Structural and mechanistic basis of Parl activity and regulation (original) (raw)

• Koonin EV, Makarova KS, Rogozin IB, Davidovic L, Letellier MC, Pellegrini L . The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers. Genome Biol 2003; 4: R19.
  Article Google Scholar
• Urban S, Lee JR, Freeman M . Drosophila rhomboid-1 defines a family of putative intramembrane serine proteases. Cell 2001; 107: 173–182.
  Article CAS Google Scholar
• Urban S . Rhomboid proteins: conserved membrane proteases with divergent biological functions. Genes Dev 2006; 20: 3054–3068.
  Article CAS Google Scholar
• Urban S, Wolfe MS . Reconstitution of intramembrane proteolysis in vitro reveals that pure rhomboid is sufficient for catalysis and specificity. Proc Natl Acad Sci USA 2005; 102: 1883–1888.
  Article CAS Google Scholar
• Wang Y, Zhang Y, Ha Y . Crystal structure of a rhomboid family intramembrane protease. Nature 2006; 444: 179–180.
  Article CAS Google Scholar
• Wu Z, Yan N, Feng L, Oberstein A, Yan H, Baker RP et al. Structural analysis of a rhomboid family intramembrane protease reveals a gating mechanism for substrate entry. Nat Struct Mol Biol 2006; 13: 1084–1091.
  Article CAS Google Scholar
• Ben-Shem A, Fass D, Bibi E . Structural basis for intramembrane proteolysis by rhomboid serine proteases. Proc Natl Acad Sci USA 2007; 104: 462–466.
  Article CAS Google Scholar
• Lemieux MJ, Fischer SJ, Cherney MM, Bateman KS, James MN . The crystal structure of the rhomboid peptidase from Haemophilus influenzae provides insight into intramembrane proteolysis. Proc Natl Acad Sci USA 2007; 104: 750–754.
  Article CAS Google Scholar
• Bondar AN, del Val C, White SH . Rhomboid protease dynamics and lipid interactions. Structure 2009; 17: 395–405.
  Article CAS Google Scholar
• Clemmer KM, Sturgill GM, Veenstra A, Rather PN . Functional characterization of Escherichia coli GlpG and additional rhomboid proteins using an aarA mutant of Providencia stuartii. J Bacteriol 2006; 188: 3415–3419.
  Article CAS Google Scholar
• Erez E, Fass D, Bibi E . How intramembrane proteases bury hydrolytic reactions in the membrane. Nature 2009; 459: 371–378.
  Article CAS Google Scholar
• Ha Y . Structure and mechanism of intramembrane protease. Semin Cell Dev Biol 2009; 20: 240–250.
  Article CAS Google Scholar
• Cipolat S, Rudka T, Hartmann D, Costa V, Serneels L, Craessaerts K et al. Mitochondrial rhomboid PARL regulates cytochrome c release during apoptosis via OPA1-dependent cristae remodeling. Cell 2006; 126: 163–175.
  Article CAS Google Scholar
• Jeyaraju DV, Xu L, Letellier MC, Bandaru S, Zunino R, Berg EA et al. Phosphorylation and cleavage of presenilin-associated rhomboid-like protein (PARL) promotes changes in mitochondrial morphology. Proc Natl Acad Sci USA 2006; 103: 18562–18567.
  Article CAS Google Scholar
• Civitarese AE, MacLean PS, Carling S, Kerr-Bayles L, McMillan RP, Pierce A et al. Regulation of skeletal muscle oxidative capacity and insulin signaling by the mitochondrial rhomboid protease PARL. Cell Metab 2010; 11: 412–426.
  Article CAS Google Scholar
• Sík A, Passer BJ, Koonin EV, Pellegrini L . Self-regulated cleavage of the mitochondrial intramembrane-cleaving protease PARL yields Pbeta, a nuclear-targeted peptide. J Biol Chem 2004; 279: 15323–15329.
  Article Google Scholar
• Hill RB, Pellegrini L . The PARL family of mitochondrial rhomboid proteases. Semin Cell Dev Biol 2010; 21: 582–592.
  Article CAS Google Scholar
• Deas E, Plun-Favreau H, Gandhi S, Desmond H, Kjaer S, Loh S et al. PINK1 Cleavage at position A103 by the mitochondrial protease PARL. Hum Mol Genet 2010; 20: 867–879.
  Article Google Scholar
• Jin SM, Lazarou M, Wang C, Kane LA, Narendra DP, Youle RJ . Mitochondrial membrane potential regulates PINK1 import and proteolytic destabilization by PARL. J Cell Biol 2010; 191: 933–942.
  Article CAS Google Scholar
• Shi G, Lee JR, Grimes DA, Racacho L, Ye D, Yang H et al. Functional alteration of PARL contributes to mitochondrial dysregulation in Parkinson's disease. Hum Mol Genet 2011 (E-pub ahead of print 25 February 2011).
• Baker RP, Young K, Feng L, Shi Y, Urban S . Enzymatic analysis of a rhomboid intramembrane protease implicates transmembrane helix 5 as the lateral substrate gate. Proc Natl Acad Sci USA 2007; 104: 8257–8262.
  Article CAS Google Scholar
• Koonin EV, Wolf YI . Constraints and plasticity in genome and molecular-phenome evolution. Nat Rev Genetics 2010; 11: 487–498.
  Article CAS Google Scholar
• Rawlings ND, Barrett AJ . Families of serine peptidases. Methods Enzymol 1994; 244: 19–61.
  Article CAS Google Scholar
• MacKenzie KR, Fleming KG . Association energetics of membrane spanning alpha-helices. Curr Opin Struct Biol 2008; 18: 412–419.
  Article CAS Google Scholar
• Maegawa S, Koide K, Ito K, Akiyama Y . The intramembrane active site of GlpG, an E. coli rhomboid protease, is accessible to water and hydrolyses an extramembrane peptide bond of substrates. Mol Microbiol 2007; 64: 435–447.
  Article CAS Google Scholar
• Tsukada H, Blow DM . Structure of alpha-chymotrypsin refined at 1.68 A resolution. J Mol Biol 1985; 184: 703–711.
  Article CAS Google Scholar
• Bernstein HD, Poritz MA, Strub K, Hoben PJ, Brenner S, Walter P . Model for signal sequence recognition from amino-acid sequence of 54K subunit of signal recognition particle. Nature 1989; 340: 482–486.
  Article CAS Google Scholar
• O′Neil KT, Erickson-Viitanen S, DeGrado WF . Photolabeling of calmodulin with basic, amphiphilic alpha-helical peptides containing p-benzoylphenylalanine. J Biol Chem 1989; 264: 14571–14578.
  PubMed Google Scholar
• Gellman SH . On the role of methionine residues in the sequence-independent recognition of nonpolar protein surfaces. Biochemistry 1991; 30: 6633–6636.
  Article CAS Google Scholar
• McGregor MJ, Islam SA, Sternberg MJ . Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J Mol Biol 1987; 198: 295–310.
  Article CAS Google Scholar
• Jeyaraju DV, Cisbani G, De Brito OM, Koonin EV, Pellegrini L . Hax1 lacks BH modules and is peripherally associated to heavy membranes: implications for Omi/HtrA2 and PARL activity in the regulation of mitochondrial stress and apoptosis. Cell Death Differ 2009; 16: 1622–1629.
  Article CAS Google Scholar
• Wang Y, Ha Y . Open-cap conformation of intramembrane protease GlpG. Proc Natl Acad Sci USA 2007; 104: 2098–2102.
  Article CAS Google Scholar
• Wang Y, Maegawa S, Akiyama Y, Ha Y . The role of L1 loop in the mechanism of rhomboid intramembrane protease GlpG. J Mol Biol 2007; 374: 1104–1113.
  Article CAS Google Scholar
• Muñoz V, Serrano L . Development of the multiple sequence approximation within the AGADIR model of alpha-helix formation: comparison with Zimm-Bragg and Lifson-Roig formalisms. Biopolymers 1997; 41: 495–509.
  Article Google Scholar
• Arnold K, Bordoli L, Kopp J, Schwede T . The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 2006; 22: 195–201.
  Article CAS Google Scholar
• Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY et al. Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci 2007 Chapter 2: Unit 2.9.
• Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 2010; 66: 12–21.
  Article CAS Google Scholar
• DeLano WL . The PyMOL molecular graphics system. DeLano Scientific 2002.