title: A self-compartmentalizing hexamer serine protease from Pyrococcus horikoshii: substrate selection achieved through multimerization.
abstract: Oligopeptidases impose a size limitation on their substrates, the mechanism of which has long been under debate. Here we present the structure of a hexameric serine protease, an oligopeptidase from Pyrococcus horikoshii (PhAAP), revealing a complex, self-compartmentalized inner space, where substrates may access the monomer active sites passing through a double-gated "check-in" system, first passing through a pore on the hexamer surface and then turning to enter through an even smaller opening at the monomers' domain interface. This substrate screening strategy is unique within the family. We found that among oligopeptidases, a residue of the catalytic apparatus is positioned near an amylogenic β-edge, which needs to be protected to prevent aggregation, and we found that different oligopeptidases use different strategies to achieve such an end. We propose that self-assembly within the family results in characteristically different substrate selection mechanisms coupled to different multimerization states.
authors: Protein Modeling Research Group, Hungarian Academy of Sciences, Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary.
authors: Dóra K
authors: DK
authors: Menyhárd
authors: Anna
authors: A
authors: Kiss-Szemán
authors: Éva
authors: É
authors: Tichy-Rács
authors: Balázs
authors: B
authors: Hornung
authors: Krisztina
authors: K
authors: Rádi
authors: Zoltán
authors: Z
authors: Szeltner
authors: Klarissza
authors: K
authors: Domokos
authors: Ilona
authors: I
authors: Szamosi
authors: Gábor
authors: G
authors: Náray-Szabó
authors: László
authors: L
authors: Polgár
authors: Veronika
authors: V
authors: Harmat
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry*; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004791:Enzyme Inhibitors / Q000737:chemistry; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry; D055503:Protein Multimerization; D055550:Protein Stability; D020836:Protein Structure, Quaternary; D043902:Pyrococcus horikoshii / Q000201:enzymology*; D012697:Serine Endopeptidases / Q000737:chemistry*; D013379:Substrate Specificity
chemical_list: D019843:Archaeal Proteins; D004791:Enzyme Inhibitors; D010455:Peptides; D012697:Serine Endopeptidases
keywords: Acylaminoacyl Peptidase; Aggregation; Amylogenic β-Strand; Peptide Interactions; Protein Self-assembly; Self-compartmentalization; Serine Protease; Substrate Size Selection; X-ray Crystallography
references: Acta Crystallogr D Biol Crystallogr. 1994 Sep 1;50(Pt 5):760-3
references: 15299374
references: EMBO Rep. 2007 Aug;8(8):737-42
references: 17668004
references: Nat Chem Biol. 2009 Jan;5(1):15-22
references: 19088715
references: J Mol Biol. 1990 Jul 20;214(2):497-525
references: 2380986
references: PLoS One. 2011;6(10):e25888
references: 22016782
references: J Lab Clin Med. 1992 Oct;120(4):546-52
references: 1328432
references: Proc Natl Acad Sci U S A. 2005 Mar 8;102(10):3599-604
references: 15738423
references: EMBO J. 1998 Jan 2;17(1):1-9
references: 9427736
references: Cell. 1998 Jul 24;94(2):161-70
references: 9695945
references: Proteins. 2005 Aug 15;60(3):504-12
references: 15971204
references: Biochim Biophys Acta. 2009 Aug;1794(8):1204-10
references: 19303951
references: J Mol Biol. 1998 Jun 19;279(4):889-900
references: 9642069
references: J Chem Theory Comput. 2008 Mar;4(3):435-47
references: 26620784
references: Biochem Biophys Res Commun. 2003 Mar 21;302(4):849-54
references: 12646248
references: Biophys J. 2005 Dec;89(6):4234-44
references: 16169977
references: J Struct Biol. 2008 May;162(2):312-23
references: 18325786
references: Structure. 1997 Dec 15;5(12):1571-84
references: 9438866
references: Protein Sci. 2004 Feb;13(2):412-21
references: 14718659
references: Cell Mol Life Sci. 2002 Feb;59(2):349-62
references: 11915948
references: Biochim Biophys Acta. 2008 Sep;1784(9):1176-83
references: 18590836
references: J Comput Chem. 2004 Aug;25(11):1400-15
references: 15185334
references: Biochim Biophys Acta. 2004 Dec 24;1739(1):5-25
references: 15607113
references: EMBO J. 1991 Jun;10(6):1297-302
references: 2026135
references: Genomics. 1989 Apr;4(3):355-61
references: 2565880
references: Proteins. 2007 Nov 15;69(3):633-43
references: 17623862
references: J Mol Biol. 2002 Dec 13;324(5):1041-50
references: 12470958
references: Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):12-21
references: 20057044
references: Acta Crystallogr D Biol Crystallogr. 2007 Feb;63(Pt 2):179-87
references: 17242511
references: Acta Crystallogr D Biol Crystallogr. 1997 May 1;53(Pt 3):240-55
references: 15299926
references: Oncogene. 1991 Jul;6(7):1293-5
references: 1861871
references: Acta Crystallogr D Biol Crystallogr. 1999 Jan;55(Pt 1):191-205
references: 10089410
references: Curr Protein Pept Sci. 2008 Feb;9(1):96-107
references: 18336325
references: Science. 1995 Aug 18;269(5226):945-50
references: 7638617
references: J Biol Chem. 2008 Aug 1;283(31):21827-36
references: 18524775
references: Proc Natl Acad Sci U S A. 2003 Apr 29;100(9):5063-8
references: 12690074
references: Angew Chem Int Ed Engl. 2010 Aug 16;49(35):6111-5
references: 20645368
references: Mol Pharmacol. 2000 Sep;58(3):577-83
references: 10953051
references: J Biol Chem. 2002 Nov 8;277(45):42613-22
references: 12202494
references: J Struct Biol. 2011 Sep;175(3):362-71
references: 21741480
references: Appl Environ Microbiol. 2007 Mar;73(6):2005-8
references: 17259360
references: Bioorg Med Chem Lett. 2010 Jan 15;20(2):571-5
references: 19969453
references: Nature. 2003 Dec 18;426(6968):884-90
references: 14685248
references: Acta Crystallogr D Biol Crystallogr. 2006 Sep;62(Pt 9):1002-11
references: 16929101
references: J Pharmacol Exp Ther. 2001 Nov;299(2):528-35
references: 11602663
references: Nature. 1991 Jul 18;352(6332):213-8
references: 1857417
references: Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67
references: 22505256
references: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
references: 15572765
references: Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):125-32
references: 20124692
references: EMBO J. 2010 Oct 20;29(20):3520-30
references: 20834233
references: J Biol Chem. 2010 Jul 9;285(28):21487-95
references: 20444688
references: J Mol Biol. 2007 Apr 27;368(2):509-20
references: 17350041
references: Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2754-9
references: 11880627
references: EMBO J. 2002 Oct 15;21(20):5343-52
references: 12374735
references: J Biol Chem. 2011 Jan 21;286(3):1987-98
references: 21084296
references: Nat Methods. 2010 Mar;7(3):237-42
references: 20154676
references: J Biol Chem. 2010 Dec 10;285(50):39249-59
references: 20926390
references: J Mol Biol. 2008 Sep 12;381(4):897-912
references: 18585390
references: J Mol Biol. 2006 Jan 27;355(4):768-83
references: 16330047
references: J Chem Theory Comput. 2010 Feb 9;6(2):459-66
references: 26617301
references: Protein Sci. 2005 Mar;14(3):653-62
references: 15689507
references: Acta Crystallogr A. 2008 Jan;64(Pt 1):112-22
references: 18156677