Structural comparison of substrate entry gate for rhomboid intramembrane peptidases

Biochemistry and Cell Biology

Volumn 89, Issue 2, 2011, Pages 216-223

  Lazareno Saez, Christelle ^a   Brooks, Cory L ^a   Lemieux, M Joanne ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

GlpG; Intramembrane peptidase; Membrane protein; Rhomboid protease; Serine peptidase; Substrate entry gate

Indexed keywords

GLPG; INTRAMEMBRANE PEPTIDASE; MEMBRANE PROTEIN; RHOMBOID PROTEASE; SERINE PEPTIDASE;

AMINO ACIDS; BIOLOGICAL MEMBRANES; CONFORMATIONS; CRYSTAL STRUCTURE; ESCHERICHIA COLI; HYDROPHOBICITY; PLANTS (BOTANY); PROTEINS; SUBSTRATES;

HYDROLASES;

ECGLPG PROTEIN; HIGLPG PROTEIN; MEMBRANE PROTEIN; PEPTIDASE; RHOMBOID; SERINE PROTEINASE; UNCLASSIFIED DRUG;

ALPHA HELIX; CARBOXY TERMINAL SEQUENCE; CHANNEL GATING; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME SUBSTRATE; ESCHERICHIA COLI; HAEMOPHILUS INFLUENZAE; HYDROPHOBICITY; NONHUMAN; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DEGRADATION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; REGULATORY MECHANISM; REVIEW;

AMINO ACID SEQUENCE; BINDING SITES; ESCHERICHIA COLI PROTEINS; MEMBRANE PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE HYDROLASES; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SUBSTRATE SPECIFICITY;

EID: 79953747761     PISSN: 08298211     EISSN: 12086002     Source Type: Journal    
DOI: 10.1139/O10-161     Document Type: Review

References (25)

1. Armougom, F., Moretti, S., Poirot, O., Audic, S., Dumas, P., Schaeli, B., et al. 2006. Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucleic Acids Res. 34(Suppl. 2): W604-W608. doi:10.1093/nar/gkl092. PMID:16845081. (Pubitemid 44529841)
2. Baker, R.P., Young, K., Feng, L., Shi, Y., and Urban, S. 2007. Enzymatic analysis of a rhomboid intramembrane protease implicates transmembrane helix 5 as the lateral substrate gate. Proc. Natl. Acad. Sci. U.S.A. 104(20): 8257-8262. doi:10.1073/pnas.0700814104. PMID:17463085. (Pubitemid 47175475)
3. Ben-Shem, A., Fass, D., and Bibi, E. 2007. Structural basis for intramembrane proteolysis by rhomboid serine proteases. Proc. Natl. Acad. Sci. U.S.A. 104(2): 462-466. doi:10.1073/pnas.0609773104. PMID:17190827. (Pubitemid 46123048)
4. Brooks, C.L., Lazareno-Saez, C., Lamoureux, J.S., Mak, M.W., and Lemieux, M.J. 2011. Insights into substrate gating in H. influenzae rhomboid. J. Mol. Biol. In press. doi:10.1016/j.jmb.2011.01.046. PMID:21295583.
5. Brossier, F., Jewett, T.J., Sibley, L.D., and Urban, S. 2005. A spatially localized rhomboid protease cleaves cell surface adhesins essential for invasion by Toxoplasma. Proc. Natl. Acad. Sci. U.S.A. 102(11): 4146-4151. doi:10.1073/pnas.0407918102.PMID:15753289. (Pubitemid 40388570)
6. Cipolat, S., Rudka, T., Hartmann, D., Costa, V., Serneels, L., Craessaerts, K., et al. 2006. Mitochondrial rhomboid PARL regulates cytochrome c release during apoptosis via OPA1-dependent cristae remodeling. Cell, 126(1): 163-175. doi:10.1016/j.cell.2006.06.021. PMID:16839884.
7. Girard, E., Marchal, S., Perez, J., Finet, S., Kahn, R., Fourme, R., et al. 2010. Structure-function perturbation and dissociation of tetrameric urate oxidase by high hydrostatic pressure. Biophys. J. 98(10): 2365-2373. doi:10.1016/j.bpj.2010.01.058. PMID:20483346.
8. Gottlieb, E. 2006. OPA1 and PARL keep a lid on apoptosis. Cell, 126(1): 27-29. doi:10.1016/j.cell.2006.06.030. PMID:16839872.
9. Gouet, P., Courcelle, E., Stuart, D.I., and Metoz, F. 1999. ESPript: multiple sequence alignments in PostScript. Bioinformatics, 15(4): 305-308. doi:10.1093/bioinformatics/15.4.305. (Pubitemid 29213756)
10. Hatunic, M., Stapleton, M., Hand, E., DeLong, C., Crowley, V.E., and Nolan, J.J. 2009. The Leu262Val polymorphism of presenilin associated rhomboid like protein (PARL) is associated with earlier onset of type 2 diabetes and increased urinary microalbumin creatinine ratio in an Irish case-control population. Diabetes Res. Clin. Pract. 83(3): 316-319. doi:10.1016/j.diabres. 2008.12.004. PMID:19185381.
11. Howell, S.A., Hackett, F., Jongco, A.M., Withers-Martinez, C., Kim, K., Carruthers, V.B., and Blackman, M.J. 2005. Distinct mechanisms govern proteolytic shedding of a key invasion protein in apicomplexan pathogens. Mol. Microbiol. 57(5): 1342-1356. doi:10.1111/j.1365-2958.2005.04772.x. PMID:16102004. (Pubitemid 41176527)
12. Lee, J.R., Urban, S., Garvey, C.F., and Freeman, M. 2001. Regulated intracellular ligand transport and proteolysis control EGF signal activation in Drosophila. Cell, 107(2): 161-171. doi:10.1016/S0092-8674(01)00526-8. PMID:11672524. (Pubitemid 33035943)
13. Lemberg, M.K., and Freeman, M. 2007. Functional and evolutionary implications of enhanced genomic analysis of rhomboid intramembrane proteases. Genome Res. 17(11): 1634-1646.doi:10.1101/gr.6425307. PMID:17938163. (Pubitemid 350074859)
14. Lemieux, M.J., Fischer, S.J., Cherney, M.M., Bateman, K.S., and James, M.N. 2007. The crystal structure of the rhomboid peptidase from Haemophilus influenzae provides insight into intramembrane proteolysis. Proc. Natl. Acad. Sci. U.S.A. 104(3): 750-754. doi:10.1073/pnas.0609981104. PMID:17210913. (Pubitemid 46154682)
15. Sheiner, L., Dowse, T.J., and Soldati-Favre, D. 2008. Identification of trafficking determinants for polytopic rhomboid proteases in Toxoplasma gondii. Traffic, 9(5): 665-677. doi:10.1111/j.1600-0854.2008.00736.x. PMID:18346213. (Pubitemid 351494299)
16. Strisovsky, K., Sharpe, H.J., and Freeman, M. 2009. Sequencespecific intramembrane proteolysis: identification of a recognition motif in rhomboid substrates. Mol. Cell, 36(6): 1048-1059. doi:10.1016/j.molcel.2009.11.006. PMID:20064469.
17. Urban, S. 2010. Taking the plunge: integrating structural, enzymaticand computational insights into a unified model for membrane-immersed rhomboid proteolysis. Biochem. J. 425(3): 501-512. doi:10.1042/BJ20090861. PMID:20070259.
18. Urban, S., and Freeman, M. 2003. Substrate specificity of rhomboid intramembrane proteases is governed by helix-breaking residues in the substrate transmembrane domain. Mol. Cell, 11(6): 1425-1434. doi:10.1016/S1097-2765(03) 00181-3. PMID:12820957. (Pubitemid 36776530)
19. Vinothkumar, K.R., Strisovsky, K., Andreeva, A., Christova, Y., Verhelst, S., and Freeman, M. 2010. The structural basis for catalysis and substrate specificity of a rhomboid protease. EMBO J. 29(22): 3797-3809. doi:10.1038/emboj.2010.243. PMID:20890268.
20. Wang, Y., and Ha, Y. 2007. Open-cap conformation of intramembrane protease GlpG. Proc. Natl. Acad. Sci. U.S.A. 104(7): 2098-2102. doi:10.1073/pnas.0611080104. PMID:17277078. (Pubitemid 46391358)
21. Wang, Y., Zhang, Y., and Ha, Y. 2006. Crystal structure of a rhomboid family intramembrane protease. Nature, 444(7116): 179-180. doi:10.1038/ nature05255. PMID:17051161.
22. Wang, Y., Maegawa, S., Akiyama, Y., and Ha, Y. 2007. The role of L1 loop in the mechanism of rhomboid intramembrane protease GlpG. J. Mol. Biol. 374(4): 1104-1113. doi:10.1016/j.jmb.2007.10.014. PMID:17976648. (Pubitemid 350052106)
23. Whitworth, A.J., Lee, J.R., Ho, V.M.W., Flick, R., Chowdhury, R., and McQuibban, G.A. 2008. Rhomboid-7 and HtrA2/Omi act in a common pathway with the Parkinson's disease factors Pink1 and Parkin. Dis. Model. Mech. 1(2-3): 168-174. doi:10.1242/dmm.000109.
24. Wu, Z., Yan, N., Feng, L., Oberstein, A., Yan, H., Baker, R.P., et al. 2006. Structural analysis of a rhomboid family intramembrane protease reveals a gating mechanism for substrate entry. Nat. Struct. Mol. Biol. 13(12): 1084-1091. doi:10.1038/nsmb1179. PMID:17099694. (Pubitemid 44885918)
25. Yan, Z., Zou, H., Tian, F., Grandis, J.R., Mixson, A.J., Lu, P.Y., and Li, L.Y. 2008. Human rhomboid family-1 gene silencing causes apoptosis or autophagy to epithelial cancer cells and inhibits xenograft tumor growth. Mol. Cancer Ther. 7(6): 1355-1364. doi:10.1158/1535-7163.MCT-08-0104. PMID:18524845.