Molecular determinants of the ATP hydrolysis asymmetry of the CCT chaperonin complex

Proteins: Structure, Function and Bioinformatics

Volumn 82, Issue 5, 2014, Pages 703-707

  Chagoyen, Mónica ^a   Carrascosa, José L ^a   Pazos, Florencio ^a   Valpuesta, José M ^a  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

Assisted protein folding; Hetero oligomer; SDP analysis; Sequence analysis; Specificity determining positions

Indexed keywords

ADENOSINE TRIPHOSPHATE; CHAPERONIN CCT1; CHAPERONIN CCT2; CHAPERONIN CCT3; CHAPERONIN CCT4; CHAPERONIN CCT5; CHAPERONIN CCT6; CHAPERONIN CCT7; CHAPERONIN CCT8; CHAPERONIN CONTAINING TCP1; UNCLASSIFIED DRUG; PROTEIN SUBUNIT;

ARTICLE; BINDING SITE; GENE DUPLICATION; HYDROLYSIS; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE; SACCHAROMYCES CEREVISIAE; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; NUCLEOTIDE SEQUENCE; PROTEIN DATABASE; PROTEIN SUBUNIT;

EUKARYOTA;

ADENOSINE TRIPHOSPHATE; CHAPERONIN CONTAINING TCP-1; CONSERVED SEQUENCE; DATABASES, PROTEIN; HYDROLYSIS; MODELS, MOLECULAR; PROTEIN SUBUNITS;

EID: 84898037231     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24510     Document Type: Article

References (33)

1. Horwich AL, Fenton WA. Chaperonin-mediated protein folding: using a central cavity to kinetically assist polypeptide chain folding. Q Rev Biophys 2009;42:83-116.
2. Gomez-Puertas P, Martin-Benito J, Carrascosa JL, Willison KR, Valpuesta JM. The substrate recognition mechanisms in chaperonins. J Mol Recognit 2004;17:85-94.
3. Valpuesta JM, Carrascosa JL, Willison KR. Structure and function of the cytosolic chaperonin CCT. In: Buchner J, Kiefhaber T, editors. Protein folding handbook. Weinheim: Wiley-VCH; 2005. pp 725-755.
4. Yebenes H, Mesa P, Munoz IG, Montoya G, Valpuesta JM. Chaperonins: two rings for folding. Trends Biochem Sci 2011;36:424-432.
5. Rivenzon-Segal D, Wolf SG, Shimon L, Willison KR, Horovitz A. Sequential ATP-induced allosteric transitions of the cytoplasmic chaperonin containing TCP-1 revealed by EM analysis. Nat Struct Mol Biol 2005;12:233-237.
6. Reissmann S, Joachimiak LA, Chen B, Meyer AS, Nguyen A, Frydman J. A gradient of ATP affinities generates an asymmetric power stroke driving the chaperonin TRIC/CCT folding cycle. Cell Rep 2012;2:866-877.
7. de Juan D, Pazos F, Valencia A. Emerging methods in protein co-evolution. Nat Rev Genet 2013;14:249-261.
8. Uniprot. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 2012;40(Database issue):D71-D75.
9. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003;4:41.
10. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32:1792-1797.
11. Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol 2011;7:e1002195.
12. Armougom F, Moretti S, Poirot O, Audic S, Dumas P, Schaeli B, Keduas V, Notredame C. Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucleic Acids Res 2006;34(Web Server issue):W604-W608.
13. Muth T, Garcia-Martin JA, Rausell A, Juan D, Valencia A, Pazos F. JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. Bioinformatics 2012;28:584-586.
14. Rausell A, Juan D, Pazos F, Valencia A. Protein interactions and ligand binding: from protein subfamilies to functional specificity. Proc Natl Acad Sci USA 2010;107:1995-2000.
15. Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 1995;8:127-134.
16. Leitner A, Joachimiak LA, Bracher A, Monkemeyer L, Walzthoeni T, Chen B, Pechmann S, Holmes S, Cong Y, Ma B, Ludtke S, Chiu W, Hartl FU, Aebersold R, Frydman J. The molecular architecture of the eukaryotic chaperonin TRiC/CCT. Structure 2012;20:814-825.
17. Douglas NR, Reissmann S, Zhang J, Chen B, Jakana J, Kumar R, Chiu W, Frydman J. Dual action of ATP hydrolysis couples lid closure to substrate release into the group II chaperonin chamber. Cell 2011;144:240-252.
18. Kalisman N, Adams CM, Levitt M. Subunit order of eukaryotic TRiC/CCT chaperonin by cross-linking, mass spectrometry, and combinatorial homology modeling. Proc Natl Acad Sci USA 2012;109:2884-2889.
19. Kalisman N, Schroder GF, Levitt M. The crystal structures of the eukaryotic chaperonin CCT reveal its functional partitioning. Structure 2013;21:540-549.
20. Archibald JM, Logsdon JM Jr, Doolittle WF. Origin and evolution of eukaryotic chaperonins: phylogenetic evidence for ancient duplications in CCT genes. Mol Biol Evol 2000;17:1456-1466.
21. Fares MA, Wolfe KH. Positive selection and subfunctionalization of duplicated CCT chaperonin subunits. Mol Biol Evol 2003;20:1588-1597.
22. Willison KR, Horwich AL. Structure and function of chaperonins in archaebacteria and eukaryotic cytosol. In: Ellis RJ, editor. The chaperonins. San Diego: Academic Press; 1996. pp 107-136.
23. Willison KR, Kubota H. The structure, function and genetics of the chaperonin containing TCP-1 (CCT) in eukaryotic cytosol. In: Morimoto RI, Tissieres A, Georgopolulos C, editors. The biology of heat shock proteins and molecular chaperones. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 1994. pp 299-312.
24. Amit M, Weisberg SJ, Nadler-Holly M, McCormack EA, Feldmesser E, Kaganovich D, Willison KR, Horovitz A. Equivalent mutations in the eight subunits of the chaperonin CCT produce dramatically different cellular and gene expression phenotypes. J Mol Biol 2010;401:532-543.
25. Lin P, Sherman F. The unique hetero-oligomeric nature of the subunits in the catalytic cooperativity of the yeast Cct chaperonin complex. Proc Natl Acad Sci USA 1997;94:10780-10785.
26. Llorca O, Martin-Benito J, Grantham J, Ritco-Vonsovici M, Willison KR, Carrascosa JL, Valpuesta JM. The 'sequential allosteric ring' mechanism in the eukaryotic chaperonin-assisted folding of actin and tubulin. EMBO J 2001;20:4065-4075.
27. Muñoz IG, Yebenes H, Zhou M, Mesa P, Serna M, Park AY, Bragado-Nilsson E, Beloso A, de Carcer G, Malumbres M, Robinson CV, Valpuesta JM, Montoya G. Crystal structure of the open conformation of the mammalian chaperonin CCT in complex with tubulin. Nat Struct Mol Biol 2011;18:14-19.
28. Llorca O, Martin-Benito J, Ritco-Vonsovici M, Grantham J, Hynes GM, Willison KR, Carrascosa JL, Valpuesta JM. Eukaryotic chaperonin CCT stabilizes actin and tubulin folding intermediates in open quasi-native conformations. EMBO J 2000;19:5971-5979.
29. Llorca O, McCormack EA, Hynes G, Grantham J, Cordell J, Carrascosa JL, Willison KR, Fernandez JJ, Valpuesta JM. Eukaryotic type II chaperonin CCT interacts with actin through specific subunits. Nature 1999;402:693-696.
30. Hynes GM, Willison KR. Individual subunits of the eukaryotic cytosolic chaperonin mediate interactions with binding sites located on subdomains of beta-actin. J Biol Chem 2000;275:18985-18994.
31. Ritco-Vonsovici M, Willison KR. Defining the eukaryotic cytosolic chaperonin-binding sites in human tubulins. J Mol Biol 2000;304:81-98.
32. Villebeck L, Moparthi SB, Lindgren M, Hammarstrom P, Jonsson BH. Domain-specific chaperone-induced expansion is required for beta-actin folding: a comparison of beta-actin conformations upon interactions with GroEL and tail-less complex polypeptide 1 ring complex (TRiC). Biochemistry 2007;46:12639-12647.
33. Villebeck L, Persson M, Luan SL, Hammarstrom P, Lindgren M, Jonsson BH. Conformational rearrangements of tail-less complex polypeptide 1 (TCP-1) ring complex (TRiC)-bound actin. Biochemistry 2007;46:5083-5093.