29:
1586:
314:
447:, depending on the substrates or substrate analogs bound. The first state, exhibited when pdxJ has either pyridoxine-5'-phosphate or no substrates bound, is classified as the "open" conformation. This conformation is characterized by an active site freely accessible by solvent. In contrast, when DXP and an HAP
455:
or undesirable side reactions. Binding of phosphate alone is not capable of causing a transition between the open and closed states. A third, "partially open" intermediate has also been reported upon binding of DXP alone.
1040:
Ahmad S, Raza S, et al. (2018). "From phylogeny to protein dynamics: A computational hierarchical quest for potent drug identification against an emerging enteropathogen "Yersinia enterocolitica"".
854:
Nagano N, Orengo CA, Thornton JM (August 2002). "One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions".
973:
Garrido-Franco M, Huber R, Schmidt FS, et al. (2000). "Crystallization and preliminary X-ray crystallographic analysis of PdxJ, the pyridoxine 50-phosphate synthesizing enzyme".
263:
590:
Garrido-Franco M, Laber B, Huber R, Clausen T (August 2002). "Enzyme-ligand complexes of pyridoxine 5'-phosphate synthase: implications for substrate binding and catalysis".
1142:
463:
under biological conditions. This octamer can be thought of as a tetramer of dimers, and it is likely that the dimer is the active unit of the protein. In each dimer, an
938:
Yeh JI, Du S, Pohl E, Cane DE (2002). "Multistate binding in pyridoxine 5′-phosphate synthase: 1.96 Å crystal structure in complex with 1-deoxy-D-xylulose phosphate".
179:
198:
891:"Vitamin B6 biosynthesis: formation of pyridoxine 5'-phosphate from 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate by PdxA and PdxJ protein"
1222:
1013:
Mittenhuber G (January 2001). "Phylogenetic analyses and comparative genomics of vitamin B6 (pyridoxine) and pyridoxal phosphate biosynthesis pathways".
1212:
440:
through their phosphate groups explains a previously discovered specificity for the substrates over their respective non-phosphorylated alcohols.
1135:
663:
Cane DE, Du S, Robinson J (1999). "Biosynthesis of vitamin B6: Enzymatic conversion of 1-deoxy-D-xylulose-5-phosphate to pyridoxol phosphate".
1611:
1227:
555:
development. However, there may be limits to this approach as pdxJ is not found in obligate parasites. pdxJ and more generally vitamin B
432:
moieties, and the phosphate-binding site responsible for binding to HAP and pyridoxine 5'-phosphate is a conserved motif found in many
1305:
1128:
420:
compared to the classical TIM fold. These three extra helices are important for mediating inter-subunit contacts in the assembled
1202:
191:
317:
Arrow-pushing mechanism of the reaction catalyzed by pdxJ. Other mechanisms have been proposed but differ only in the timing of
501:
1-deoxy-D-xylulose-5-phosphate:3-amino-2-oxopropyl phosphate 3-amino-2-oxopropyltransferase (phosphate-hydrolysing; cyclizing)
278:
158:
134:
1461:
1576:
625:
Mukherjee T, Hanes J, Tews I, Ealick SE, Begley TP (November 2011). "Pyridoxal phosphate: biosynthesis and catabolism".
282:
349:. The enol eliminates the phosphate derived from DXP, and water is added to the resulting double bond to reform the
1217:
690:
Cane DE, Du S, Spenser ID (2000). "Biosynthesis of vitamin B6: Origin of the oxygen atoms of pyridoxol phosphate".
1446:
1562:
1549:
1536:
1523:
1510:
1497:
1484:
1263:
1244:
1207:
1168:
551:. This identification seems to have validity, as other approaches have also identified pdxJ as a good target for
408:
protein, although it exhibits some departures from this motif. Most significantly, the central tunnel of pdxJ is
1456:
152:
28:
1410:
1353:
1159:
770:
Garrido-Franco M (April 2003). "Pyridoxine 5'-phosphate synthase: de novo synthesis of vitamin B6 and beyond".
274:
224:
57:
139:
1358:
1180:
452:
248:
203:
1379:
1298:
437:
326:
127:
1451:
1197:
1415:
540:
536:
389:
302:
286:
155:
79:
1606:
1348:
1253:
1058:
920:
373:
1107:
1076:
Scott TA, Quintaneiro LM, Norvaisas P, Lui PP, Wilson MP, Leung KY, et al. (April 2017).
1022:
990:
955:
912:
871:
836:
787:
747:
642:
607:
544:
448:
444:
381:
377:
239:
146:
38:
1394:
1389:
1363:
1291:
1097:
1089:
1050:
982:
947:
902:
863:
826:
818:
779:
737:
699:
672:
634:
599:
487:, specifically those transferring nitrogenous groups transferring other nitrogenous groups.
1120:
115:
1441:
1425:
1338:
496:
807:"Two independent routes of de novo vitamin B6 biosynthesis: not that different after all"
91:
62:
1590:
1479:
1420:
1102:
1077:
831:
806:
174:
907:
890:
867:
783:
742:
725:
603:
451:
are bound, loop 4 of the protein folds over the active site, preventing the escape of
1600:
1384:
1343:
366:
358:
342:
1062:
924:
805:
Fitzpatrick TB, Amrhein N, Kappes B, Macheroux P, Tews I, Raschle T (October 2007).
1333:
1172:
354:
338:
1054:
638:
1557:
1492:
1328:
1151:
548:
484:
468:
417:
413:
409:
362:
334:
1585:
1093:
986:
560:
532:
524:
433:
425:
416:
central tunnel observed in most TIM barrel proteins, and pdxJ has three extra
405:
216:
1531:
1505:
535:
of pyridoxal phosphate. The DXP-dependent pathway is found predominantly in
472:
429:
393:
385:
318:
313:
298:
235:
1111:
1026:
994:
959:
916:
875:
840:
791:
751:
646:
611:
1155:
464:
460:
1078:"Host-Microbe Co-metabolism Dictates Cancer Drug Efficacy in C. elegans"
543:. Because of this distribution, pdxJ has been identified as a potential
424:. However, there are also important similarities in function: like many
227:
103:
822:
726:"Structural basis for the function of pyridoxine 5'-phosphate synthase"
421:
122:
951:
703:
676:
42:
1544:
1314:
564:
231:
186:
98:
86:
74:
245:
1-deoxy-D-xylulose 5-phosphate + 3-hydroxy-1-aminoacetone phosphate
1518:
889:
Laber B, Maurer W, Scharf S, Stepusin K, Schmidt FS (April 1999).
563:
have also been shown to alter the effects of certain compounds on
330:
312:
290:
1232:
1190:
1185:
552:
350:
346:
110:
1287:
1124:
627:
Biochimica et
Biophysica Acta (BBA) - Proteins and Proteomics
388:
residue, Glu72, is positioned ideally to perform most of the
396:
residues His45 and His193 appearing to play roles as well.
1283:
252:
428:
proteins, pdxJ binds its substrates primarily by their
372:
3-hydroxy-1-aminoacetone phosphate is unstable, so the
369:, completing the synthesis of pyridoxine-5'-phosphate.
1574:
724:
Franco MG, Laber B, Huber R, Clausen T (March 2001).
251:
765:
763:
761:
719:
717:
715:
713:
585:
583:
581:
579:
1470:
1434:
1403:
1372:
1321:
1262:
1243:
1167:
1015:
Journal of
Molecular Microbiology and Biotechnology
376:cannot be confirmed directly. Nonetheless, C and O
197:
185:
173:
168:
145:
133:
121:
109:
97:
85:
73:
68:
56:
51:
21:
1008:
1006:
1004:
257:
404:Pyridoxine-5'-phosphate synthase, or pdxJ, is a
471:in the other monomer, where it helps bind both
1299:
1136:
384:studies, support the mechanism shown here. A
8:
301:, and pyridoxine-5'-phosphate (a vitamer of
1306:
1292:
1284:
1223:Branched-chain amino acid aminotransferase
1143:
1129:
1121:
658:
656:
165:
1101:
906:
830:
741:
265:pyridoxine-5'-phosphate + phosphate + 2 H
250:
1581:
575:
345:on C4 of DXP is eliminated, forming an
18:
483:This enzyme belongs to the family of
365:. A deprotonation causes the ring to
7:
1213:Kynurenine—oxoglutarate transaminase
505:pyridoxine 5-phosphate phospho lyase
503:. Other names in common use include
357:to close the ring and the resulting
436:proteins. The fact that pdxJ binds
258:{\displaystyle \rightleftharpoons }
283:3-hydroxy-1-aminoacetone phosphate
14:
392:required in this mechanism, with
353:. This enol then attacks the HAP
36:pyridoxine 5'-phosphate synthase
1584:
1273:Pyridoxine 5'-phosphate synthase
467:residue Arg20 forms part of the
443:pdxJ exhibits several different
221:pyridoxine 5'-phosphate synthase
27:
22:Pyridoxine 5'-phosphate synthase
1228:Alanine—glyoxylate transaminase
279:1-deoxy-D-xylulose 5-phosphate
1:
908:10.1016/S0014-5793(99)00393-2
868:10.1016/S0022-2836(02)00649-6
784:10.1016/s1570-9639(03)00065-7
772:Biochimica et Biophysica Acta
743:10.1016/S0969-2126(01)00584-6
604:10.1016/S0022-2836(02)00695-2
1612:Enzymes of unknown structure
1055:10.1016/j.molliq.2018.06.013
1043:Journal of Molecular Liquids
856:Journal of Molecular Biology
639:10.1016/j.bbapap.2011.06.018
592:Journal of Molecular Biology
523:This enzyme participates in
531:. pdxJ plays a role in the
1628:
1218:Ornithine aminotransferase
1094:10.1016/j.cell.2017.03.040
325:In the first step of this
1462:Michaelis–Menten kinetics
1208:Tyrosine aminotransferase
987:10.1107/S0907444900007368
164:
26:
1354:Diffusion-limited enzyme
499:of this enzyme class is
380:experiments, as well as
361:is eliminated to form a
811:The Biochemical Journal
1181:Aspartate transaminase
975:Acta Crystallographica
453:reaction intermediates
322:
259:
1447:Eadie–Hofstee diagram
1380:Allosteric regulation
1247:: Oximinotransferases
533:DXP-dependent pathway
459:pdxJ assembles as an
333:group of HAP forms a
327:condensation reaction
316:
285:(HAP), whereas its 3
260:
1457:Lineweaver–Burk plot
1198:Alanine transaminase
249:
541:Alphaproteobacteria
537:Gammaproteobacteria
412:in contrast to the
390:acid-base catalysis
303:pyridoxal phosphate
277:of this enzyme are
1416:Enzyme superfamily
1349:Enzyme promiscuity
1254:Oximinotransferase
1088:(3): 442–456.e18.
823:10.1042/bj20070765
559:metabolism in the
374:reaction mechanism
323:
255:
1572:
1571:
1281:
1280:
1203:GABA transaminase
952:10.1021/bi026292t
704:10.1021/ja000224h
677:10.1021/ja9914947
378:isotopic labeling
240:chemical reaction
213:
212:
209:
208:
128:metabolic pathway
1619:
1589:
1588:
1580:
1452:Hanes–Woolf plot
1395:Enzyme activator
1390:Enzyme inhibitor
1364:Enzyme catalysis
1308:
1301:
1294:
1285:
1145:
1138:
1131:
1122:
1116:
1115:
1105:
1073:
1067:
1066:
1037:
1031:
1030:
1010:
999:
998:
970:
964:
963:
946:(39): 11649–57.
935:
929:
928:
910:
886:
880:
879:
851:
845:
844:
834:
802:
796:
795:
767:
756:
755:
745:
721:
708:
707:
692:J. Am. Chem. Soc
687:
681:
680:
665:J. Am. Chem. Soc
660:
651:
650:
622:
616:
615:
587:
264:
262:
261:
256:
166:
45:
34:Escherichia coli
31:
19:
16:Class of enzymes
1627:
1626:
1622:
1621:
1620:
1618:
1617:
1616:
1597:
1596:
1595:
1583:
1575:
1573:
1568:
1480:Oxidoreductases
1466:
1442:Enzyme kinetics
1430:
1426:List of enzymes
1399:
1368:
1339:Catalytic triad
1317:
1312:
1282:
1277:
1258:
1239:
1163:
1149:
1119:
1075:
1074:
1070:
1039:
1038:
1034:
1012:
1011:
1002:
972:
971:
967:
937:
936:
932:
888:
887:
883:
853:
852:
848:
804:
803:
799:
769:
768:
759:
723:
722:
711:
698:(17): 4213–14.
689:
688:
684:
671:(33): 7722–23.
662:
661:
654:
633:(11): 1585–96.
624:
623:
619:
589:
588:
577:
573:
558:
528:
521:
519:Biological role
497:systematic name
493:
481:
402:
311:
294:
268:
247:
246:
47:
37:
17:
12:
11:
5:
1625:
1623:
1615:
1614:
1609:
1599:
1598:
1594:
1593:
1570:
1569:
1567:
1566:
1553:
1540:
1527:
1514:
1501:
1488:
1474:
1472:
1468:
1467:
1465:
1464:
1459:
1454:
1449:
1444:
1438:
1436:
1432:
1431:
1429:
1428:
1423:
1418:
1413:
1407:
1405:
1404:Classification
1401:
1400:
1398:
1397:
1392:
1387:
1382:
1376:
1374:
1370:
1369:
1367:
1366:
1361:
1356:
1351:
1346:
1341:
1336:
1331:
1325:
1323:
1319:
1318:
1313:
1311:
1310:
1303:
1296:
1288:
1279:
1278:
1276:
1275:
1269:
1267:
1260:
1259:
1257:
1256:
1250:
1248:
1241:
1240:
1238:
1237:
1236:
1235:
1225:
1220:
1215:
1210:
1205:
1200:
1195:
1194:
1193:
1188:
1177:
1175:
1165:
1164:
1150:
1148:
1147:
1140:
1133:
1125:
1118:
1117:
1068:
1032:
1000:
981:(8): 1045–48.
965:
930:
881:
846:
797:
757:
709:
682:
652:
617:
574:
572:
569:
556:
526:
520:
517:
492:
489:
480:
479:Classification
477:
401:
398:
359:hydroxyl group
343:hydroxyl group
310:
307:
292:
271:
270:
266:
254:
211:
210:
207:
206:
201:
195:
194:
189:
183:
182:
177:
171:
170:
162:
161:
150:
143:
142:
137:
131:
130:
125:
119:
118:
113:
107:
106:
101:
95:
94:
89:
83:
82:
77:
71:
70:
66:
65:
60:
54:
53:
49:
48:
32:
24:
23:
15:
13:
10:
9:
6:
4:
3:
2:
1624:
1613:
1610:
1608:
1605:
1604:
1602:
1592:
1587:
1582:
1578:
1564:
1560:
1559:
1554:
1551:
1547:
1546:
1541:
1538:
1534:
1533:
1528:
1525:
1521:
1520:
1515:
1512:
1508:
1507:
1502:
1499:
1495:
1494:
1489:
1486:
1482:
1481:
1476:
1475:
1473:
1469:
1463:
1460:
1458:
1455:
1453:
1450:
1448:
1445:
1443:
1440:
1439:
1437:
1433:
1427:
1424:
1422:
1421:Enzyme family
1419:
1417:
1414:
1412:
1409:
1408:
1406:
1402:
1396:
1393:
1391:
1388:
1386:
1385:Cooperativity
1383:
1381:
1378:
1377:
1375:
1371:
1365:
1362:
1360:
1357:
1355:
1352:
1350:
1347:
1345:
1344:Oxyanion hole
1342:
1340:
1337:
1335:
1332:
1330:
1327:
1326:
1324:
1320:
1316:
1309:
1304:
1302:
1297:
1295:
1290:
1289:
1286:
1274:
1271:
1270:
1268:
1265:
1261:
1255:
1252:
1251:
1249:
1246:
1242:
1234:
1231:
1230:
1229:
1226:
1224:
1221:
1219:
1216:
1214:
1211:
1209:
1206:
1204:
1201:
1199:
1196:
1192:
1189:
1187:
1184:
1183:
1182:
1179:
1178:
1176:
1174:
1173:Transaminases
1170:
1166:
1161:
1157:
1153:
1146:
1141:
1139:
1134:
1132:
1127:
1126:
1123:
1113:
1109:
1104:
1099:
1095:
1091:
1087:
1083:
1079:
1072:
1069:
1064:
1060:
1056:
1052:
1048:
1044:
1036:
1033:
1028:
1024:
1020:
1016:
1009:
1007:
1005:
1001:
996:
992:
988:
984:
980:
976:
969:
966:
961:
957:
953:
949:
945:
941:
934:
931:
926:
922:
918:
914:
909:
904:
900:
896:
892:
885:
882:
877:
873:
869:
865:
862:(5): 741–65.
861:
857:
850:
847:
842:
838:
833:
828:
824:
820:
816:
812:
808:
801:
798:
793:
789:
785:
781:
778:(1–2): 92–7.
777:
773:
766:
764:
762:
758:
753:
749:
744:
739:
736:(3): 245–53.
735:
731:
727:
720:
718:
716:
714:
710:
705:
701:
697:
693:
686:
683:
678:
674:
670:
666:
659:
657:
653:
648:
644:
640:
636:
632:
628:
621:
618:
613:
609:
605:
601:
598:(4): 601–12.
597:
593:
586:
584:
582:
580:
576:
570:
568:
566:
562:
554:
550:
546:
542:
538:
534:
530:
518:
516:
514:
510:
506:
502:
498:
490:
488:
486:
478:
476:
474:
470:
466:
462:
457:
454:
450:
446:
445:conformations
441:
439:
435:
431:
427:
423:
419:
418:alpha helices
415:
411:
407:
399:
397:
395:
391:
387:
383:
379:
375:
370:
368:
364:
360:
356:
352:
348:
344:
340:
336:
332:
328:
320:
315:
308:
306:
304:
300:
296:
288:
284:
280:
276:
244:
243:
242:
241:
237:
233:
229:
226:
222:
218:
205:
202:
200:
196:
193:
190:
188:
184:
181:
178:
176:
172:
167:
163:
160:
157:
154:
151:
148:
144:
141:
138:
136:
132:
129:
126:
124:
120:
117:
114:
112:
108:
105:
104:NiceZyme view
102:
100:
96:
93:
90:
88:
84:
81:
78:
76:
72:
67:
64:
61:
59:
55:
50:
44:
40:
35:
30:
25:
20:
1558:Translocases
1555:
1542:
1529:
1516:
1503:
1493:Transferases
1490:
1477:
1334:Binding site
1272:
1085:
1081:
1071:
1046:
1042:
1035:
1018:
1014:
978:
974:
968:
943:
940:Biochemistry
939:
933:
898:
895:FEBS Letters
894:
884:
859:
855:
849:
814:
810:
800:
775:
771:
733:
729:
695:
691:
685:
668:
664:
630:
626:
620:
595:
591:
522:
512:
509:PNP synthase
508:
504:
500:
494:
491:Nomenclature
485:transferases
482:
458:
442:
403:
371:
355:ketone group
341:of DXP. The
339:ketone group
324:
272:
220:
214:
92:BRENDA entry
33:
1329:Active site
1156:nitrogenous
1152:Transferase
1021:(1): 1–20.
901:(1): 45–8.
817:(1): 1–13.
549:antibiotics
545:drug target
469:active site
414:hydrophobic
410:hydrophilic
363:double bond
335:Schiff base
80:IntEnz view
52:Identifiers
1601:Categories
1532:Isomerases
1506:Hydrolases
1373:Regulation
1049:: 372–89.
571:References
561:microbiome
529:metabolism
438:substrates
434:TIM barrel
426:TIM barrel
406:TIM barrel
382:structural
281:(DXP) and
275:substrates
217:enzymology
149:structures
116:KEGG entry
1607:EC 2.6.99
1411:EC number
730:Structure
539:and some
525:vitamin B
473:phosphate
430:phosphate
400:Structure
394:histidine
386:glutamate
367:aromatize
337:with the
319:phosphate
309:Mechanism
299:phosphate
253:⇌
236:catalyzes
69:Databases
1435:Kinetics
1359:Cofactor
1322:Activity
1158:groups (
1112:28431245
1063:90481778
1027:11200221
995:10944349
960:12269807
925:33542088
917:10225425
876:12206759
841:17822383
792:12686115
752:11286891
647:21767669
612:12206776
475:groups.
465:arginine
321:removal.
287:products
273:The two
230:) is an
228:2.6.99.2
204:proteins
192:articles
180:articles
153:RCSB PDB
63:2.6.99.2
1591:Biology
1545:Ligases
1315:Enzymes
1266:: Other
1103:5406385
832:2267407
567:hosts.
461:octamer
422:octamer
140:profile
123:MetaCyc
46:
1577:Portal
1519:Lyases
1264:2.6.99
1110:
1100:
1061:
1025:
993:
958:
923:
915:
874:
839:
829:
790:
750:
645:
610:
565:animal
511:, and
449:analog
329:, the
232:enzyme
187:PubMed
169:Search
159:PDBsum
99:ExPASy
87:BRENDA
75:IntEnz
58:EC no.
1471:Types
1245:2.6.3
1169:2.6.1
1059:S2CID
921:S2CID
331:amine
234:that
135:PRIAM
1563:list
1556:EC7
1550:list
1543:EC6
1537:list
1530:EC5
1524:list
1517:EC4
1511:list
1504:EC3
1498:list
1491:EC2
1485:list
1478:EC1
1233:AGXT
1191:GOT2
1186:GOT1
1162:2.6)
1108:PMID
1082:Cell
1023:PMID
991:PMID
956:PMID
913:PMID
872:PMID
837:PMID
788:PMID
776:1647
748:PMID
643:PMID
631:1814
608:PMID
553:drug
547:for
513:PdxJ
495:The
351:enol
347:enol
289:are
238:the
219:, a
199:NCBI
156:PDBe
111:KEGG
43:1M5W
1098:PMC
1090:doi
1086:169
1051:doi
1047:265
983:doi
948:doi
903:doi
899:449
864:doi
860:321
827:PMC
819:doi
815:407
780:doi
738:doi
700:doi
696:122
673:doi
669:121
635:doi
600:doi
596:321
305:).
215:In
175:PMC
147:PDB
39:PDB
1603::
1171::
1160:EC
1154::
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897:.
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870:.
858:.
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825:.
813:.
809:.
786:.
774:.
760:^
746:.
732:.
728:.
712:^
694:.
667:.
655:^
641:.
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606:.
594:.
578:^
515:.
507:,
297:,
225:EC
41::
1579::
1565:)
1561:(
1552:)
1548:(
1539:)
1535:(
1526:)
1522:(
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1509:(
1500:)
1496:(
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740::
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637::
614:.
602::
557:6
527:6
295:O
293:2
291:H
269:O
267:2
223:(
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