{"action":"created","issue":{"url":"https://api.github.com/repos/geneontology/go-ontology/issues/15051","repository_url":"https://api.github.com/repos/geneontology/go-ontology","labels_url":"https://api.github.com/repos/geneontology/go-ontology/issues/15051/labels{/name}","comments_url":"https://api.github.com/repos/geneontology/go-ontology/issues/15051/comments","events_url":"https://api.github.com/repos/geneontology/go-ontology/issues/15051/events","html_url":"https://github.com/geneontology/go-ontology/issues/15051","id":295076341,"number":15051,"title":"Review parentage of \"malonyl-CoA synthetase activity\"","user":{"login":"sjm41","id":16306861,"avatar_url":"https://avatars2.githubusercontent.com/u/16306861?v=4","gravatar_id":"","url":"https://api.github.com/users/sjm41","html_url":"https://github.com/sjm41","followers_url":"https://api.github.com/users/sjm41/followers","following_url":"https://api.github.com/users/sjm41/following{/other_user}","gists_url":"https://api.github.com/users/sjm41/gists{/gist_id}","starred_url":"https://api.github.com/users/sjm41/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sjm41/subscriptions","organizations_url":"https://api.github.com/users/sjm41/orgs","repos_url":"https://api.github.com/users/sjm41/repos","events_url":"https://api.github.com/users/sjm41/events{/privacy}","received_events_url":"https://api.github.com/users/sjm41/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"ukemi","id":11067494,"avatar_url":"https://avatars3.githubusercontent.com/u/11067494?v=4","gravatar_id":"","url":"https://api.github.com/users/ukemi","html_url":"https://github.com/ukemi","followers_url":"https://api.github.com/users/ukemi/followers","following_url":"https://api.github.com/users/ukemi/following{/other_user}","gists_url":"https://api.github.com/users/ukemi/gists{/gist_id}","starred_url":"https://api.github.com/users/ukemi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ukemi/subscriptions","organizations_url":"https://api.github.com/users/ukemi/orgs","repos_url":"https://api.github.com/users/ukemi/repos","events_url":"https://api.github.com/users/ukemi/events{/privacy}","received_events_url":"https://api.github.com/users/ukemi/received_events","type":"User","site_admin":false},"assignees":[{"login":"ukemi","id":11067494,"avatar_url":"https://avatars3.githubusercontent.com/u/11067494?v=4","gravatar_id":"","url":"https://api.github.com/users/ukemi","html_url":"https://github.com/ukemi","followers_url":"https://api.github.com/users/ukemi/followers","following_url":"https://api.github.com/users/ukemi/following{/other_user}","gists_url":"https://api.github.com/users/ukemi/gists{/gist_id}","starred_url":"https://api.github.com/users/ukemi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ukemi/subscriptions","organizations_url":"https://api.github.com/users/ukemi/orgs","repos_url":"https://api.github.com/users/ukemi/repos","events_url":"https://api.github.com/users/ukemi/events{/privacy}","received_events_url":"https://api.github.com/users/ukemi/received_events","type":"User","site_admin":false}],"milestone":null,"comments":5,"created_at":"2018-02-07T10:07:15Z","updated_at":"2018-02-08T14:36:06Z","closed_at":null,"author_association":"NONE","body":"I think \"malonyl-CoA synthetase activity\" GO:0090409 should (also) be a child of \"CoA-ligase activity\" (GO:0016405).\r\n\r\n **GO:0090409 - malonyl-CoA synthetase activity**\r\n Catalysis of the reaction: malonate + ATP + coenzyme A = malonyl-CoA + AMP + diphosphate. \r\n\r\n **GO:0016405 - CoA-ligase activity**\r\nCatalysis of the reaction: substrate + ATP + CoASH = AMP + diphosphate + substrate-CoA."},"comment":{"url":"https://api.github.com/repos/geneontology/go-ontology/issues/comments/364130178","html_url":"https://github.com/geneontology/go-ontology/issues/15051#issuecomment-364130178","issue_url":"https://api.github.com/repos/geneontology/go-ontology/issues/15051","id":364130178,"user":{"login":"deustp01","id":12737623,"avatar_url":"https://avatars2.githubusercontent.com/u/12737623?v=4","gravatar_id":"","url":"https://api.github.com/users/deustp01","html_url":"https://github.com/deustp01","followers_url":"https://api.github.com/users/deustp01/followers","following_url":"https://api.github.com/users/deustp01/following{/other_user}","gists_url":"https://api.github.com/users/deustp01/gists{/gist_id}","starred_url":"https://api.github.com/users/deustp01/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/deustp01/subscriptions","organizations_url":"https://api.github.com/users/deustp01/orgs","repos_url":"https://api.github.com/users/deustp01/repos","events_url":"https://api.github.com/users/deustp01/events{/privacy}","received_events_url":"https://api.github.com/users/deustp01/received_events","type":"User","site_admin":false},"created_at":"2018-02-08T14:36:06Z","updated_at":"2018-02-08T14:36:06Z","author_association":"NONE","body":"@ukemi according to the authorities, \"Ligases are enzymes that catalyze the joining of two molecules or two parts of a molecule with concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. Ligase is often used for the common name but in a few cases synthase[sic*] or carboxylase is used. Synthetase may be used in place of synthase for enzymes in this class.\" (http://www.brenda-enzymes.org/ecexplorer.php?browser=1&f[nodes]=&f[action]=open&f[change]=286 - mouse over a class name to see a tooltip with its definition)\r\n*My Ochoa trained colleagues disagree - synthetase is correct; synthase is not - the latter term should be reserved for bond formation not accompanied by nucleotide triphosphate hydrolysis.\r\nI guess that cleavage of ATP to AMP + PPi fits this definition, as well as cleavage to ADP + Pi.\r\nThe general dictionary definition of \"ligase\" deviates from this. I think we go with the biochemists here (ignoring the syn(the)tase issue and ignore the general, which is (Wikipedia):\r\n\r\n> In biochemistry, a ligase is an enzyme that can catalyze the joining of two large molecules by forming a new chemical bond, usually with accompanying hydrolysis of a small pendant chemical group on one of the larger molecules or the enzyme catalyzing the linking together of two compounds, e.g., enzymes that catalyze joining of C-O, C-S, C-N, etc. In general, a ligase catalyzes the following reaction:\r\n\r\n    Ab + C → A–C + b\r\n\r\nor sometimes\r\n\r\n    Ab + cD → A–D + b + c + d + e + f\r\n\r\nwhere the lowercase letters signify the small, dependent groups. Ligase can join two complementary fragments of nucleic acid and repair single stranded breaks that arise in double stranded DNA during replication.\r\n"}}
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