Structural basis for recognition of S-adenosylhomocysteine by riboswitches

被引:68
作者
Edwards, Andrea L. [1 ]
Reyes, Francis E. [1 ]
Heroux, Annie [2 ]
Batey, Robert T. [1 ]
机构
[1] Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
[2] Brookhaven Natl Lab, Dept Biol, Upton, NY 11973 USA
基金
美国国家卫生研究院;
关键词
riboswitch; S-adenosylhomocysteine; X-ray crystallography; isothermal titration calorimetry; chemical probing; RNA STRUCTURE-ANALYSIS; SHAPE CHEMISTRY; TERTIARY INTERACTIONS; CRYSTAL-STRUCTURE; HEAT-CAPACITY; BINDING; ADENOSYLMETHIONINE; TRANSCRIPTION; BOX; CONFORMATION;
D O I
10.1261/rna.2341610
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
S-adenosyl-(L)-homocysteine (SAH) riboswitches are regulatory elements found in bacterial mRNAs that up-regulate genes involved in the S-adenosyl-(L)-methionine (SAM) regeneration cycle. To understand the structural basis of SAH-dependent regulation by RNA, we have solved the structure of its metabolite-binding domain in complex with SAH. This structure reveals an unusual pseudoknot topology that creates a shallow groove on the surface of the RNA that binds SAH primarily through interactions with the adenine ring and methionine main chain atoms and discriminates against SAM through a steric mechanism. Chemical probing and calorimetric analysis indicate that the unliganded RNA can access bound-like conformations that are significantly stabilized by SAH to direct folding of the downstream regulatory switch. Strikingly, we find that metabolites bearing an adenine ring, including ATP, bind this aptamer with sufficiently high affinity such that normal intracellular concentrations of these compounds may influence regulation of the riboswitch.
引用
收藏
页码:2144 / 2155
页数:12
相关论文
共 57 条
[1]   PHENIX:: building new software for automated crystallographic structure determination [J].
Adams, PD ;
Grosse-Kunstleve, RW ;
Hung, LW ;
Ioerger, TR ;
McCoy, AJ ;
Moriarty, NW ;
Read, RJ ;
Sacchettini, JC ;
Sauter, NK ;
Terwilliger, TC .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2002, 58 :1948-1954
[2]   THE CCP4 SUITE - PROGRAMS FOR PROTEIN CRYSTALLOGRAPHY [J].
BAILEY, S .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1994, 50 :760-763
[3]   Structural and energetic analysis of metal ions essential to SRP signal recognition domain assembly [J].
Batey, RT ;
Doudna, JA .
BIOCHEMISTRY, 2002, 41 (39) :11703-11710
[4]   Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine [J].
Batey, RT ;
Gilbert, SD ;
Montange, RK .
NATURE, 2004, 432 (7015) :411-415
[5]   Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli [J].
Bennett, Bryson D. ;
Kimball, Elizabeth H. ;
Gao, Melissa ;
Osterhout, Robin ;
Van Dien, Stephen J. ;
Rabinowitz, Joshua D. .
NATURE CHEMICAL BIOLOGY, 2009, 5 (08) :593-599
[6]   Riboswitches as antibacterial drug targets [J].
Blount, Kenneth F. ;
Breaker, Ronald R. .
NATURE BIOTECHNOLOGY, 2006, 24 (12) :1558-1564
[7]   Allosteric properties of inosine monophosphate dehydrogenase revealed through the thermodynamics of binding of inosine 5'-monophosphate and mycophenolic acid. Temperature dependent heat capacity of binding as a signature of ligand-coupled conformational equilibria [J].
Bruzzese, FJ ;
Connelly, PR .
BIOCHEMISTRY, 1997, 36 (34) :10428-10438
[8]   Stimulation of-1 programmed ribosomal frameshifting by a metabolite-responsive RNA pseudoknot [J].
Chou, Ming-Yuan ;
Lin, Szu-Chieh ;
Chang, Kung-Yao .
RNA, 2010, 16 (06) :1236-1244
[9]   MolProbity: structure validation and all-atom contact analysis for nucleic acids and their complexes [J].
Davis, IW ;
Murray, LW ;
Richardson, JS ;
Richardson, DC .
NUCLEIC ACIDS RESEARCH, 2004, 32 :W615-W619
[10]   Crystal structure of a hepatitis delta virus ribozyme [J].
Ferré-D'Amaré, AR ;
Zhou, KH ;
Doudna, JA .
NATURE, 1998, 395 (6702) :567-574