HDAC6 and Ubp-M BUZ domains recognize specific C-terminal sequences of proteins

Biochemistry

Volumn 49, Issue 50, 2010, Pages 10737-10746

  Hard, Ryan L ^a   Liu, Jiangxin ^b   Shen, Juan ^a   Zhou, Pei ^b   Pei, Dehua ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PARTNERS; BINDING PEPTIDE; C-TERMINAL SEQUENCES; DATABASE SEARCHES; DEACETYLASE; DOMAIN SPECIFICITY; FLUORESCENCE POLARIZATION; HIGH AFFINITY; HISTONE H3; HISTONE H4; HUMAN PROTEOME; IN-VITRO; N-TERMINALS; PEPTIDE LIBRARY; PEPTIDE SEQUENCES; POTENTIAL PARTNERS; PROTEIN COMPLEXES; PROTEIN-BINDING; SEQUENCE ANALYSIS; SEQUENCE SPECIFICITY; TETRAMERS; UBIQUITIN; UBIQUITIN LIGASES;

AMINO ACIDS; OLIGOMERS; ROUGH SET THEORY; SEARCH ENGINES;

PEPTIDES;

HISTONE DEACETYLASE 6; HISTONE H3; HISTONE H4; PEPTIDE LIBRARY; PROTEIN; PROTEIN BUZ; PROTEIN UBP M; TETRAMER; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; FLUORESCENCE POLARIZATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN SYNTHESIS; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; HISTONE DEACETYLASES; HUMANS; PEPTIDE LIBRARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; UBIQUITIN THIOLESTERASE;

EID: 78650323748     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi101014s     Document Type: Article

References (41)

1. Ciechanover, A. (1998) The Ubiquitin-Proteasome Pathway: On Protein Death and Cell Life EMBO J. 17, 7151-7160
2. Wickliffe, K., Williamson, A., Jin, L., and Rape, M. (2009) The Multiple Layers of Ubiquitin Dependent Cell Cycle Control Chem. Rev. 109, 1537-1548
3. Met30-Mediated Inactivation of the Transcription Factor Met4 Cell 102, 303-314
4. Conaway, R. (2002) Emerging Roles of Ubiquitin in Transcription Regulation Science 296, 1254-1258
5. Reyes-Turcu, F., Ventii, K., and Wilkinson, K. (2009) Regulation and Cellular Roles of Ubiquitin-Specific Deubiquitinating Enzymes Annu. Rev. Biochem. 78, 363-397
6. Bonnet, J., Romier, C., Tora, L., and Devys, D. (2008) Zinc-finger UBPs: Regulators of Deubiquitylation Trends Biochem. Sci. 33, 369-375
7. Bilodeau, P., Urbanowski, J., Winistorfer, S., and Piper, R. (2002) The Vps27p-Hse1p Complex Binds Ubiquitin and Mediates Endosomal Protein Sorting Nat. Cell Biol. 4, 534-539
8. Kawaguchi, Y., Kovacs, J., McLaurin, A., Vance, J., Ito, A., and Yao, T. (2003) The Deacetylase HDAC6 Regulates Aggresome Formation and Cell Viability in Response to Misfolded Protein Stress Cell 115, 727-738
9. Hofmann, K. and Bucher, P. (1996) The UBA Domain: A Sequence Motif Present in Multiple Enzyme Classes of the Ubiquitination Pathway Trends Biochem. Sci. 21, 172-173
10. Hurley, J., Lee, S., and Prag, G. (2006) Ubiquitin Binding Domains Biochem. J. 399, 361-372
11. Beal, R. E., Toscano-Cantaffa, D., Young, P., Rechsteiner, M., and Pickart, C. M. (1998) The Hydrophobic Effect Contributes to Polyubiquitin Chain Recognition Biochemistry 37, 2925-2934
12. Mueller, T. D. and Feigon, J. (2002) Solution Structures of UBA Domains Reveal a Conserved Hydrophobic Surface for Protein-Protein Interactions J. Mol. Biol. 319, 1243-1255
13. Pai, M., Tzeng, S., Kovacs, J., Keaton, M., Li, S., Yao, T., and Zhou, P. (2007) Solution Structure of the Ubp-M BUZ Domain, a Highly Specific Protein Module that Recognizes the C-terminal Tail of Free Ubiquitin J. Mol. Biol. 370, 290-302
14. Reyes-Turcu, F. E., Horton, J. R., Mullally, J. E., Heroux, A., Cheng, X., and Wilkinson, K. D. (2006) The Ubiquitin Binding Domain Znf UBP Recognizes the C-terminal Diglycine Motif of Unanchored Ubiquitin Cell 124, 1197-1208
15. Allen, M. D. and Bycroft, M. (2007) The Solution Structure of the Znf UBP Domain of USP33/VDU1 Protein Sci. 16, 2072-2075
16. Boyault, C., Gilquin, B., Zhang, Y., Rybin, V., Garman, E., Meyer-Klaucke, W., Matthias, P., Müller, C., and Khochbin, S. (2006) HDAC6-p97/VCP Controlled Polyubiquitin Chain Turnover EMBO J. 25, 3357-3366
17. Matheny, S. A., Chen, C., Kortum, R., Razidlo, G., Lewis, R., and White, M. (2004) Ras Regulates Assembly of Mitogenic Signaling Complexes Through the Effector Protein IMP Nature 427, 256-260
18. Hook, S. S., Orian, A., Cowley, S., and Eisenman, R. (2002) Histone Deacetylase 6 Binds Polyubiquitin Through its Zinc Finger (PAZ) Domain and Co-Purifies with Deubiquitinating Enzymes Proc. Natl. Acad. Sci. U.S.A. 99, 13425-13430
19. Seigneurin-Berny, D., Verdel, A., Curtet, S., Lemercier, C., Garin, J., Rousseaux, S., and Kochbin, S. (2001) Identification of Components of the Murine Histone Deacetylase 6 Complex: Link Between Acetylation and Ubiquitination Signaling Pathways Mol. Cell. Biol. 21, 8035-8044
20. Dang, L. C., Stein, R., and Merli, F. (1998) Kinetic and Mechanistic Studies on the Hydrolysis of Ubiquitin C-Terminal 7-Amido-4-Methylcoumarin by Deubiquitinating Enzymes Biochemistry 37, 1868-1879
21. Stein, R. L., Chen, Z., and Melandri, F. (1995) Kinetic Studies of Isopeptidase T: Modulation of Peptidase Activity by Ubiquitin Biochemistry 34, 12616-12623
22. Pei, D. and Wavreille, A.-S. (2007) Reverse Interactomics: Decoding protein-protein interactions with combinatorial chemistry Mol. BioSyst. 3, 536-541
23. Joo, S. H. and Pei, D. (2008) Synthesis and Screening of Support-Bound Combinatorial Peptide Libraries with Free C-Termini: Determination of the Sequence Specificity of PDZ Domains Biochemistry 47, 3061-3072
24. Sweeney, M. C. and Pei, D. (2003) An improved method for rapid sequencing of support-bound peptides by partial Edman degradation and mass spectrometry J. Comb. Chem. 5, 218-222
25. Thakkar, A., Wavreille, A. S., and Pei, D. (2006) Traceless capping agent for peptide sequencing by partial Edman degradation and mass spectrometry Anal. Chem. 78, 5935-5939
26. Luger, K., Rechsteiner, T., and Richmond, T. J. (1999) Expression and purification of recombinant histones, and nucleosome reconstitution Methods Enzymol. 304, 3-19
27. Wavreille, A.-S., Garaud, M., Zhang, Y., and Pei, D. (2007) Defining SH2 domain and PTP specificity by screening combinatorial peptide libraries Methods 42, 207-219
28. 2 domains Biochemistry 44, 14932-14947
29. Garaud, M. and Pei, D. (2007) Substrate profiling of protein tyrosine phosphatase PTP1B by screening a combinatorial library J. Am. Chem. Soc. 129, 5366-5367
30. Lam, K. S. and Lebl, M. (1992) Streptavidin and avidin recognize peptide ligands with different motifs ImmunoMethods 1, 11-15
31. Barylko, B., Binns, D., Lin, K.-M., Atkinson, M., Jameson, D., Yin, H., and Albanesi, J. (1998) Synergistic Activation of Dynamin GTPase by Grb2 and Phosphoinositides J. Biol. Chem. 273, 3791-3797
32. Craig, K. L. and Tyers, M. (1999) The F-box: A new motif for ubiquitin dependent proteolysis in cell cycle regulation and signal transduction Prog. Biophys. Mol. Biol. 72, 299-328
33. Mimnaugh, E. G., Kayastha, G., McGovern, N. B., Hwang, S. G., Marcu, M. G., Trepel, J., Cai, S., Marchesi, V., and Neckers, L. (2001) Caspase-dependent deubiquitination of monoubiquitinated nucleosomal histone H2A induced by diverse apoptogenic stimuli Cell Death Differ. 8, 1182-1196
34. Benedit, P., Paciucci, R., Thompson, T., Valeri, M., Nadal, M., Cáceres, C., Torres, I., Estivill, X., Lozano, J., Morote, J., and Reventós, J. (2001) PTOV1, a novel protein overexpressed in prostate cancer containing a new class of protein homology blocks Oncogene 20, 1455-1464
35. Kalveram, B., Schmidtke, G., and Groettrup, M. (2008) The ubiquitin-like modifier FAT10 interacts with HDAC6 and localizes to aggresomes under proteasome inhibition J. Cell Sci. 121, 4079-4088
36. Ingvarsdottir, K., Krogan, N., Emre, N., Wyce, A., Thompson, N., Emili, A., Hughes, T., Greenblatt, J., and Berger, S. (2005) H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisae SAGA complex Mol. Cell. Biol. 25, 1162-1172
37. Kay, B., Adey, N., and Sparks, A. (1995) Reagents binding vinculin, dynein, and glutathione S-transferase from peptide libraries. PCT Int. Appl., pp 110 CODEN: PIXXD2 WO9520601 A1 19950803 CAN 123:250695 AN 1995:826768 CAPLUS.
38. Propheter, D. C., Hsu, K.-L., and Mahal, L. K. (2010) Fabrication of an oriented lectin microarray ChemBioChem 11, 1-5
39. Songyang, Z., Fanning, A., Fu, C., Xu, J., Marfatia, S., Chishti, A., Crompton, A., Chan, A., Anderson, J., and Cantley, L. (1997) Recognition of unique carboxyl-terminal motifs by distinct PDZ domains Science 275, 73-77
40. Hoffmuller, U., Russwurm, M., Kleinjung, F., Ashurst, J., Oschkinat, H., Volker-Engert, R., Koesling, D., and Schneider-Mergener, J. (1999) Interaction of a PDZ protein domain with a synthetic library of all human protein C-termini Angew. Chem., Int. Ed. 38, 2000-2004
41. Boisguerin, P., Leben, R., Ay, B., Radziwill, G., Moelling, K., Dong, L., and Volkmer-Engert, R. (2004) An improved method for the synthesis of cellulose membrane-bound peptides with free C-termini is useful for PDZ domain binding studies Chem. Biol. 11, 449-459