title: The complete VS ribozyme in solution studied by small-angle X-ray scattering.
abstract: We have used small-angle X-ray solution scattering to obtain ab initio shape reconstructions of the complete VS ribozyme. The ribozyme occupies an electron density envelope with an irregular shape, into which helical sections have been fitted. The ribozyme is built around a core comprising a near-coaxial stack of three helices, organized by two three-way helical junctions. An additional three-way junction formed by an auxiliary helix directs the substrate stem-loop, juxtaposing the cleavage site with an internal loop to create the active complex. This is consistent with the current view of the probable mechanism of trans-esterification in which adenine and guanine nucleobases contributed by the interacting loops combine in general acid-base catalysis.
authors.affiliation: Department of Physics, Geballe Laboratory of Advanced Materials, Stanford University, Stanford, CA 94305, USA.
authors.forename: Jan
authors.initials: J
authors.lastname: Lipfert
authors.forename: Jonathan
authors.initials: J
authors.lastname: Ouellet
authors.forename: David G
authors.initials: DG
authors.lastname: Norman
authors.forename: Sebastian
authors.initials: S
authors.lastname: Doniach
authors.forename: David M J
authors.initials: DM
authors.lastname: Lilley
mesh_terms: D001483:Base Sequence; D002021:Buffers; D020134:Catalytic Domain; D004722:Endoribonucleases / Q000737:chemistry*; D008274:Magnesium / Q000378:metabolism / Q000494:pharmacology; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry*; D053838:Scattering, Small Angle; D014961:X-Ray Diffraction
chemical_list: D002021:Buffers; D016337:RNA, Catalytic; D004722:Endoribonucleases; C438195:varkud satellite ribozyme; D008274:Magnesium
references.citation: EMBO J. 2001 Mar 15;20(6):1415-24
references.pmid: 11250907
references.citation: Chem Biol. 2007 Jan;14(1):97-105
references.pmid: 17196404
references.citation: Science. 2006 Sep 22;313(5794):1752-6
references.pmid: 16990543
references.citation: Biophys J. 1999 Jun;76(6):2879-86
references.pmid: 10354416
references.citation: Biochemistry. 2004 Feb 3;43(4):1118-25
references.pmid: 14744158
references.citation: Biochemistry. 2006 Jun 27;45(25):7861-71
references.pmid: 16784238
references.citation: Annu Rev Biophys Biomol Struct. 2007;36:307-27
references.pmid: 17284163
references.citation: EMBO J. 2002 May 15;21(10):2461-71
references.pmid: 12006498
references.citation: J Mol Biol. 2001 Nov 9;313(5):1013-9
references.pmid: 11700057
references.citation: J Mol Biol. 2001 Sep 28;312(4):663-74
references.pmid: 11575922
references.citation: Nat Struct Biol. 2003 Sep;10(9):708-12
references.pmid: 12881719
references.citation: EMBO J. 1996 Jun 3;15(11):2820-5
references.pmid: 8654379
references.citation: Cell. 1990 May 18;61(4):685-96
references.pmid: 2160856
references.citation: Chem Rev. 2001 Jun;101(6):1763-78
references.pmid: 11709998
references.citation: RNA. 2004 May;10(5):880-8
references.pmid: 15100442
references.citation: Nucleic Acids Res. 2001 Dec 15;29(24):5115-20
references.pmid: 11812844
references.citation: Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9308-13
references.pmid: 12883002
references.citation: EMBO J. 2007 May 16;26(10):2489-500
references.pmid: 17464286
references.citation: Biochemistry. 2003 Apr 15;42(14):4265-76
references.pmid: 12680781
references.citation: Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7003-8
references.pmid: 12782785
references.citation: EMBO J. 1995 Jan 16;14(2):368-76
references.pmid: 7835347
references.citation: J Am Chem Soc. 2004 Sep 8;126(35):10848-9
references.pmid: 15339162
references.citation: EMBO J. 2001 Oct 1;20(19):5461-9
references.pmid: 11574478
references.citation: Nat Struct Biol. 1999 Jun;6(6):544-9
references.pmid: 10360357
references.citation: J Mol Biol. 2004 Aug 20;341(4):935-49
references.pmid: 15328609
references.citation: J Mol Biol. 2002 Jul 12;320(3):443-54
references.pmid: 12096902
references.citation: J Am Chem Soc. 2005 Apr 13;127(14):5026-7
references.pmid: 15810830
references.citation: J Mol Biol. 2007 Feb 2;365(5):1393-406
references.pmid: 17118400
references.citation: Biochemistry. 1999 Aug 24;38(34):11040-50
references.pmid: 10460159
references.citation: Proc Natl Acad Sci U S A. 1995 May 9;92(10):4686-90
references.pmid: 7753865
references.citation: EMBO J. 2002 Sep 2;21(17):4691-8
references.pmid: 12198171
references.citation: RNA. 2006 Jan;12(1):83-93
references.pmid: 16373494
references.citation: Mol Cell. 1998 May;1(6):873-81
references.pmid: 9660970
references.citation: J Magn Reson. 2003 Jan;160(1):65-73
references.pmid: 12565051
references.citation: J Appl Crystallogr. 2009 Apr 1;42(Pt 2):342-346
references.pmid: 27630371