Molecular Structure of a Novel Membrane Protease Specific for a Stomatin Homolog from the Hyperthermophilic Archaeon Pyrococcus horikoshii

Journal of Molecular Biology

Volumn 358, Issue 4, 2006, Pages 1152-1164

  Yokoyama, Hideshi ^a   Matsui, Eriko ^a   Akiba, Toshihiko ^a   Harata, Kazuaki ^a   Matsui, Ikuo ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

archaea; ClpP; membrane protease; Pyrococcus horikoshii; stomatin

Indexed keywords

ENDOPEPTIDASE CLP; LYSINE; MEMBRANE ENZYME; OLIGOMER; PROTEIN 1510 N; PROTEIN PH1511; PROTEINASE; SERINE; STOMATIN; UNCLASSIFIED DRUG;

ALPHA HELIX; ARCHAEBACTERIUM; ARTICLE; BETA SHEET; CATALYSIS; CRYSTAL STRUCTURE; DIMERIZATION; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME SPECIFICITY; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; ENZYME SUBUNIT; ESCHERICHIA COLI; HYDROPHOBICITY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PYROCOCCUS HORIKOSHII; STRUCTURAL HOMOLOGY;

ARCHAEA; ESCHERICHIA COLI; PYROCOCCUS HORIKOSHII;

EID: 33646090402     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.02.052     Document Type: Article

References (37)

1. Arnold I., and Langer T. Membrane protein degradation by AAA proteases in mitochondria. Biochim. Biophys. Acta 1592 (2002) 89-96
2. Brown M.S., Ye J., Rawson R.B., and Goldstein J.L. Regulated intramembrane proteolysis: a control mechanism conserved from bacteria to humans. Cell 100 (2000) 391-398
3. Wolfe M.S., and Kopan R. Intramembrane proteolysis: theme and variation. Science 305 (2004) 1119-1123
4. Stewart G.W., Argent A.C., and Dash B.C.J. Stomatin: a putative cation transport regulator in the red cell membrane. Biochim. Biophys. Acta 1225 (1993) 15-25
5. Price M.P., Thompson R.J., Eshcol J.O., Wemmie J.A., and Benson C.J. Stomatin modulates gating of acid-sensing ion channels. J. Biol. Chem. 279 (2004) 53886-53891
6. Zhang J.Z., Hayashi H., Ebina Y., Prohaska R., and Ismail-Beigi F. Association of stomatin (band 7.2b) with Glut1 glucose transporter. Arch. Biochem. Biophys. 372 (1999) 173-178
7. Zhang J.Z., Abbud W., Prohaska R., and Ismail-Beigi F. Overexpression of stomatin depresses GLUT-1 glucose transporter activity. Am. J. Physiol. Cell Physiol. 280 (2001) C1277-C1283
8. Zhang S., Arnadottir J., Keller C., Caldwell G.A., Yao C.A., and Chalfie M. MEC-2 is recruited to the putative mechanosensory complex in C. elegans touch receptor neurons through its stomatin-like domain. Curr. Biol. 14 (2004) 1888-1896
9. Tavernarakis N., Driscoll M., and Kyrpides N.C. The SPFH domain: implicated in regulating targeted protein turnover in stomatins and other membrane-associated proteins. Trends Biochem. Sci. 24 (1999) 425-427
10. Kihara A., Akiyama Y., and Ito K. A protease complex in the Escherichia coli plasma membrane: HflKC (HflA) forms a complex with FtsH (HflB), regulating its proteolytic activity against SecY. EMBO J. 15 (1996) 6122-6131
11. Langer T., Käser M., Klanner C., and Leonhard K. AAA proteases of mitochondria: quality control of membrane proteins and regulatory functions during mitochondrial biogenesis. Biochem. Soc. Trans. 29 (2001) 431-436
12. Green J.B., Fricke B., Chetty M.C., von Düring M., Preston G.F., and Stewart G.W. Eukaryotic and prokaryotic stomatins: the proteolytic link. Blood Cells, Mol. Dis. 32 (2004) 411-422
13. Yokoyama H., and Matsui I. A novel thermostable membrane protease forming an operon with a stomatin homolog from the hyperthermophilic archaebacterium Pyrococcus horikoshii. J. Biol. Chem. 280 (2005) 6588-6594
14. Wickner S., Maurizi M.R., and Gottesman S. Posttranslational quality control: folding, refolding, and degrading proteins. Science 286 (1999) 1888-1893
15. Ermolaeva M.D., White O., and Salzberg S.L. Prediction of operons in microbial genomes. Nucl. Acids Res. 29 (2001) 1216-1221
16. Hirokawa T., Boon-Chieng S., and Mitaku S. SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics 14 (1998) 378-379
17. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26 (1993) 283-291
18. Vega M.C., Martínez J.C., and Serrano L. Thermodynamic and structural characterization of Asn and Ala residues in the disallowed II′ region of the Ramachandran plot. Protein Sci. 9 (2000) 2322-2328
19. Hutchinson E.G., and Thornton J.M. A revised set of potentials for β-turn formation in proteins. Protein Sci. 3 (1994) 2207-2216
20. Wang J., Hartling J.A., and Flanagan J.M. The structure of ClpP at 2.3 Å resolution suggests a model for ATP-dependent proteolysis. Cell 91 (1997) 447-456
21. Krissinel E., and Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallog. sect. D 60 (2004) 2256-2268
22. Kang S.G., Maurizi M.R., Thompson M., Mueser T., and Ahvazi B. Crystallography and mutagenesis point to an essential role for the N-terminus of human mitochondrial ClpP. J. Struct. Biol. 148 (2004) 338-352
23. Paetzel M., and Dalbey R.E. Catalytic hydroxyl/amine dyads within serine proteases. Trends Biochem. Sci. 22 (1997) 28-31
24. Paetzel M., Dalbey R.E., and Strynadka N.C.J. Crystal structure of a bacterial signal peptidase in complex with a β-lactam inhibitor. Nature 396 (1998) 186-190
25. Jansèn T., Kidron H., Soitamo A., Salminen T., and Mäenpää P. Transcriptional regulation and structural modelling of the Synechocystis sp. PCC 6803 carboxyl-terminal endoprotease family. FEMS Microbiol. Letters 228 (2003) 121-128
26. Bendtsen J.D., Nielsen H., von Heijne G., and Brunak S. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340 (2004) 783-795
27. Snyers L., Umlauf E., and Prohaska R. Oligomeric nature of the integral membrane protein stomatin. J. Biol. Chem. 273 (1998) 17221-17226
28. Umlauf E., Csaszar E., Moertelmaier M., Schuetz G.J., Parton R.G., and Prohaska R. Association of stomatin with lipid bodies. J. Biol. Chem. 279 (2004) 23699-23709
29. 15N heteronuclear NMR studies of Escherichia coli thioredoxin in samples isotopically labeled by residue type. Biochemistry 24 (1985) 7263-7268
30. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
31. De la Fortelle E., and Bricogne G. Maximum-likelihood heavy atom parameter refinement in the MIR and MAD methods. Methods Enzymol. 276 (1997) 472-494
32. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D 50 (1994) 760-763
33. McRee D.E. XtalView/Xfit-a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125 (1999) 156-165
34. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallog. sect. D 54 (1998) 905-921
35. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24 (1991) 946-950
36. Merritt E.A., and Bacon D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277 (1997) 505-524
37. Gouet P., Courcelle E., Stuart D.I., and Métoz F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15 (1999) 305-308