Nucleotide-dependent substrate handoff from the SspB adaptor to the AAA+ ClpXP protease

Molecular Cell

Volumn 16, Issue 3, 2004, Pages 343-350

  Bolon, Daniel N ^a   Grant, Robert A ^a   Baker, Tania A ^a,b   Sauer, Robert T ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTOR PROTEIN; ADENOSINE TRIPHOSPHATE; ENDOPEPTIDASE CLPX; NUCLEOTIDE; PROTEIN SSPB; PROTEINASE; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL ENGINEERING; COVALENT BOND; CRYSTAL STRUCTURE; DISULFIDE BOND; ENZYME SUBSTRATE; HYDROLYSIS; MOLECULAR INTERACTION; MOLECULAR PROBE; MOLECULAR RECOGNITION; NONHUMAN; PROTEIN FOLDING;

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATASES; ADENOSINE TRIPHOSPHATE; CARRIER PROTEINS; DISULFIDES; ENDOPEPTIDASE CLP; ESCHERICHIA COLI PROTEINS; HAEMOPHILUS INFLUENZAE; HYDROLYSIS; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEIN SUBUNITS; RECOMBINANT FUSION PROTEINS; RNA, BACTERIAL; SUBSTRATE SPECIFICITY;

EID: 5344266886     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2004.10.001     Document Type: Article

References (32)

1. Bailey S. The Ccp4 suite. programs for protein crystallography Acta Crystallogr. D Biol. Crystallogr. 50:1994;760-763
2. Bolon D.N., Wah D.A., Hersch G.L., Baker T.A., Sauer R.T. Bivalent tethering of SspB to ClpXP is required for efficient substrate delivery. a protein-design study Mol. Cell. 13:2004;443-449
3. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S., et al. Crystallography & NMR system. a new software suite for macromolecular structure determination Acta Crystallogr. D Biol. Crystallogr. 54:1998;905-921
4. Burton R.E., Hunt J.A., Fierke C.A., Oas T.G. Novel disulfide engineering in human carbonic anhydrase II using the PAIRWISE side-chain geometry database. Protein Sci. 9:2000;776-785
5. Burton R.E., Siddiqui S.M., Kim Y.I., Baker T.A., Sauer R.T. Effects of protein stability and structure on substrate processing by the ClpXP unfolding and degradation machine. EMBO J. 20:2001;3092-3100
6. Burton R.E., Baker T.A., Sauer R.T. Energy-dependent degradation. linkage between ClpX-catalyzed nucleotide hydrolysis and protein-substrate processing Protein Sci. 12:2003;893-902
7. Deshaies R.J. Make it or break it. the role of ubiquitin-dependent proteolysis in cellular regulation Trends Cell Biol. 5:1995;428-434
8. Dougan D.A., Mogk A., Zeth K., Turgay K., Bukau B. AAA+ proteins and substrate recognition, it all depends on their partner in crime. FEBS Lett. 529:2002;6-10
9. Flynn J.M., Levchenko I., Seidel M., Wickner S.H., Sauer R.T., Baker T.A. Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis. Proc. Natl. Acad. Sci. USA. 98:2001;10584-10589
10. Flynn J.M., Neher S.B., Kim Y.I., Sauer R.T., Baker T.A. Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals. Mol. Cell. 11:2003;671-683
11. Gottesman S. Proteolysis in bacterial regulatory circuits. Annu. Rev. Cell Dev. Biol. 19:2003;565-587
12. Gottesman S., Roche E., Zhou Y., Sauer R.T. The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system. Genes Dev. 12:1998;1338-1347
13. Hersch G.L., Baker T.A., Sauer R.T. SspB delivery of substrates for ClpXP proteolysis probed by the design of improved degradation tags. Proc. Natl. Acad. Sci. USA. 101:2004;12136-12141
14. Hoskins J.R., Sharma S., Sathyanarayana B.K., Wickner S. Clp ATPases and their role in protein unfolding and degradation. Adv. Protein Chem. 59:2001;413-429
15. Jones T.A., Zou J.Y., Cowan S.W., Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A. 47:1991;110-119
16. Joshi S.A., Hersch G.L., Baker T.A., Sauer R.T. Communication between ClpX and ClpP during substrate processing and degradation. Nat. Struct. Mol. Biol. 11:2004;404-411
17. Keiler K.C., Waller P.R., Sauer R.T. Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science. 271:1996;990-993
18. Kenniston J.A., Baker T.A., Fernandez J.M., Sauer R.T. Linkage between ATP consumption and mechanical unfolding during the protein processing reactions of an AAA+ degradation machine. Cell. 114:2003;511-520
19. Kenniston J.A., Burton R.E., Siddiqui S.M., Baker T.A., Sauer R.T. Effects of local protein stability and the geometric position of the substrate degradation tag on the efficiency of ClpXP denaturation and degradation. J. Struct. Biol. 146:2004;130-140
20. Kim Y.I., Burton R.E., Burton B.M., Sauer R.T., Baker T.A. Dynamics of substrate denaturation and translocation by the ClpXP degradation machine. Mol. Cell. 5:2000;639-648
21. Levchenko I., Seidel M., Sauer R.T., Baker T.A. A specificity-enhancing factor for the ClpXP degradation machine. Science. 289:2000;2354-2356
22. Levchenko I., Grant R.A., Wah D.A., Sauer R.T., Baker T.A. Structure of a delivery protein for an AAA+ protease in complex with a peptide degradation tag. Mol. Cell. 12:2003;365-372
23. Navaza J., Saludjian P. AMoRe. an automated molecular replacement program package Carter C.W., Sweet R.M. Macromolecular Crystallography. 1997;581-594 Academic Press, San Diego, CA
24. Neher S.B., Sauer R.T., Baker T.A. Distinct peptide signals in the UmuD and UmuD′ subunits of UmuD/D′ mediate tethering and substrate processing by the ClpXP protease. Proc. Natl. Acad. Sci. USA. 100:2003;13219-13224
25. Ortega J., Singh S.K., Ishikawa T., Maurizi M.R., Steven A.C. Visualization of substrate binding and translocation by the ATP-dependent protease, ClpXP. Mol. Cell. 6:2000;1515-1521
26. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Carter C.W., Sweet R.M. Macromolecular Crystallography. 1997;307-326 Academic Press, San Diego, CA
27. Pickart C.M., Cohen R.E. Proteasomes and their kin. proteases in the machine age Nat. Rev. Mol. Cell Biol. 5:2004;177-187
28. Siddiqui, S.M. (2004). Dissecting the steps of substrate processing by the energy-dependent protease ClpXP. Ph.D. thesis, Massachusetts Institute of Technology, Cambridge, Massachusetts.
29. Song H.K., Eck M.J. Structural basis of degradation signal recognition by SspB, a specificity-enhancing factor for the ClpXP proteolytic machine. Mol. Cell. 12:2003;75-86
30. Wah D.A., Levchenko I., Baker T.A., Sauer R.T. Characterization of a specificity factor for an AAA+ ATPase. assembly of SspB dimers with ssrA-tagged proteins and the ClpX hexamer Chem. Biol. 9:2002;1237-1245
31. Wah D.A., Levchenko I., Rieckhof G.E., Bolon D.N., Baker T.A., Sauer R.T. Flexible linkers leash the substrate binding domain of SspB to a peptide module that stabilizes delivery complexes with the AAA+ ClpXP protease. Mol. Cell. 12:2003;355-363
32. Wang J., Hartling J.A., Flanagan J.M. The structure of ClpP at 2.3 A resolution suggests a model for ATP-dependent proteolysis. Cell. 91:1997;447-456