Skip to content

Contributor submission DynA #162

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
mite-bot wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Contributor submission DynA #162

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
67 changes: 67 additions & 0 deletions mite_data/data/3e1f2498-e4a0-11f0-b8d3-8218ec668ab3.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,67 @@
{
"accession": "MITE9999999",
"status": "pending",
"comment": "Cleavage of precursor peptide to mature dynobactin A by an unclustered (likely generic) protease.",
"changelog": [
{
"version": "1",
"date": "2025-12-29",
"contributors": [
"AAAAAAAAAAAAAAAAAAAAAAAA"
],
"reviewers": [
"BBBBBBBBBBBBBBBBBBBBBBBB"
],
"comment": "New entry."
}
],
"enzyme": {
"name": "DynA",
"description": "Radical SAM enzyme",
"references": [
"doi:10.1021/jacs.4c10425",
"doi:10.31635/ccschem.024.202404983"
],
"databaseIds": {
"uniprot": "A0A1C0U7F5",
"genpept": "OCQ53858.1"
},
"cofactors": {
"organic": [
"SAM"
],
"inorganic": [
"FeS"
]
}
},
"reactions": [
{
"tailoring": [
"Cyclization"
],
"description": "Macrocyclization of DynB precursor peptide. Available information indicates that full leader peptide is required for substrate recognition.",
"reactionSMARTS": "[#6:1]-[#6:2]-[#6:3](-[#6:5](-[#6:146](-[#7:148]-[#6:149](-[#6:154](-[#7:156]-[#6:157](-[#6:160](-[#7:162]-[#6:163](-[#6:469](-[#6:471])-[#6:470])-[#6:164](-[#7:166]-[#6:167]-[#6:168](-[#7:170]-[#6:171](-[#6:177](-[#7:179]-[#6:180](-[#6:186](-[#7:188]-[#6:189](-[#6:192](-[#7:194]-[#6:195](-[#6:200](-[#7:202]-[#6:203](-[#6:206](-[#7:208]-[#6:209](-[#6:214](-[#7:216]-[#6:217](-[#6:223](-[#7:225]-[#6:226]-[#6:227](-[#7:229]-[#6:230](-[#6:236](-[#7:238]1-[#6:242](-[#6:243](-[#7:245]-[#6:246](-[#6:465](-[#6:467]-[#6:468])-[#6:466])-[#6:247](-[#7:249]-[#6:250](-[#6:258](-[#7:260]-[#6:261](-[#6:264](-[#7:266]-[#6:267](-[#6:272](-[#7:274]-[#6:275](-[#6:281](-[#7:283]-[#6:284](-[#6:462](-[#6:464])-[#6:463])-[#6:285](-[#7:287]-[#6:288](-[#6:294](-[#7:296]-[#6:297](-[#6:303](-[#7:305]-[#6:306](-[#6:311](-[#7:313]-[#6:314](-[#6:459](-[#6:461])-[#6:460])-[#6:315](-[#7:317]-[#6:318](-[#6:324](-[#7:326]-[#6:327](-[#6:330](-[#7:332]-[#6:333](-[#6:335](-[#7:337]-[#6:338](-[#6:456](-[#8:458])-[#6:457])-[#6:339](-[#7:341]-[#6:342](-[#6:452](-[#6:454]-[#6:455])-[#6:453])-[#6:343](-[#7:345]2-[#6:349](-[#6:350](-[#7:352]-[#6:353](-[#6:356](-[#7:358]-[#6:359](-[#6:370](-[#7:372]-[#6:373](-[#6:378](-[#7:380]-[#6:381](-[#6:384](-[#7:386]-[#6:387](-[#6:392](-[#7:394]-[#6:395](-[#6:449](-[#6:451])-[#6:450])-[#6:396](-[#7:398]-[#6:399](-[#6:406](-[#7:408]-[#6:409](-[#6:412](-[#7:414]-[#6:415](-[#6:424](-[#7:426]-[#6:427](-[#6:435](-[#7:437]-[#6:438](-[#6:446](-[#8:448])=[#8:447])-[#6:439]-[#6:440]3:[#6:445]:[#6:444]:[#6:443]:[#6:442]:[#6:441]:3)=[#8:436])-[#6:428]-[#6:429]-[#6:430]-[#7:431]-[#6:432](-[#7:434])=[#7:433])=[#8:425])-[#6:416]-[#6:417]3:[#6:423]:[#6:422]:[#6:420](-[#8:421]):[#6:419]:[#6:418]:3)=[#8:413])-[#6:410]-[#8:411])=[#8:407])-[#6:400]-[#6:401]3:[#7:405]:[#6:404]:[#7:403]:[#6:402]:3)=[#8:397])=[#8:393])-[#6:388]-[#6:389](=[#8:391])-[#7:390])=[#8:385])-[#6:382]-[#8:383])=[#8:379])-[#6:374]-[#6:375](=[#8:377])-[#7:376])=[#8:371])-[#6:360]-[#6:361]3:[#6:369]4:[#6:364](:[#6:365]:[#6:366]:[#6:367]:[#6:368]:4):[#7:363]:[#6:362]:3)=[#8:357])-[#6:354]-[#8:355])=[#8:351])-[#6:348]-[#6:347]-[#6:346]-2)=[#8:344])=[#8:340])=[#8:336])-[#6:334])=[#8:331])-[#6:328]-[#8:329])=[#8:325])-[#6:319]-[#6:320]-[#6:321](=[#8:323])-[#7:322])=[#8:316])=[#8:312])-[#6:307]-[#6:308](-[#6:310])-[#6:309])=[#8:304])-[#6:298]-[#6:299]-[#6:300]-[#6:301]-[#7:302])=[#8:295])-[#6:289]-[#6:290]-[#6:291](-[#8:293])=[#8:292])=[#8:286])=[#8:282])-[#6:276]-[#6:277]-[#6:278]-[#6:279]-[#7:280])=[#8:273])-[#6:268]-[#6:269](=[#8:271])-[#7:270])=[#8:265])-[#6:262]-[#8:263])=[#8:259])-[#6:251]-[#6:252]-[#6:253]-[#7:254]-[#6:255](-[#7:257])=[#7:256])=[#8:248])=[#8:244])-[#6:241]-[#6:240]-[#6:239]-1)=[#8:237])-[#6:231]-[#6:232]-[#6:233]-[#6:234]-[#7:235])=[#8:228])=[#8:224])-[#6:218]-[#6:219]-[#6:220](=[#8:222])-[#7:221])=[#8:215])-[#6:210]-[#6:211](-[#6:213])-[#6:212])=[#8:207])-[#6:204]-[#8:205])=[#8:201])-[#6:196]-[#6:197](=[#8:199])-[#7:198])=[#8:193])-[#6:190]-[#8:191])=[#8:187])-[#6:181]-[#6:182]-[#6:183]-[#6:184]-[#7:185])=[#8:178])-[#6:172]-[#6:173]-[#6:174]-[#6:175]-[#7:176])=[#8:169])=[#8:165])=[#8:161])-[#6:158]-[#16:159])=[#8:155])-[#6:150]-[#6:151](-[#8:153])=[#8:152])=[#8:147])-[#7:6]-[#6:7](-[#6:9](-[#7:14]-[#6:15](-[#6:17](-[#7:19]-[#6:20](-[#6:22](-[#7:28]-[#6:29](-[#6:31](-[#7:36]-[#6:37](-[#6:39](-[#7:50]-[#6:51](-[#6:53](-[#6:143](-[#8:145])-[#6:144])-[#7:54]-[#6:55](-[#6:57](-[#7:63]-[#6:64](-[#6:66](-[#7:71]-[#6:72](-[#6:74](-[#7:80]-[#6:81](-[#6:83](-[#7:86]-[#6:87](-[#6:89]1-[#7:93](-[#6:94](-[#6:96](-[#7:102]-[#6:103](-[#6:105](-[#7:108]-[#6:109](-[#6:111](-[#7:116]-[#6:117](-[#6:119](-[#7:125]-[#6:126](-[#6:128](-[#7:134]-[#6:135](-[#6:137](-[#6:139]-[#6:140]-[#16:141]-[#6:142])-[#7:138])=[#8:136])-[#6:129]-[#6:130]-[#6:131]-[#6:132]-[#7:133])=[#8:127])-[#6:120]-[#6:121]-[#6:122]-[#6:123]-[#7:124])=[#8:118])-[#6:112]-[#6:113](-[#6:115])-[#6:114])=[#8:110])-[#6:106]-[#8:107])=[#8:104])-[#6:97]-[#6:98]-[#6:99]-[#6:100]-[#7:101])=[#8:95])-[#6:92]-[#6:91]-[#6:90]-1)=[#8:88])-[#6:84]-[#8:85])=[#8:82])-[#6:75]-[#6:76]-[#6:77](=[#8:79])-[#7:78])=[#8:73])-[#6:67]-[#6:68](=[#8:70])-[#7:69])=[#8:65])-[#6:58]-[#6:59]-[#6:60]-[#6:61]-[#7:62])=[#8:56])=[#8:52])-[#6:40]-[#6:41]1:[#6:49]2:[#6:44](:[#6:45]:[#6:46]:[#6:47]:[#6:48]:2):[#7:43]:[#6:42]:1)=[#8:38])-[#6:32]-[#6:33](=[#8:35])-[#7:34])=[#8:30])-[#6:23]-[#6:24]-[#6:25]-[#6:26]-[#7:27])=[#8:21])-[#6:18])=[#8:16])-[#6:10]-[#6:11](-[#6:13])-[#6:12])=[#8:8])-[#6:4]>>[#6:1]-[#6:2]-[#6:3](-[#6:5](-[#6:146](-[#7:148]-[#6:149](-[#6:154](-[#7:156]-[#6:157](-[#6:160](-[#7:162]-[#6:163](-[#6:469](-[#6:471])-[#6:470])-[#6:164](-[#7:166]-[#6:167]-[#6:168](-[#7:170]-[#6:171](-[#6:177](-[#7:179]-[#6:180](-[#6:186](-[#7:188]-[#6:189](-[#6:192](-[#7:194]-[#6:195](-[#6:200](-[#7:202]-[#6:203](-[#6:206](-[#7:208]-[#6:209](-[#6:214](-[#7:216]-[#6:217](-[#6:223](-[#7:225]-[#6:226]-[#6:227](-[#7:229]-[#6:230](-[#6:236](-[#7:238]1-[#6:242](-[#6:243](-[#7:245]-[#6:246](-[#6:465](-[#6:467]-[#6:468])-[#6:466])-[#6:247](-[#7:249]-[#6:250](-[#6:258](-[#7:260]-[#6:261](-[#6:264](-[#7:266]-[#6:267](-[#6:272](-[#7:274]-[#6:275](-[#6:281](-[#7:283]-[#6:284](-[#6:462](-[#6:464])-[#6:463])-[#6:285](-[#7:287]-[#6:288](-[#6:294](-[#7:296]-[#6:297](-[#6:303](-[#7:305]-[#6:306](-[#6:311](-[#7:313]-[#6:314](-[#6:459](-[#6:461])-[#6:460])-[#6:315](-[#7:317]-[#6:318](-[#6:324](-[#7:326]-[#6:327](-[#6:330](-[#7:332]-[#6:333](-[#6:335](-[#7:337]-[#6:338](-[#6:456](-[#8:458])-[#6:457])-[#6:339](-[#7:341]-[#6:342](-[#6:452](-[#6:454]-[#6:455])-[#6:453])-[#6:343](-[#7:345]2-[#6:349](-[#6:350](-[#7:352]-[#6:353](-[#6:356](-[#7:358]-[#6:359]3-[#6:370](-[#7:372]-[#6:373](-[#6:378](-[#7:380]-[#6:381](-[#6:384](-[#7:386]-[#6:387](-[#6:392](-[#7:394]-[#6:395](-[#6:449](-[#6:451])-[#6:450])-[#6:396](-[#7:398]-[#6:399]4-[#6:406](-[#7:408]-[#6:409](-[#6:412](-[#7:414]-[#6:415](-[#6:424](-[#7:426]-[#6:427](-[#6:435](-[#7:437]-[#6:438](-[#6:446](-[#8:448])=[#8:447])-[#6:439]-[#6:440]5:[#6:441]:[#6:442]:[#6:443]:[#6:444]:[#6:445]:5)=[#8:436])-[#6:428]-[#6:429]-[#6:430]-[#7:431]-[#6:432](-[#7:434])=[#7:433])=[#8:425])-[#6:416](-[#7:403]5:[#6:404]:[#7:405]:[#6:401](:[#6:402]:5)-[#6:400]-4)-[#6:417]4:[#6:423]:[#6:422]:[#6:420](-[#8:421]):[#6:419]:[#6:418]:4)=[#8:413])-[#6:410]-[#8:411])=[#8:407])=[#8:397])=[#8:393])-[#6:388](-[#6:366]4:[#6:367]:[#6:368]:[#6:369]5:[#6:364](:[#6:365]:4):[#7:363]:[#6:362]:[#6:361]:5-[#6:360]-3)-[#6:389](=[#8:391])-[#7:390])=[#8:385])-[#6:382]-[#8:383])=[#8:379])-[#6:374]-[#6:375](=[#8:377])-[#7:376])=[#8:371])=[#8:357])-[#6:354]-[#8:355])=[#8:351])-[#6:348]-[#6:347]-[#6:346]-2)=[#8:344])=[#8:340])=[#8:336])-[#6:334])=[#8:331])-[#6:328]-[#8:329])=[#8:325])-[#6:319]-[#6:320]-[#6:321](=[#8:323])-[#7:322])=[#8:316])=[#8:312])-[#6:307]-[#6:308](-[#6:309])-[#6:310])=[#8:304])-[#6:298]-[#6:299]-[#6:300]-[#6:301]-[#7:302])=[#8:295])-[#6:289]-[#6:290]-[#6:291](-[#8:293])=[#8:292])=[#8:286])=[#8:282])-[#6:276]-[#6:277]-[#6:278]-[#6:279]-[#7:280])=[#8:273])-[#6:268]-[#6:269](=[#8:271])-[#7:270])=[#8:265])-[#6:262]-[#8:263])=[#8:259])-[#6:251]-[#6:252]-[#6:253]-[#7:254]-[#6:255](-[#7:257])=[#7:256])=[#8:248])=[#8:244])-[#6:241]-[#6:240]-[#6:239]-1)=[#8:237])-[#6:231]-[#6:232]-[#6:233]-[#6:234]-[#7:235])=[#8:228])=[#8:224])-[#6:218]-[#6:219]-[#6:220](=[#8:222])-[#7:221])=[#8:215])-[#6:210]-[#6:211](-[#6:212])-[#6:213])=[#8:207])-[#6:204]-[#8:205])=[#8:201])-[#6:196]-[#6:197](=[#8:199])-[#7:198])=[#8:193])-[#6:190]-[#8:191])=[#8:187])-[#6:181]-[#6:182]-[#6:183]-[#6:184]-[#7:185])=[#8:178])-[#6:172]-[#6:173]-[#6:174]-[#6:175]-[#7:176])=[#8:169])=[#8:165])=[#8:161])-[#6:158]-[#16:159])=[#8:155])-[#6:150]-[#6:151](-[#8:153])=[#8:152])=[#8:147])-[#7:6]-[#6:7](-[#6:9](-[#7:14]-[#6:15](-[#6:17](-[#7:19]-[#6:20](-[#6:22](-[#7:28]-[#6:29](-[#6:31](-[#7:36]-[#6:37](-[#6:39](-[#7:50]-[#6:51](-[#6:53](-[#6:143](-[#8:145])-[#6:144])-[#7:54]-[#6:55](-[#6:57](-[#7:63]-[#6:64](-[#6:66](-[#7:71]-[#6:72](-[#6:74](-[#7:80]-[#6:81](-[#6:83](-[#7:86]-[#6:87](-[#6:89]1-[#7:93](-[#6:94](-[#6:96](-[#7:102]-[#6:103](-[#6:105](-[#7:108]-[#6:109](-[#6:111](-[#7:116]-[#6:117](-[#6:119](-[#7:125]-[#6:126](-[#6:128](-[#7:134]-[#6:135](-[#6:137](-[#6:139]-[#6:140]-[#16:141]-[#6:142])-[#7:138])=[#8:136])-[#6:129]-[#6:130]-[#6:131]-[#6:132]-[#7:133])=[#8:127])-[#6:120]-[#6:121]-[#6:122]-[#6:123]-[#7:124])=[#8:118])-[#6:112]-[#6:113](-[#6:114])-[#6:115])=[#8:110])-[#6:106]-[#8:107])=[#8:104])-[#6:97]-[#6:98]-[#6:99]-[#6:100]-[#7:101])=[#8:95])-[#6:92]-[#6:91]-[#6:90]-1)=[#8:88])-[#6:84]-[#8:85])=[#8:82])-[#6:75]-[#6:76]-[#6:77](=[#8:79])-[#7:78])=[#8:73])-[#6:67]-[#6:68](=[#8:70])-[#7:69])=[#8:65])-[#6:58]-[#6:59]-[#6:60]-[#6:61]-[#7:62])=[#8:56])=[#8:52])-[#6:40]-[#6:41]1:[#6:49]2:[#6:44](:[#6:45]:[#6:46]:[#6:47]:[#6:48]:2):[#7:43]:[#6:42]:1)=[#8:38])-[#6:32]-[#6:33](=[#8:35])-[#7:34])=[#8:30])-[#6:23]-[#6:24]-[#6:25]-[#6:26]-[#7:27])=[#8:21])-[#6:18])=[#8:16])-[#6:10]-[#6:11](-[#6:12])-[#6:13])=[#8:8])-[#6:4]",
"reactions": [
{
"substrate": "CC[C@H](C)[C@H](NC(=O)[C@H](CC(C)C)NC(=O)[C@H](C)NC(=O)[C@H](CCCCN)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@@H](NC(=O)[C@H](CCCCN)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CCC(N)=O)NC(=O)[C@H](CO)NC(=O)[C@@H]1CCCN1C(=O)[C@H](CCCCN)NC(=O)[C@H](CO)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CCCCN)NC(=O)[C@H](CCCCN)NC(=O)[C@@H](N)CCSC)[C@@H](C)O)C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](CS)C(=O)N[C@H](C(=O)NCC(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CO)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@@H](CO)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CCC(N)=O)C(=O)NCC(=O)N[C@@H](CCCCN)C(=O)N1CCC[C@H]1C(=O)N[C@H](C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](CO)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@@H](CCCCN)C(=O)N[C@H](C(=O)N[C@@H](CCC(=O)O)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CC(C)C)C(=O)N[C@H](C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CO)C(=O)N[C@@H](C)C(=O)N[C@H](C(=O)N[C@H](C(=O)N1CCC[C@H]1C(=O)N[C@@H](CO)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@@H](CO)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@H](C(=O)N[C@@H](Cc1c[nH]cn1)C(=O)N[C@@H](CO)C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](Cc1ccccc1)C(=O)O)C(C)C)[C@@H](C)CC)[C@@H](C)O)C(C)C)C(C)C)[C@@H](C)CC)C(C)C",
"products": [
"CC[C@H](C)[C@H](NC(=O)[C@H](CC(C)C)NC(=O)[C@H](C)NC(=O)[C@H](CCCCN)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@@H](NC(=O)[C@H](CCCCN)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CCC(N)=O)NC(=O)[C@H](CO)NC(=O)[C@@H]1CCCN1C(=O)[C@H](CCCCN)NC(=O)[C@H](CO)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CCCCN)NC(=O)[C@H](CCCCN)NC(=O)[C@@H](N)CCSC)[C@@H](C)O)C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](CS)C(=O)N[C@H](C(=O)NCC(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CO)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@@H](CO)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CCC(N)=O)C(=O)NCC(=O)N[C@@H](CCCCN)C(=O)N1CCC[C@H]1C(=O)N[C@H](C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](CO)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@@H](CCCCN)C(=O)N[C@H](C(=O)N[C@@H](CCC(=O)O)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CC(C)C)C(=O)N[C@H](C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CO)C(=O)N[C@@H](C)C(=O)N[C@H](C(=O)N[C@H](C(=O)N1CCC[C@H]1C(=O)N[C@@H](CO)C(=O)N[C@H]1Cc2c[nH]c3cc(ccc23)C(C(N)=O)[C@@H](C(=O)N[C@H](C(=O)N[C@H]2Cc3cn(cn3)C(c3ccc(O)cc3)[C@@H](C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](Cc3ccccc3)C(=O)O)NC(=O)[C@H](CO)NC2=O)C(C)C)NC(=O)[C@H](CO)NC(=O)[C@H](CC(N)=O)NC1=O)[C@@H](C)CC)[C@@H](C)O)C(C)C)C(C)C)[C@@H](C)CC)C(C)C"
],
"isIntermediate": true,
"description": "Macrocyclization of DynB precursor peptide into macrocyclized intermediate before cleavage to mature dynobactin A. "
}
],
"evidence": {
"evidenceCode": [
"Heterologous expression",
"In vitro assay"
],
"references": [
"doi:10.1021/jacs.4c10425",
"doi:10.31635/ccschem.024.202404983"
]
}
}
]
}