Modeling AAA+ ring complexes from monomeric structures

Journal of Structural Biology

Volumn 156, Issue 1, 2006, Pages 230-243

  Diemand, Alexander V ^a   Lupas, Andrei N ^a  

^a MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

Author keywords

AAA+; Apaf 1; Apoptosome; ClpB; MalT; Molecular modeling

Indexed keywords

AAA+ PROTEIN; ADENOSINE TRIPHOSPHATASE; APOPTOSOME; APOPTOTIC PROTEASE ACTIVATING FACTOR 1; BINDING PROTEIN; MALT PROTEIN; MONOMER; PROTEIN; PROTEIN CLPB; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; BETA SHEET; CARBOXY TERMINAL SEQUENCE; COMPLEX FORMATION; MOLECULAR MODEL; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE;

ADENOSINE TRIPHOSPHATASES; ALGORITHMS; AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; ENDOPEPTIDASE CLP; ESCHERICHIA COLI PROTEINS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MONTE CARLO METHOD; NUCLEOTIDES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 33749234149     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2006.04.011     Document Type: Article

References (48)

1. Acehan D., Jiang X., Morgan D.G., Heuser J.E., Wang X., and Akey C.W. Three-dimensional structure of the apoptosome: implications for assembly, procaspase-9 binding, and activation. Mol. Cell 9 (2002) 423-432
2. Bochtler M., Hartmann C., Song H.K., Bourenkov G.P., Bartunik H.D., and Huber R. The structures of HsIU and the ATP-dependent protease HsIU-HsIV. Nature 403 (2000) 800-805
3. Botos I., Melnikov E.E., Cherry S., Khalatova A.G., Rasulova F.S., Tropea J.E., Maurizi M.R., Rotanova T.V., Gustchina A., and Wlodawer A. Crystal structure of the AAA+ alpha domain of E. coli Lon protease at 1.9 Å resolution. J. Struct. Biol. 146 (2004) 113-122
4. Botos I., Melnikov E.E., Cherry S., Tropea J.E., Khalatova A.G., Rasulova F.S., Dauter Z., Maurizi M.R., Rotanova T.V., Wlodawer A., and Gustchina A. The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site. J. Biol. Chem. 279 (2004) 8140-8148
5. Comeau S.R., Gatchell D.W., Vajda S., and Camacho C.J. ClusPro: an automated docking and discrimination method for the prediction of protein complexes.p. Bioinformatics 20 (2004) 45-50
6. DeLaBarre B., and Brunger A.T. Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains. Nat. Struct. Biol. 10 (2003) 856-863
7. DeLaBarre B., and Brunger A.T. Nucleotide dependent motion and mechanism of action of p97/VCP. J. Mol. Biol. 347 (2005) 437-452
8. Diemand A.V., and Scheib H. Moltalk-a programming library for protein structures and structure analysis. BMC Bioinformatics 5 (2004) 39
9. Diemand A.V., and Scheib H. iMolTalk: an interactive, internet-based protein structure analysis server. Nucleic Acids Res. 32 (2004) W512-W516
10. Gray J.J., Moughon S., Wang C., Schueler-Furman O., Kuhlman B., Rohl C.A., and Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Mol. Biol. 331 (2003) 281-299
11. Guex N., and Peitsch M.C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18 (1997) 2714-2723
12. Guo F., Maurizi M.R., Esser L., and Xia D. Crystal structure of ClpA, an Hsp100 chaperone and regulator of ClpAP protease. J. Biol. Chem. 277 (2002) 46743-46752
13. Humphrey W., Dalke A., and Schulten K. VMD-visual molecular dynamics. J. Mol. Graph. 14 (1996) 33-38
14. Huyton T., Pye V.E., Briggs L.C., Flynn T.C., Beuron F., Kondo H., Ma J., Zhang X., and Freemont P.S. The crystal structure of murine p97/VCP at 3.6 Å. J. Struct. Biol. 144 (2003) 337-348
15. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24 (1991) 946-950
16. Krzywda S., Brzozowski A.M., Verma C., Karata K., Ogura T., and Wilkinson A.J. The crystal structure of the AAA domain of the ATP-dependent protease FtsH of Escherichia coli at 1.5 Å resolution. Structure 10 (2002) 1073-1083
17. Kwon A.R., Kessler B.M., Overkleeft H.S., and McKay D.B. Structure and reactivity of an asymmetric complex between HslV and I-domain deleted HslU, a prokaryotic homolog of the eukaryotic proteasome. J. Mol. Biol. 330 (2003) 185-195
18. Lee A.Y., Hsu C.H., and Wu S.H. Functional domains of Brevibacillus thermoruber lon protease for oligomerization and DNA binding: role of N-terminal and sensor and substrate discrimination domains. J. Biol. Chem. 279 (2004) 34903-34912
19. Lee S.Y., DeLaTorre A., Yan D., Kustu S., Nixon B.T., and Wemmer D.E. Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains. Genes Dev. 17 (2003) 2552-2563
20. Lee S., Sowa M.E., Watanabe Y.H., Sigler P.B., Chiu W., Yoshida M., and Tsai F.T. The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state. Cell 115 (2003) 229-240
21. Lenzen C.U., Steinmann D., Whiteheart S.W., and Weis W.I. Crystal structure of the hexamerization domain of N-ethylmaleimide-sensitive fusion protein. Cell 94 (1998) 525-536
22. Li J., and Sha B. Crystal structure of E. coli Hsp100 ClpB nucleotide-binding domain 1 (NBD1) and mechanistic studies on ClpB ATPase activity. J. Mol. Biol. 318 (2002) 1127-1137
23. Lupas A.N., and Martin J. AAA proteins. Curr. Opin. Struct. Biol. 12 (2002) 746-753
24. Mancini E.J., Kainov D.E., Grimes J.M., Tuma R., Bamford D.H., and Stuart D.I. Atomic snapshots of an RNA packaging motor reveal conformational changes linking ATP hydrolysis to RNA translocation. Cell 118 (2004) 743-755
25. Merritt E.A., and Bacon D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277 (1997) 505-524
26. Metropolis N., Rosenbluth A.W., Rosenbluth M.N., Teller A.H., and Teller E. Equation of state calculations by fast computing machines. J. Chem. Phys. 21 (1953) 1087-1092
27. Niwa H., Tsuchiya D., Makyio H., Yoshida M., and Morikawa K. Hexameric ring structure of the ATPase domain of the membrane-integrated metalloprotease FtsH from Thermus thermophilus HB8. Structure 10 (2002) 1415-1423
28. Park E., Rho Y.M., Koh O.J., Ahn S.W., Seong I.S., Song J.J., Bang O., Seol J.H., Wang J., Eom S.H., and Chung C.H. Role of the GYVG pore motif of HslU ATPase in protein unfolding and translocation for degradation by HslV peptidase. J. Biol. Chem. 280 (2005) 22892-22898
29. Putnam C.D., Clancy S.B., Tsuruta H., Gonzalez S., Wetmur J.G., and Tainer J.A. Structure and mechanism of the RuvB Holliday junction branch migration motor. J. Mol. Biol. 311 (2001) 297-310
30. Riedl S., Li W., Chao Y., Schwarzenbacher R., and Shi Y. Structure of the apoptotic protease-activating factor 1 bound to ADP. Nature 434 (2005) 926-933
31. Rohrwild M., Pfeifer G., Santarius U., Muller S.A., Huang H.C., Engel A., Baumeister W., and Goldberg A.L. The ATP-dependent HslVU protease from Escherichia coli is a four-ring structure resembling the proteasome. Nat. Struct. Biol. 4 (1997) 133-139
32. Rudyak S.G., Brenowitz M., and Shrader T.E. Mg2+-linked oligomerization modulates the catalytic activity of the Lon (La) protease from Mycobacterium smegmatis. Biochemistry 40 (2001) 9317-9323
33. Sali A., and Blundell T.L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234 (1993) 779-815
34. Sallai L., and Tucker P.A. Crystal structure of the central and C-terminal domain of the sigma(54)-activator ZraR. J. Struct. Biol. 151 (2005) 160-170
35. Sayle R.A., and Milner-White E.J. RASMOL: biomolecular graphics for all. Trends Biochem. Sci. 20 (1995) 374
36. Singleton M.R., Sawaya M.R., Ellenberger T., and Wigley D.B. Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides. Cell 101 (2000) 589-600
37. Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (2005) 951-960
38. Soding J., Biegert A., and Lupas A.N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33 (2005) W244-W248
39. Sousa M.C., Kessler B.M., Overkleeft H.S., and McKay D.B. Crystal structure of HslUV complexed with a vinyl sulfone inhibitor: corroboration of a proposed mechanism of allosteric activation of HslV by HslU. J. Mol. Biol. 318 (2002) 779-785
40. Sousa M.C., Trame C.B., Tsuruta H., Wilbanks S.M., Reddy V.S., and McKay D.B. Crystal and solution structures of an HslUV protease-chaperone complex. Cell 103 (2000) 633-643
41. Stahlberg H., Kutejova E., Suda K., Wolpensinger B., Lustig A., Schatz G., Engel A., and Suzuki C.K. Mitochondrial Lon of Saccharomyces cerevisiae is a ring-shaped protease with seven flexible subunits. Proc. Natl. Acad. Sci. USA 96 (1999) 6787-6790
42. Wang C., Schueler-Furman O., and Baker D. Improved side-chain modeling for protein-protein docking. Protein Sci. 14 (2005) 1328-1339
43. Wang J., Song J.J., Franklin M.C., Kamtekar S., Im Y.J., Rho S.H., Seong I.S., Lee C.S., Chung C.H., and Eom S.H. Crystal structures of the HslVU peptidase-ATPase complex reveal an ATP-dependent proteolysis mechanism. Structure 9 (2001) 177-184
44. Xia D., Esser L., Singh S.K., Guo F., and Maurizi M.R. Crystallographic investigation of peptide binding sites in the N-domain of the ClpA chaperone. J. Struct. Biol. 146 (2004) 166-179
45. Yan N., Chai J., Lee E.S., Gu L., Liu Q., He J., Wu J.W., Kokel D., Li H., Hao Q., Xue D., and Shi Y. Structure of the CED-4-CED-9 complex provides insights into programmed cell death in Caenorhabditis elegans. Nature 437 (2005) 831-837
46. Yu R.C., Hanson P.I., Jahn R., and Brunger A.T. Structure of the ATP-dependent oligomerization domain of N-ethylmaleimide sensitive factor complexed with ATP. Nat. Struct. Biol. 5 (1998) 803-811
47. Yu X., Acehan D., Menetret J.F., Booth C.R., Ludtke S.J., Riedl S.J., Shi Y., Wang X., and Akey C.W. A structure of the human apoptosome at 12.8 a resolution provides insights into this cell death platform. Structure 13 (2005) 1725-1735
48. Zhang X., Shaw A., Bates P.A., Newman R.H., Gowen B., Orlova E., Gorman M.A., Kondo H., Dokurno P., Lally J., Leonard G., Meyer H., van Heel M., and Freemont P.S. Structure of the AAA ATPase p97. Mol. Cell 6 (2000) 1473-1484