Structure of rhomboid protease in a lipid environment.
Structures of the prokaryotic homologue of rhomboid proteases reveal a core of six transmembrane helices, with the active-site residues residing in a hydrophilic cavity. The native environment of rhomboid protease is a lipid bilayer, yet all the structures determined thus far are in a nonnative detergent environment. There remains a possibility of structural artefacts arising from the use of detergents. In an attempt to address the effect of detergents on the structure of rhomboid protease, crystals of GlpG, an Escherichia coli rhomboid protease in a lipid environment, were obtained using two alternative approaches. The structure of GlpG refined to 1. 7-Å resolution was obtained from crystals grown in the presence of lipid bicelles. This structure reveals well-ordered and partly ordered lipid molecules forming an annulus around the protein. Lipid molecules adapt to the surface features of protein and arrange such that they match the hydrophobic thickness of GlpG. Virtually identical two-dimensional crystals were also obtained after detergent removal by dialysis. A comparison of an equivalent structure determined in a completely delipidated detergent environment provides insights on how detergent substitutes for lipid. A detergent molecule is also observed close to the active site, helping to postulate a model for substrate binding and hydrolysis in rhomboids.
MRC Laboratory of Molecular Biology, Cambridge, UK. vkumar@mrc-lmb.cam.ac.uk
Kutti R
KR
Vinothkumar
D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D003902:Detergents / Q000378:metabolism; D010450:Endopeptidases / Q000737:chemistry / Q000378:metabolism; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism; D006868:Hydrolysis; D057927:Hydrophobic and Hydrophilic Interactions; D008051:Lipid Bilayers / Q000378:metabolism*; D008565:Membrane Proteins / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D010447:Peptide Hydrolases / Q000737:chemistry / Q000378:metabolism; D017433:Protein Structure, Secondary; D013379:Substrate Specificity
D004268:DNA-Binding Proteins; D003902:Detergents; D029968:Escherichia coli Proteins; C102898:GlpG protein, E coli; D008051:Lipid Bilayers; D008565:Membrane Proteins; D010450:Endopeptidases; D010447:Peptide Hydrolases
Mol Cell. 2009 Dec 25;36(6):1048-59
20064469
Biochim Biophys Acta. 2004 Nov 3;1666(1-2):62-87
15519309
J Mol Biol. 1983 May 15;166(2):211-7
6854644
Proc Natl Acad Sci U S A. 2007 May 15;104(20):8257-62
17463085
Biochim Biophys Acta. 2004 Nov 3;1666(1-2):2-18
15519305
Semin Cell Dev Biol. 2009 Apr;20(2):240-50
19059492
Biochim Biophys Acta. 1976 Jul 20;441(1):38-47
782533
Science. 2005 Apr 29;308(5722):654-9
15802565
Genome Res. 2007 Nov;17(11):1634-46
17938163
Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):1883-8
15684070
Biophys J. 2005 Apr;88(4):2626-37
15665131
Acta Crystallogr D Biol Crystallogr. 1994 Sep 1;50(Pt 5):760-3
15299374
Nature. 2006 Nov 9;444(7116):179-80
17051161
Q Rev Biophys. 2010 Feb;43(1):65-158
20667175
Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):72-82
16369096
J Mol Biol. 2007 Dec 7;374(4):1104-13
17976648
J Struct Biol. 1999 Apr-May;125(2-3):223-8
10222278
J Struct Biol. 1996 Jan-Feb;116(1):9-16
8742717
Science. 2004 Aug 20;305(5687):1119-23
15326347
EMBO J. 2010 Nov 17;29(22):3797-809
20890268
Q Rev Biophys. 1988 Nov;21(4):429-77
3071823
Ultramicroscopy. 2007 Feb-Mar;107(2-3):73-80
16872749
J Mol Biol. 1999 Aug 27;291(4):899-911
10452895
Curr Opin Struct Biol. 2008 Aug;18(4):406-11
18495472
J Mol Biol. 1996 Jun 14;259(3):393-421
8676377
Micron. 2001 Jul;32(5):517-40
11163725
Proc Natl Acad Sci U S A. 2007 Jan 9;104(2):462-6
17190827
Biochim Biophys Acta. 1998 Nov 10;1376(3):401-15
9805000
Mol Cell. 2003 Jun;11(6):1425-34
12820957
Nature. 2005 Dec 1;438(7068):633-8
16319884
Biochem J. 2010 Jan 15;425(3):501-12
20070259
Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):48-57
16369093
Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
15572765
Structure. 2009 Mar 11;17(3):395-405
19278654
Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
20124702
Chem Rev. 2009 Apr;109(4):1599-612
19226105
Acta Crystallogr D Biol Crystallogr. 2007 Jan;63(Pt 1):32-41
17164524
Structure. 2004 Nov;12(11):2009-14
15530365
EMBO J. 2010 May 19;29(10):1652-8
20389283
Genes Dev. 2000 Jul 1;14(13):1651-63
10887159
Mol Microbiol. 2007 May;64(4):1028-37
17501925
Trends Biochem Sci. 2007 Jun;32(6):259-70
17481903
J Mol Biol. 2002 Feb 8;316(1):1-6
11829498
Nature. 2007 Nov 15;450(7168):376-82
18004376
J Mol Biol. 1994 Jul 22;240(4):281-7
8035455
Biophys J. 2008 May 15;94(10):3996-4013
18234817
Q Rev Biophys. 1992 Feb;25(1):1-49
1589568
Proc Natl Acad Sci U S A. 2007 Jan 16;104(3):750-4
17210913
Nat Struct Mol Biol. 2006 Dec;13(12):1084-91
17099694
Annu Rev Genet. 2008;42:191-210
18605900
J Biol Chem. 2001 Aug 31;276(35):32395-8
11432876