206:
886:
Watson JD, Milner-White EJ (January 2002). "A novel main-chain anion-binding site in proteins: the nest. A particular combination of phi,psi values in successive residues gives rise to anion-binding sites that occur commonly and are found often at functionally important regions".
316:
comprising the four residues xxGK, as above, whose main chain atoms form a phosphate-sized concavity with the NH groups pointing inwards. The synthetic hexapeptide SGAGKT has been shown to bind inorganic phosphate strongly; since such a short peptide does not form an
469:'s fold phosphate binding motif because of the shared principles in the location of the binding loop between the first β-strand and α-helix in the αβα sandwich fold and positioning of the functionally important aspartate on the tip of the second β-strand.
104:, while the B motif is a much less conserved downstream region. The P-loop is best known for its presence in ATP- and GTP-binding proteins, and is also found in a variety of proteins with phosphorylated substrates. Major lineages include:
209:
Alignment of the H-Ras mutant A59G mutants in complex with GppNHp (green cartoon) and GDP (cyan cartoon). The P-loop main chain is shown in red, the Mg ion as green sphere and the side chains of the amino acids K16 and S17 are shown as
360:
reaction) contain a motif which folds into a P-loop-like structure with an arginine in the place of the conserved lysine. The conserved sequence of this motif is C-x(5)-R-, where C and R denote
457:. There is considerable variability in the sequence of this motif, with the only invariant features being a negatively charged residue following a stretch of bulky, hydrophobic amino acids.
922:
Bianchi A, Giorgi C, Ruzza P, Toniolo C, Milner-White EJ (May 2012). "A synthetic hexapeptide designed to resemble a proteinaceous P-loop nest is shown to bind inorganic phosphate".
1049:"A common set of conserved motifs in a vast variety of putative nucleic acid-dependent ATPases including MCM proteins involved in the initiation of eukaryotic DNA replication"
413:
in most P-loop proteins situated well downstream of the A-motif. The consensus sequence of this motif was reported to be -x(3)-G-x(3)-LhhhD, where R, K, G, L and D denote
332:, but stays bound to the remaining phosphate groups. Walker motif A-binding has been shown to cause structural changes in the bound nucleotide, along the line of the
588:"Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold"
488:
553:
518:
1008:"The A-loop, a novel conserved aromatic acid subdomain upstream of the Walker A motif in ABC transporters, is critical for ATP binding"
1170:
687:
313:
508:
398:, essential for ATP-binding, found in about 25 amino acids upstream of the Walker A motif in a subset of P-loop proteins.
349:
289:; these features are typically part of an α/β domain with four strands sandwiched between two helices on each side. The
1096:
Longo LM, Jabłońska J, Vyas P, Kanade M, Kolodny R, Ben-Tal N, Tawfik DS (December 2020). Deane CM, Boudker O (eds.).
967:"Crystal structure of a human low molecular weight phosphotyrosyl phosphatase. Implications for substrate specificity"
744:
Saraste M, Sibbald PR, Wittinghofer A (November 1990). "The P-loop--a common motif in ATP- and GTP-binding proteins".
503:
82:
705:"A conformational analysis of Walker motif A [GXXXXGKT (S)] in nucleotide-binding and other proteins"
498:
563:
262:
258:
86:
329:
312:
Apart from the conserved lysine, a feature of the P-loop used in phosphate binding is a compound LRLR
840:
543:
483:
395:
371:
1098:"On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment"
947:
809:
558:
538:
465:
There is a hypothesis that the Walker A phosphate binding motif can be evolutionarily related to
829:"Ca2+ activates human homologous recombination protein Rad51 by modulating its ATPase activity"
1129:
1078:
1029:
988:
939:
904:
868:
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78:
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478:
357:
353:
290:
273:(K) residue in the Walker A motif, together with the main chain NH atoms, are crucial for
155:
844:
453:. The aspartate residue co-ordinates magnesium ions, and the glutamate is essential for
1150:
1124:
1097:
603:
528:
493:
454:
433:
residues respectively, x represents any of the 20 standard amino acids and h denotes a
94:
74:
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1048:
863:
828:
612:
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430:
159:
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112:
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1007:
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58:
721:
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318:
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282:
833:
Proceedings of the
National Academy of Sciences of the United States of America
784:
Hanson PI, Whiteheart SW (July 2005). "AAA+ proteins: have engine, will work".
328:
Upon nucleotide hydrolysis the loop does not significantly change the protein
322:
294:
274:
266:
254:
189:
185:
1064:
983:
966:
853:
442:
438:
306:
298:
246:
234:
101:
100:
Of the two motifs, the A motif is the main "P-loop" responsible for binding
1133:
1033:
943:
908:
900:
872:
805:
730:
660:
652:
1082:
992:
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621:
237:
binding. The motif has the pattern G-x(4)-GK-, where G, K, T and S denote
450:
446:
414:
365:
361:
230:
169:
131:
123:
90:
53:
1114:
935:
426:
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205:
127:
1155:
17:
418:
337:
270:
250:
242:
193:
181:
116:
797:
637:"Classification and evolution of P-loop GTPases and related ATPases"
636:
437:
amino acid. This motif was changed to be hhhhDE, where E denotes a
204:
352:) that catalyse the hydrolysis of an inorganic phosphate from a
108:
321:, this suggests that it is the nest, rather than being at the
965:
Zhang M, Stauffacher CV, Lin D, Van Etten RL (August 1998).
325:
of a helix, that is the main phosphate binding feature.
1006:
Ambudkar SV, Kim IW, Xia D, Sauna ZE (February 2006).
635:
Leipe DD, Wolf YI, Koonin EV, Aravind L (March 2002).
703:
Ramakrishnan C, Dani VS, Ramasarma T (October 2002).
297:
are also coordinated to a divalent cation such as a
52:
44:
39:
35:
P-loop containing nucleoside triphosphate hydrolase
34:
675:
586:Walker JE, Saraste M, Runswick MJ, Gay NJ (1982).
265:utilizing proteins; it is the β phosphate of the
779:
777:
775:
581:
579:
8:
378:have also been said to resemble a P-loop.
1151:Prosite entry for Walker A motif, PS00017
1123:
1113:
1072:
1023:
982:
862:
852:
720:
611:
253:residues respectively, and x denotes any
1156:Prosite entry for DEAD box motif PS51195
148:STAND NTPases including MJ, PH, AP, and
674:Stryer L, Berg JM, Tymoczko JL (2002).
575:
81:motifs, known to have highly conserved
786:Nature Reviews. Molecular Cell Biology
554:Thymidine kinase in clinical chemistry
519:Phosphatidylinositol phosphate kinases
489:Ca/calmodulin-dependent protein kinase
445:and glutamate also form a part of the
31:
7:
971:The Journal of Biological Chemistry
27:ATP-binding protein sequence motifs
827:Bugreev DV, Mazin AV (July 2004).
604:10.1002/j.1460-2075.1982.tb01276.x
25:
394:ring of ATP) refers to conserved
374:(PLP) utilizing enzymes such as
122:Nucleic acid-dependent ATPases:
682:. San Francisco: W.H. Freeman.
85:. These were first reported in
746:Trends in Biochemical Sciences
1:
1025:10.1016/j.febslet.2005.12.051
509:Nucleoside-diphosphate kinase
390:residue interacting with the
350:protein tyrosine phosphatases
889:Journal of Molecular Biology
758:10.1016/0968-0004(90)90281-f
641:Journal of Molecular Biology
83:three-dimensional structures
1187:
504:G protein-coupled receptor
356:residue (the reverse of a
1171:Protein structural motifs
722:10.1093/protein/15.10.783
281:-rich loop preceded by a
984:10.1074/jbc.273.34.21714
461:Evolutionary connections
257:. It is present in many
233:that is associated with
97:and co-workers in 1982.
1047:Koonin EV (June 1993).
854:10.1073/pnas.0402105101
499:Cyclin-dependent kinase
368:residues respectively.
1065:10.1093/nar/21.11.2541
1053:Nucleic Acids Research
901:10.1006/jmbi.2001.5227
653:10.1006/jmbi.2001.5378
564:Wall-associated kinase
227:phosphate-binding loop
211:
208:
396:aromatic amino acids
217:, also known as the
1115:10.7554/eLife.64415
977:(34): 21714–21720.
845:2004PNAS..101.9988B
709:Protein Engineering
544:Signal transduction
484:Autophosphorylation
372:Pyridoxal phosphate
285:and followed by an
269:that is bound. The
119:(α and β subunits).
936:10.1002/prot.24038
559:Thymidylate kinase
539:Phosphotransferase
277:-binding. It is a
212:
166:Nucleotide kinases
1059:(11): 2541–2547.
839:(27): 9988–9993.
376:cysteine synthase
334:induced fit model
182:G domain proteins
64:
63:
16:(Redirected from
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592:The EMBO Journal
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549:Thymidine kinase
449:motifs found in
291:phosphate groups
229:, is a motif in
79:protein sequence
32:
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798:10.1038/nrm1684
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752:(11): 430–434.
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534:Phosphorylation
479:Activation loop
475:
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404:
384:
358:tyrosine kinase
354:phosphotyrosine
346:
203:
28:
23:
22:
15:
12:
11:
5:
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1145:External links
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895:(2): 171–182.
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494:Cell signaling
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455:ATP hydrolysis
407:Walker B motif
403:
402:Walker B motif
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215:Walker A motif
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201:Walker A motif
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344:Similar folds
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678:Biochemistry
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647:(1): 41–72.
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524:Phospholipid
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406:
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386:The A-loop (
385:
370:
347:
330:conformation
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226:
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214:
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173:
144:AAA proteins
135:
130:, and PhoH (
113:ATP synthase
99:
71:
67:
65:
29:
514:Phosphatase
435:hydrophobic
319:alpha helix
287:alpha helix
283:beta strand
219:Walker loop
40:Identifiers
1108:: e64415.
570:References
323:N-terminus
309:(II) ion.
295:nucleotide
275:nucleotide
267:nucleotide
255:amino acid
190:transducin
186:G-proteins
111:and rotor
451:helicases
447:DEAD/DEAH
443:aspartate
439:glutamate
340:binding.
307:manganese
299:magnesium
247:threonine
235:phosphate
175:IPR000850
137:IPR003714
124:helicases
102:phosphate
89:-binding
59:IPR027417
1165:Category
1134:33295875
1034:16412422
944:22275093
924:Proteins
909:11779237
873:15226506
814:27830342
806:16072036
731:12468712
661:11916378
473:See also
415:arginine
388:aromatic
366:arginine
362:cysteine
231:proteins
170:InterPro
132:InterPro
91:proteins
72:Walker B
68:Walker A
54:InterPro
1125:7758060
1083:8332451
993:9705307
952:5401588
841:Bibcode
766:2126155
622:6329717
467:Rossman
427:leucine
423:glycine
392:adenine
303:calcium
293:of the
279:glycine
239:glycine
210:sticks.
172::
162:ATPases
152:ATPases
134::
117:ATPases
1132:
1122:
1081:
1074:309579
1071:
1032:
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942:
907:
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864:454202
861:
812:
804:
764:
729:
686:
659:
620:
613:553140
610:
419:lysine
382:A-loop
348:PTPs (
338:enzyme
271:lysine
251:serine
243:lysine
223:P-loop
194:myosin
95:Walker
75:motifs
45:Symbol
18:P-loop
1102:eLife
948:S2CID
810:S2CID
411:motif
409:is a
305:, or
225:, or
221:, or
150:NACHT
1130:PMID
1079:PMID
1030:PMID
989:PMID
940:PMID
905:PMID
869:PMID
802:PMID
762:PMID
727:PMID
684:ISBN
657:PMID
618:PMID
429:and
364:and
314:nest
249:and
160:PilT
128:Swi2
109:RecA
77:are
70:and
66:The
1120:PMC
1110:doi
1069:PMC
1061:doi
1020:doi
1016:580
979:doi
975:273
932:doi
897:doi
893:315
859:PMC
849:doi
837:101
794:doi
754:doi
717:doi
649:doi
645:317
608:PMC
600:doi
336:of
263:GTP
261:or
259:ATP
192:),
156:ABC
93:by
87:ATP
1167::
1128:.
1118:.
1104:.
1100:.
1077:.
1067:.
1057:21
1055:.
1051:.
1028:.
1014:.
1010:.
987:.
973:.
969:.
946:.
938:.
928:80
926:.
903:.
891:.
867:.
857:.
847:.
835:.
831:.
808:.
800:.
788:.
774:^
760:.
750:15
748:.
725:.
713:15
711:.
707:.
655:.
643:.
639:.
616:.
606:.
594:.
590:.
578:^
425:,
421:,
417:,
301:,
245:,
241:,
184::
126:,
115:/
1136:.
1112::
1106:9
1085:.
1063::
1036:.
1022::
995:.
981::
954:.
934::
911:.
899::
875:.
851::
843::
816:.
796::
790:6
768:.
756::
733:.
719::
692:.
663:.
651::
624:.
602::
596:1
196:.
188:(
178:)
168:(
158:-
140:)
48:?
20:)
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