably thermodynamically favourable, an energy source is needed for the reversal. The reaction represented below is trying to be too generic to the point of causing confusion.

Ab + C → A–C + b

A better version would be:

A-OH + B-H + ATP → A-B + ADP + Pi or A-OH + B-H + ATP → A-B + AMP + PPi

The H2O formed in the ligase reaction is consumed by the hydrolysis of ATP. 96.54.32.44 (talk) 19:55, 17 February 2011 (UTC)

Wiki Education assignment: CHEM 300

This article was the subject of a Wiki Education Foundation–supported course assignment, between 9 January 2023 and 28 April 2023. Further details are available on the course page. Student editor(s): Re332168 (article contribs). Peer reviewers: Dasiomo. (UTC)

— Assignment last updated by RS UBC800 (talk) 21:05, 2 April 2023 (UTC)

- The introductory section with the general reactions are confusing, particularly the 2nd one with the lowercase letters appearing out of nowhere: "Ab + cD → A–D + b + c + d + e + f where the lowercase letters can signify the small, dependent groups". I think bringing in an example of an actual reaction catalyzed by ligase may illustrate this better. - The nomenclature section seems irrelevant, particularly the 2nd paragraph describing the difference between synthase, synthetase, lyase. Ligase enzymes classified as EC 6 come in various names including synth(et)ase and carboxylase, so that should be clarified, but the focus on synthase vs. synthetase and comparison to lyase should be removed since that doesn't have to do with ligases. - There is an uncited source in the references and the other 2 lead to archived sites. I want to try to update them and find more sources. — Preceding unsigned comment added by Re332168 (talk • contribs) 02:14, 3 April 2023 (UTC)