285:
29:
488:
and mapping. Unlike type I restriction enzymes, type II restriction endonucleases perform very specific cleaving of DNA. Type I restriction enzymes recognize specific sequences, but cleave DNA randomly at sites other than their recognition site whereas type II restriction enzymes cleave only at
417:
dIII. In a separate mutagenesis study it was shown that a mutation at residue 123 from Asp to Asn reduced enzymatic activity. Despite the fact that this residue is most likely responsible for the unwinding of DNA and coordination to water rather than direct interaction with the attacking
396:
sequence motif PD-(D/E)XK to coordinate Mg, a cation required to cleave DNA in most type II restriction endonucleases. The cofactor Mg is believed to bind water molecules and carry them to the catalytic sites of the enzymes, among other cations. Unlike most documented type II restriction
500:
Major uses of type II restriction enzymes include gene analysis and cloning. They have proven to be ideal modeling systems for the study of protein-nucleic acid interactions, structure-function relationships, and the mechanism of
464:
anion through to coordination of Mg. Furthermore, enzymatic function is dependent upon the correct position of the Asp-74 residue, suggesting has a role in increasing the nucleophilicity of the attacking water molecule.
452:
have led to the following proposed catalytic mechanism. It has been suggested that during the hydrolysis of DNA by EcoRV the catalytic residue Lys-92 stabilizes and orients the attacking water
445:
Despite the lack of evidence suggesting an exact mechanism for the cleavage of DNA by HindIII, site-mutagenesis analysis coupled with more detailed studies of metal ion-mediated catalysis in
472:, respectively. Lys-125 positions the attacking water molecule while Asp-108 improves its nucleophilicity. Asp-123 coordinates to Mg2+ which in turn stabilizes the leaving hydroxide ion.
468:
As a result of the site-mutagenesis experiments previously outlined, it is thus proposed that Lys-125, Asp-123, and Asp-108 of HindIII function similarly to Lys-92, Asp-90, and Asp-74 in
509:
by their ability to specifically cleave DNA to allow the removal or insertion of DNA. Through the use of restriction enzymes, scientists are able to modify, insert, or remove specific
846:
337:
347:
The structure of HindIII is complex, and consists of a homodimer. Like other type II restriction endonucleases, it is believed to contain a common structural core comprising four
413:
residues involved. In particular, substitutions of Asn for Lys at residue 125 and Leu for Asp at residue 108 significantly decreased DNA binding and the catalytic function of
489:
their specific recognition site. Since their discovery in the early 1970s, type II restriction enzymes have revolutionized the way scientists work with DNA, particularly in
118:
1148:
1143:
430:
While restriction enzymes cleave at specific DNA sequences, they are first required to bind non-specifically with the DNA backbone before localizing to the
1153:
1138:
1133:
320:
DNA. There is also evidence that suggests the restriction enzymes may act alongside modification enzymes as selfish elements, or may be involved in
171:
33:
Crystallographic structure of the HindIII restriction endonuclease dimer (cyan and green) complexed with double helical DNA (brown) based on the
1188:
1178:
1173:
1168:
1163:
1158:
636:
853:
1183:
1128:
397:
endonucleases, HindIII is unique in that it has little to no catalytic activity when Mg is substituted for other cofactors, such as Mn.
1120:
1016:
914:
442:, this bonding facilitates a conformational change of the DNA-enzyme complex which leads to the activation of catalytic centers.
176:
922:
938:
637:"Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution"
138:
1229:
542:"Mutational analyses of restriction endonuclease-HindIII mutant E86K with higher activity and altered specificity"
862:
313:
405:
Despite the uncertainty concerning the structure-catalysis relationship of type II endonucleases, site-directed
126:
191:
1224:
839:
1219:
439:
122:
831:
481:
363:
and DNA technology, little information is available concerning the mechanism of DNA recognition and
316:. Their primary function is to protect the host genome against invasion by foreign DNA, primarily
215:
284:
367:
cleavage. However, it is believed that HindIII utilizes a common mechanism of recognition and
273:
1200:
321:
790:
325:
220:
105:
239:
8:
490:
364:
359:
and the predicted molecular mass is 34,950 Da. Despite the importance of this enzyme in
295:
The cleavage of this sequence between the AA's results in 5' overhangs on the DNA called
794:
277:
that cleaves the DNA palindromic sequence AAGCTT in the presence of the cofactor Mg via
866:
813:
778:
664:
291:
dIII restrictions process results in formation of overhanging palindromic sticky ends.
268:
728:"Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases"
818:
759:
754:
727:
708:
656:
617:
612:
587:
563:
506:
494:
360:
183:
113:
35:
668:
67:
808:
798:
749:
739:
698:
648:
607:
599:
553:
431:
101:
79:
249:
558:
541:
485:
435:
409:
of the restriction endonuclease HindIII has provided much insight into the key
1213:
744:
603:
317:
803:
885:
880:
822:
712:
660:
621:
567:
513:, a very powerful tool especially when it comes to modifying an organism's
763:
890:
457:
453:
419:
406:
356:
336:
309:
296:
203:
703:
686:
348:
267:(pronounced "Hin D Three") is a type II site-specific deoxyribonuclease
861:
410:
393:
343:
II catalytic site, showing the coordination of Asp 84 and Mg with water
278:
198:
352:
188:
39:
502:
461:
368:
779:"How restriction enzymes became the workhorses of molecular biology"
973:
438:
with the bases of the recognition sequence. With the aid of other
74:
652:
946:
930:
687:"Site-directed mutagenesis of restriction endonuclease HindIII"
585:
514:
133:
1040:
1032:
1024:
1008:
954:
588:"Structure and function of type II restriction endonucleases"
510:
469:
446:
386:
379:
372:
308:
Restriction endonucleases are used as defense mechanisms in
1107:
1088:
1080:
1072:
1064:
1056:
1000:
981:
906:
95:
62:
28:
434:. On average, the restriction enzyme will form 15-20
725:
776:
484:are very useful in modern science, particularly in
1211:
371:of DNA found in other type II enzymes such as
847:
400:
854:
840:
586:Pingoud, Alfred; Jeltsch, Albert. (2001).
505:. They make good assays for the study of
27:
812:
802:
753:
743:
702:
611:
581:
579:
577:
557:
153:hindIIIR type II restriction endonuclease
335:
283:
726:Horton N, Newberry K, Perona J (1999).
539:
1212:
770:
680:
678:
634:
574:
535:
533:
531:
529:
835:
719:
628:
425:
684:
422:, its specific function is unknown.
675:
526:
475:
13:
14:
1241:
480:HindIII as well as other type II
460:of Asp-90 stabilizes the leaving
22:HindIII restriction endonuclease
863:Restriction modification system
314:restriction modification system
635:Lukacs C, et al. (2000).
1:
540:Tang, D; et al. (2000).
520:
392:. These enzymes contain the
355:. Each subunit contains 300
90:Available protein structures:
777:Roberts, Richard J. (2005).
685:Tang D, et al. (1999).
331:
7:
691:Biosci. Biotechnol. Biochem
305:3'-T T C G A| A-5'
302:5'-A |A G C T T-3'
10:
1246:
1230:Enzymes of known structure
1199:* means cleavage produces
783:Proc. Natl. Acad. Sci. USA
732:Proc. Natl. Acad. Sci. USA
440:van der Waals interactions
1197:
1119:
1100:
993:
966:
899:
873:
482:restriction endonucleases
401:Site-directed mutagenesis
245:
235:
230:
226:
214:
209:
197:
182:
170:
162:
157:
152:
132:
112:
94:
89:
85:
73:
61:
53:
48:
26:
21:
1101:Recognition sequence 8bp
994:Recognition sequence 6bp
967:Recognition sequence 5bp
900:Recognition sequence 4bp
745:10.1073/pnas.95.23.13489
559:10.1093/protein/13.4.283
804:10.1073/pnas.0500923102
604:10.1093/nar/29.18.3705
592:Nucleic Acids Research
344:
292:
274:Haemophilus influenzae
339:
322:genetic recombination
287:
43: coordinates.
1225:Restriction enzymes
795:2005PNAS..102.5905R
704:10.1271/bbb.63.1703
546:Protein Engineering
491:genetic engineering
365:phosphodiester bond
867:restriction enzyme
426:Proposed mechanism
345:
293:
269:restriction enzyme
1220:Bacterial enzymes
1207:
1206:
641:Nat. Struct. Biol
507:genetic mutations
495:molecular biology
361:molecular biology
312:organisms in the
259:
258:
255:
254:
148:
147:
144:
143:
139:structure summary
1237:
856:
849:
842:
833:
832:
827:
826:
816:
806:
774:
768:
767:
757:
747:
738:(23): 13489–94.
723:
717:
716:
706:
682:
673:
672:
632:
626:
625:
615:
583:
572:
571:
561:
537:
476:Uses in research
432:restriction site
228:
227:
150:
149:
87:
86:
42:
31:
19:
18:
1245:
1244:
1240:
1239:
1238:
1236:
1235:
1234:
1210:
1209:
1208:
1203:
1193:
1115:
1096:
989:
962:
895:
869:
860:
830:
775:
771:
724:
720:
683:
676:
633:
629:
598:(18): 3705–27.
584:
575:
538:
527:
523:
478:
428:
403:
334:
192:More structures
44:
34:
17:
12:
11:
5:
1243:
1233:
1232:
1227:
1222:
1205:
1204:
1198:
1195:
1194:
1192:
1191:
1186:
1181:
1176:
1171:
1166:
1161:
1156:
1151:
1146:
1141:
1136:
1131:
1125:
1123:
1117:
1116:
1114:
1113:
1104:
1102:
1098:
1097:
1095:
1094:
1086:
1078:
1070:
1062:
1054:
1046:
1038:
1030:
1022:
1014:
1006:
997:
995:
991:
990:
988:
987:
979:
970:
968:
964:
963:
961:
960:
952:
944:
936:
928:
920:
912:
903:
901:
897:
896:
894:
893:
888:
883:
877:
875:
871:
870:
859:
858:
851:
844:
836:
829:
828:
789:(17): 5905–8.
769:
718:
697:(10): 1703–7.
674:
627:
573:
524:
522:
519:
486:DNA sequencing
477:
474:
436:hydrogen bonds
427:
424:
402:
399:
333:
330:
271:isolated from
257:
256:
253:
252:
247:
243:
242:
237:
233:
232:
224:
223:
218:
212:
211:
207:
206:
201:
195:
194:
186:
180:
179:
174:
168:
167:
164:
160:
159:
155:
154:
146:
145:
142:
141:
136:
130:
129:
116:
110:
109:
99:
92:
91:
83:
82:
77:
71:
70:
65:
59:
58:
55:
51:
50:
46:
45:
32:
24:
23:
15:
9:
6:
4:
3:
2:
1242:
1231:
1228:
1226:
1223:
1221:
1218:
1217:
1215:
1202:
1196:
1190:
1187:
1185:
1182:
1180:
1177:
1175:
1172:
1170:
1167:
1165:
1162:
1160:
1157:
1155:
1152:
1150:
1147:
1145:
1142:
1140:
1137:
1135:
1132:
1130:
1127:
1126:
1124:
1122:
1118:
1112:
1110:
1106:
1105:
1103:
1099:
1093:
1091:
1087:
1085:
1083:
1079:
1077:
1075:
1071:
1069:
1067:
1063:
1061:
1059:
1055:
1053:
1051:
1047:
1045:
1043:
1039:
1037:
1035:
1031:
1029:
1027:
1023:
1021:
1019:
1015:
1013:
1011:
1007:
1005:
1003:
999:
998:
996:
992:
986:
984:
980:
978:
976:
972:
971:
969:
965:
959:
957:
953:
951:
949:
945:
943:
941:
937:
935:
933:
929:
927:
925:
921:
919:
917:
913:
911:
909:
905:
904:
902:
898:
892:
889:
887:
884:
882:
879:
878:
876:
874:Basic Concept
872:
868:
864:
857:
852:
850:
845:
843:
838:
837:
834:
824:
820:
815:
810:
805:
800:
796:
792:
788:
784:
780:
773:
765:
761:
756:
751:
746:
741:
737:
733:
729:
722:
714:
710:
705:
700:
696:
692:
688:
681:
679:
670:
666:
662:
658:
654:
653:10.1038/72405
650:
647:(2): 134–40.
646:
642:
638:
631:
623:
619:
614:
609:
605:
601:
597:
593:
589:
582:
580:
578:
569:
565:
560:
555:
551:
547:
543:
536:
534:
532:
530:
525:
518:
516:
512:
508:
504:
498:
496:
492:
487:
483:
473:
471:
466:
463:
459:
455:
451:
449:
443:
441:
437:
433:
423:
421:
416:
412:
408:
398:
395:
391:
389:
384:
382:
377:
375:
370:
366:
362:
358:
354:
351:and a single
350:
342:
338:
329:
327:
326:transposition
323:
319:
318:bacteriophage
315:
311:
306:
303:
300:
298:
290:
286:
282:
280:
276:
275:
270:
266:
264:
251:
248:
244:
241:
238:
234:
229:
225:
222:
219:
217:
213:
208:
205:
202:
200:
196:
193:
190:
187:
185:
181:
178:
175:
173:
169:
165:
161:
156:
151:
140:
137:
135:
131:
128:
124:
120:
117:
115:
111:
107:
103:
100:
97:
93:
88:
84:
81:
78:
76:
72:
69:
66:
64:
60:
56:
52:
47:
41:
37:
30:
25:
20:
1108:
1089:
1081:
1073:
1065:
1057:
1049:
1048:
1041:
1033:
1025:
1017:
1009:
1001:
982:
974:
955:
947:
939:
931:
923:
915:
907:
886:Neoschizomer
881:Isoschizomer
786:
782:
772:
735:
731:
721:
694:
690:
644:
640:
630:
595:
591:
552:(4): 283–9.
549:
545:
499:
479:
467:
456:, while the
447:
444:
429:
414:
404:
387:
380:
373:
346:
340:
307:
304:
301:
294:
288:
272:
262:
261:
260:
891:Isocaudomer
458:carboxylate
454:nucleophile
420:nucleophile
407:mutagenesis
357:amino acids
310:prokaryotic
297:sticky ends
240:Swiss-model
158:Identifiers
49:Identifiers
1214:Categories
1201:blunt ends
521:References
411:amino acid
394:amino acid
279:hydrolysis
236:Structures
231:Search for
210:Other data
102:structures
57:RE_Hindiii
503:evolution
462:hydroxide
369:catalysis
332:Structure
216:EC number
172:NCBI gene
80:IPR019043
823:15840723
713:10586498
669:20478739
661:10655616
622:11557805
568:10810160
349:β-sheets
250:InterPro
221:3.1.21.4
166:hindIIIR
119:RCSB PDB
75:InterPro
1149:Bsp–Bss
1144:Bsa–Bso
814:1087929
791:Bibcode
764:9811827
353:α-helix
246:Domains
199:UniProt
68:PF09518
1154:Bst–Bv
821:
811:
762:
752:
711:
667:
659:
620:
610:
566:
515:genome
385:, and
204:P43870
177:950303
163:Symbol
134:PDBsum
108:
98:
54:Symbol
16:Enzyme
1139:Bd–Bp
1134:Ba–Bc
1121:Lists
755:24846
665:S2CID
613:55916
511:genes
470:EcoRV
1050:Hind
934:III*
819:PMID
760:PMID
709:PMID
657:PMID
618:PMID
564:PMID
493:and
324:and
265:dIII
189:2e52
127:PDBj
123:PDBe
106:ECOD
96:Pfam
63:Pfam
40:2E52
1189:T-Z
1179:O-R
1174:L-N
1169:G-K
1164:E-F
1159:C-D
1109:Not
1090:Nde
1082:Pst
1074:Sac
1066:Xho
1058:Xba
1052:III
1042:Bam
1034:Eco
1028:RV*
1026:Eco
1020:II*
1018:Pov
1010:Bgl
1002:Aaa
983:Fok
977:RII
975:Eco
956:Hpa
950:III
948:Nla
940:Dpn
932:Hae
924:Alu
916:Sau
908:Taq
809:PMC
799:doi
787:102
750:PMC
740:doi
699:doi
649:doi
608:PMC
600:doi
554:doi
448:Eco
415:Hin
388:Bgl
381:Bam
374:Eco
341:Bgl
289:Hin
263:Hin
184:PDB
114:PDB
36:PDB
1216::
1044:HI
1036:RI
1012:II
958:II
942:II
926:I*
918:3A
865::
817:.
807:.
797:.
785:.
781:.
758:.
748:.
736:95
734:.
730:.
707:.
695:63
693:.
689:.
677:^
663:.
655:.
643:.
639:.
616:.
606:.
596:29
594:.
590:.
576:^
562:.
550:13
548:.
544:.
528:^
517:.
497:.
450:RV
390:II
383:HI
378:,
376:RI
328:.
299::
281:.
125:;
121:;
104:/
38::
1184:S
1129:A
1111:I
1092:I
1084:I
1076:I
1068:I
1060:I
1004:I
985:I
910:I
855:e
848:t
841:v
825:.
801::
793::
766:.
742::
715:.
701::
671:.
651::
645:7
624:.
602::
570:.
556::
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