435:
1249:
523:
239:
469:
as well as its associated iron-containing co-factor. Several species of methanogens have been characterized that express enzymes in the Hmd hydrogenase family. Between species the enzyme is found with differing numbers of sub-units and some minor amino acid sequence variations. The monomer is
528:
Although the mechanism by which Hmd acts is unknown, the iron-containing cofactor is in part responsible for the catalytic activity. High concentrations of CO inhibit the enzyme as well, implicating iron as the center of catalysis. It has been proposed that the iron functions to bind
657:
Shima S, Lyon EJ, Sordel-Klippert M, Kauss M, Kahnt J, Thauer RK, Steinbach K, Xie X, Verdier L, Griesinger C (May 2004). "The cofactor of the iron-sulfur cluster free hydrogenase hmd: structure of the light-inactivation product".
434:
503:
without the co-factor results in an inactive holoenzyme. However, hydrogenase activity can be rescued by the addition of the iron-containing co-factor taken from denatured active enzyme.
786:
193:
318:
518:. On the basis of spectroscopic characterization, Shima et al. have proposed a structure for this organic cofactor (minus the iron atom and CO molecules) as shown:
418:. The natural substrate of the enzyme is the organic compound methenyltetrahydromethanopterin. The organic compound includes a methenyl group bound to two tertiary
477:
causes the release of an iron atom and two molecules of carbon monoxide. In the holoenzyme the Fe and CO molecules are found associated with a 542 Da cofactor.
212:
506:
As mentioned, irradiation of the co-factor with UV light results in the loss of CO and Fe. In addition the 542 Da compound can be further degraded by a
407:. One step in methanogenesis entails conversion of a methenyl group (formic acid oxidation state) to a methylene group (formaldehyde oxidation state).
779:
912:
1274:
430:
to methylenetetrahydromethanopterin as shown. Eventually the methylene group is further reduced and released as a molecule of methane.
968:
772:
452:
is always added to the pro-R face. In the reverse reaction stereospecificity is maintained and the highlighted hydride is removed.
205:
375:
866:
830:
825:
156:
132:
1124:
338:
1239:
486:
1109:
1225:
1212:
1199:
1186:
1173:
1160:
1147:
927:
902:
894:
876:
858:
848:
840:
812:
150:
1119:
17:
1073:
1016:
803:
43:
326:
137:
1021:
494:
935:
884:
820:
217:
764:
522:
125:
1042:
961:
1114:
322:
60:
533:
and the substrate methenyltetrahydromethanopterin, organizing these two reactants in close proximity.
744:
380:
595:
590:
588:
485:
The iron-containing co-factor is found tightly associated with the protein. It can be released upon
153:
1269:
1078:
77:
55:
1011:
723:
613:
Lyon EJ, Shima S, Buurman G, Chowdhuri S, Batschauer A, Steinbach K, Thauer RK (January 2004).
715:
675:
636:
615:"UV-A/blue-light inactivation of the 'metal-free' hydrogenase (Hmd) from methanogenic archaea"
574:
510:(which specifically cleaves phosphate bonds). Hydrolysis of the phosphate bonds generates the
507:
490:
474:
313:
144:
410:
Among the hydrogenase family of enzymes, Hmd is unique in that it does not directly reduce CO
1057:
1052:
1026:
954:
752:
707:
667:
626:
566:
499:
113:
305:
1104:
1088:
1001:
917:
89:
48:
748:
243:
the crystal structure of the apoenzyme of the iron-sulfur-cluster-free hydrogenase (hmd)
1253:
1142:
1083:
795:
511:
445:
188:
168:
1263:
1047:
1006:
631:
614:
470:
approximately 45,000 Da in mass, although this value varies from species to species.
163:
756:
727:
267:
996:
557:
Shima S, Thauer RK (2007). "A third type of hydrogenase catalyzing H2 activation".
367:
301:
426:
before being incorporated into the substrate, which is catalytically reduced by H
279:
1220:
1155:
991:
384:
172:
1248:
515:
473:
The enzymatic activity of the enzyme is lost upon exposure to sunlight or UV.
1194:
1168:
735:
Karyakin AA, Varfolomeev SD (1986). "Catalytic
Properties of Hydrogenases".
466:
679:
671:
640:
578:
719:
238:
799:
396:
274:
101:
387:
are enzymes that either reduce protons or oxidize molecular dihydrogen.
711:
441:
404:
379:. It was discovered and first characterized by the Thauer group at the
120:
570:
1207:
977:
370:
363:
333:
200:
96:
84:
72:
448:. Given that the substrate is planar the hydride originating from H
1181:
419:
596:"EC 1.12.98.2 - 5,10-methenyltetrahydromethanopterin hydrogenase"
232:
H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase
295:
262:
108:
950:
768:
946:
1237:
600:
1133:
1097:
1066:
1035:
984:
926:
893:
875:
857:
839:
811:
332:
312:
294:
289:
273:
261:
253:
248:
231:
211:
199:
187:
182:
162:
143:
131:
119:
107:
95:
83:
71:
66:
54:
42:
37:
32:
908:5,10-Methenyltetrahydromethanopterin hydrogenase
352:5,10-methenyltetrahydromethanopterin hydrogenase
33:5,10-methenyltetrahydromethanopterin hydrogenase
18:5,10-methenyltetrahydromethanopterin hydrogenase
652:
650:
552:
550:
548:
546:
962:
780:
698:Blaut M (1994). "Metabolism of methanogens".
8:
969:
955:
947:
787:
773:
765:
286:
237:
179:
630:
465:The Hmd holoenzyme includes the protein
1244:
542:
514:guanosine monophosphate and a modified
602:. Technische Universität Braunschweig.
228:
29:
422:. The methenyl group originated as CO
7:
913:Methanosarcina-phenazine hydrogenase
395:Methanogens rely on such enzymes to
360:iron-sulfur cluster-free hydrogenase
444:transfer has also been shown to be
25:
1247:
632:10.1046/j.1432-1033.2003.03920.x
521:
497:. Expression of the Hmd gene in
456:Chemical and physical properties
433:
376:Methanothermobacter marburgensis
867:Hydrogen:quinone oxidoreductase
757:10.1070/rc1986v055n09abeh003228
831:Hydrogenase (NAD+, ferredoxin)
826:Hydrogen dehydrogenase (NADP+)
1:
290:Available protein structures:
481:Hmd iron-containing cofactor
1291:
1275:Enzymes of known structure
660:Angew. Chem. Int. Ed. Engl
1125:Michaelis–Menten kinetics
903:Coenzyme F420 hydrogenase
849:Cytochrome-c3 hydrogenase
285:
236:
178:
1017:Diffusion-limited enzyme
737:Russian Chemical Reviews
700:Antonie van Leeuwenhoek
495:guanidine hydrochloride
936:Hydrogenase (acceptor)
885:Ferredoxin hydrogenase
821:Hydrogen dehydrogenase
672:10.1002/anie.200353763
1110:Eadie–Hofstee diagram
1043:Allosteric regulation
1120:Lineweaver–Burk plot
381:Max Planck Institute
749:1986RuCRv..55..867K
559:The Chemical Record
399:the reduction of CO
1079:Enzyme superfamily
1012:Enzyme promiscuity
712:10.1007/BF00871639
1235:
1234:
944:
943:
571:10.1002/tcr.20111
508:phosphodiesterase
491:2-mercaptoethanol
358:), the so-called
348:
347:
344:
343:
339:structure summary
227:
226:
223:
222:
126:metabolic pathway
16:(Redirected from
1282:
1252:
1251:
1243:
1115:Hanes–Woolf plot
1058:Enzyme activator
1053:Enzyme inhibitor
1027:Enzyme catalysis
971:
964:
957:
948:
789:
782:
775:
766:
760:
731:
706:(1–3): 187–208.
684:
683:
654:
645:
644:
634:
610:
604:
603:
592:
583:
582:
554:
525:
437:
287:
241:
229:
180:
30:
27:Class of enzymes
21:
1290:
1289:
1285:
1284:
1283:
1281:
1280:
1279:
1260:
1259:
1258:
1246:
1238:
1236:
1231:
1143:Oxidoreductases
1129:
1105:Enzyme kinetics
1093:
1089:List of enzymes
1062:
1031:
1002:Catalytic triad
980:
975:
945:
940:
922:
918:Sulfhydrogenase
889:
871:
853:
835:
807:
796:Oxidoreductases
793:
763:
734:
697:
693:
691:Further reading
688:
687:
666:(19): 2547–51.
656:
655:
648:
619:Eur. J. Biochem
612:
611:
607:
594:
593:
586:
556:
555:
544:
539:
532:
483:
463:
458:
451:
429:
425:
417:
413:
402:
393:
391:Enzyme function
244:
28:
23:
22:
15:
12:
11:
5:
1288:
1286:
1278:
1277:
1272:
1262:
1261:
1257:
1256:
1233:
1232:
1230:
1229:
1216:
1203:
1190:
1177:
1164:
1151:
1137:
1135:
1131:
1130:
1128:
1127:
1122:
1117:
1112:
1107:
1101:
1099:
1095:
1094:
1092:
1091:
1086:
1081:
1076:
1070:
1068:
1067:Classification
1064:
1063:
1061:
1060:
1055:
1050:
1045:
1039:
1037:
1033:
1032:
1030:
1029:
1024:
1019:
1014:
1009:
1004:
999:
994:
988:
986:
982:
981:
976:
974:
973:
966:
959:
951:
942:
941:
939:
938:
932:
930:
924:
923:
921:
920:
915:
910:
905:
899:
897:
891:
890:
888:
887:
881:
879:
873:
872:
870:
869:
863:
861:
855:
854:
852:
851:
845:
843:
837:
836:
834:
833:
828:
823:
817:
815:
809:
808:
794:
792:
791:
784:
777:
769:
762:
761:
743:(9): 867–882.
732:
694:
692:
689:
686:
685:
646:
625:(1): 195–204.
605:
584:
541:
540:
538:
535:
530:
512:ribonucleotide
482:
479:
462:
461:Hmd holoenzyme
459:
457:
454:
449:
446:stereospecific
427:
423:
415:
411:
400:
392:
389:
346:
345:
342:
341:
336:
330:
329:
316:
310:
309:
299:
292:
291:
283:
282:
277:
271:
270:
265:
259:
258:
255:
251:
250:
246:
245:
242:
234:
233:
225:
224:
221:
220:
215:
209:
208:
203:
197:
196:
191:
185:
184:
176:
175:
166:
160:
159:
148:
141:
140:
135:
129:
128:
123:
117:
116:
111:
105:
104:
99:
93:
92:
87:
81:
80:
75:
69:
68:
64:
63:
58:
52:
51:
46:
40:
39:
35:
34:
26:
24:
14:
13:
10:
9:
6:
4:
3:
2:
1287:
1276:
1273:
1271:
1268:
1267:
1265:
1255:
1250:
1245:
1241:
1227:
1223:
1222:
1217:
1214:
1210:
1209:
1204:
1201:
1197:
1196:
1191:
1188:
1184:
1183:
1178:
1175:
1171:
1170:
1165:
1162:
1158:
1157:
1152:
1149:
1145:
1144:
1139:
1138:
1136:
1132:
1126:
1123:
1121:
1118:
1116:
1113:
1111:
1108:
1106:
1103:
1102:
1100:
1096:
1090:
1087:
1085:
1084:Enzyme family
1082:
1080:
1077:
1075:
1072:
1071:
1069:
1065:
1059:
1056:
1054:
1051:
1049:
1048:Cooperativity
1046:
1044:
1041:
1040:
1038:
1034:
1028:
1025:
1023:
1020:
1018:
1015:
1013:
1010:
1008:
1007:Oxyanion hole
1005:
1003:
1000:
998:
995:
993:
990:
989:
987:
983:
979:
972:
967:
965:
960:
958:
953:
952:
949:
937:
934:
933:
931:
929:
925:
919:
916:
914:
911:
909:
906:
904:
901:
900:
898:
896:
892:
886:
883:
882:
880:
878:
874:
868:
865:
864:
862:
860:
856:
850:
847:
846:
844:
842:
838:
832:
829:
827:
824:
822:
819:
818:
816:
814:
810:
805:
801:
797:
790:
785:
783:
778:
776:
771:
770:
767:
758:
754:
750:
746:
742:
738:
733:
729:
725:
721:
717:
713:
709:
705:
701:
696:
695:
690:
681:
677:
673:
669:
665:
661:
653:
651:
647:
642:
638:
633:
628:
624:
620:
616:
609:
606:
601:
597:
591:
589:
585:
580:
576:
572:
568:
564:
560:
553:
551:
549:
547:
543:
536:
534:
526:
524:
519:
517:
513:
509:
504:
502:
501:
496:
492:
488:
480:
478:
476:
471:
468:
460:
455:
453:
447:
443:
438:
436:
431:
421:
408:
406:
398:
390:
388:
386:
382:
378:
377:
372:
369:
365:
361:
357:
353:
340:
337:
335:
331:
328:
324:
320:
317:
315:
311:
307:
303:
300:
297:
293:
288:
284:
281:
278:
276:
272:
269:
266:
264:
260:
256:
252:
247:
240:
235:
230:
219:
216:
214:
210:
207:
204:
202:
198:
195:
192:
190:
186:
181:
177:
174:
170:
167:
165:
164:Gene Ontology
161:
158:
155:
152:
149:
146:
142:
139:
136:
134:
130:
127:
124:
122:
118:
115:
112:
110:
106:
103:
102:NiceZyme view
100:
98:
94:
91:
88:
86:
82:
79:
76:
74:
70:
65:
62:
59:
57:
53:
50:
47:
45:
41:
36:
31:
19:
1221:Translocases
1218:
1205:
1192:
1179:
1166:
1156:Transferases
1153:
1140:
997:Binding site
907:
798:: Acting on
740:
736:
703:
699:
663:
659:
622:
618:
608:
599:
565:(1): 37–46.
562:
558:
527:
520:
505:
498:
487:denaturation
484:
472:
464:
439:
432:
409:
394:
385:Hydrogenases
383:in Marburg.
374:
368:methanogenic
359:
355:
351:
349:
90:BRENDA entry
61:100357-01-5
992:Active site
249:Identifiers
78:IntEnz view
38:Identifiers
1270:EC 1.12.98
1264:Categories
1195:Isomerases
1169:Hydrolases
1036:Regulation
802:as donor (
537:References
516:2-pyridone
475:Photolysis
302:structures
147:structures
114:KEGG entry
1074:EC number
467:homodimer
366:found in
280:IPR004889
67:Databases
49:1.12.98.2
1098:Kinetics
1022:Cofactor
985:Activity
800:hydrogen
728:23706408
680:15127449
641:14686932
579:17304591
397:catalyze
373:such as
362:, is an
319:RCSB PDB
275:InterPro
218:proteins
206:articles
194:articles
151:RCSB PDB
1254:Biology
1208:Ligases
978:Enzymes
928:1.10.99
895:1.10.98
745:Bibcode
720:7747931
500:E. coli
442:hydride
405:methane
268:PF03201
173:QuickGO
138:profile
121:MetaCyc
56:CAS no.
1240:Portal
1182:Lyases
877:1.12.7
859:1.12.5
841:1.12.2
813:1.12.1
726:
718:
678:
639:
577:
420:amides
371:archea
364:enzyme
334:PDBsum
308:
298:
254:Symbol
201:PubMed
183:Search
169:AmiGO
157:PDBsum
97:ExPASy
85:BRENDA
73:IntEnz
44:EC no.
1134:Types
806:1.12)
724:S2CID
489:with
414:to CH
133:PRIAM
1226:list
1219:EC7
1213:list
1206:EC6
1200:list
1193:EC5
1187:list
1180:EC4
1174:list
1167:EC3
1161:list
1154:EC2
1148:list
1141:EC1
716:PMID
676:PMID
637:PMID
575:PMID
440:The
354:(or
350:The
327:PDBj
323:PDBe
306:ECOD
296:Pfam
263:Pfam
213:NCBI
154:PDBe
109:KEGG
753:doi
708:doi
668:doi
627:doi
623:271
567:doi
493:or
403:to
356:Hmd
314:PDB
257:HMD
189:PMC
145:PDB
1266::
804:EC
751:.
741:55
739:.
722:.
714:.
704:66
702:.
674:.
664:43
662:.
649:^
635:.
621:.
617:.
598:.
587:^
573:.
561:.
545:^
325:;
321:;
304:/
171:/
1242::
1228:)
1224:(
1215:)
1211:(
1202:)
1198:(
1189:)
1185:(
1176:)
1172:(
1163:)
1159:(
1150:)
1146:(
970:e
963:t
956:v
788:e
781:t
774:v
759:.
755::
747::
730:.
710::
682:.
670::
643:.
629::
581:.
569::
563:7
531:2
529:H
450:2
428:2
424:2
416:4
412:2
401:2
20:)
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