The GANC tetraloop: a novel motif in the group IIC intron structure.
Tetraloops are a common building block for RNA tertiary structure, and most tetraloops fall into one of three well-characterized classes: GNRA, UNCG, and CUYG. Here, we present the sequence and structure of a fourth highly conserved class of tetraloop that occurs only within the zeta-zeta' interaction of group IIC introns. This GANC tetraloop was identified, along with an unusual cognate receptor, in the crystal structure of the group IIC intron and through phylogenetic analysis of intron RNA sequence alignments. Unlike conventional tetraloop-receptor interactions, which are stabilized by extensive hydrogen-bonding interactions, the GANC-receptor interaction is limited to a single base stack between the conserved adenosine of the tetraloop and a single purine of the receptor, which consists of a one- to three-nucleotide bulge and does not contain an A-platform. Unlike GNRA tetraloops, the GANC tetraloop forms a sharp angle relative to the adjacent helix, bending by approximately 45 degrees toward the major groove side of the helix. These structural attributes allow GANC tetraloops to fit precisely within the group IIC intron core, thereby demonstrating that structural motifs can adapt to function in a specific niche.
Keating
Kevin S
KS
Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA.
Toor
Navtej
N
Pyle
Anna Marie
AM
D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics; D007438:Introns; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry / Q000235:genetics
D012313:RNA
Nucleic Acids Res. 2003 Aug 15;31(16):4755-61
12907716
Science. 1976 Nov 19;194(4267):796-806
790568
Science. 1996 Sep 20;273(5282):1696-9
8781229
RNA. 1996 Nov;2(11):1161-72
8903346
Nucleic Acids Res. 2006;34(22):6461-71
17130159
Science. 2008 Apr 4;320(5872):77-82
18388288
Biochemistry. 2004 Jun 29;43(25):7992-8
15209494
RNA. 2001 Apr;7(4):499-512
11345429
Nucleic Acids Res. 2003 Jan 1;31(1):424-6
12520040
Biochemistry. 1995 Nov 7;34(44):14416-27
7578046
RNA. 2003 Mar;9(3):355-63
12592009
Annu Rev Biochem. 1999;68:287-300
10872451
Nucleic Acids Res. 2005 Apr 06;33(6):2003-11
15814817
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W375-83
17452350
Nucleic Acids Res. 2000 Jan 1;28(1):235-42
10592235
Nature. 1994 Nov 3;372(6501):111-3
7526219
Mol Cell Biol. 1995 Aug;15(8):4479-88
7623838
Science. 1996 Sep 20;273(5282):1678-85
8781224
Structure. 2001 Mar 7;9(3):221-31
11286889
EMBO J. 1995 Mar 15;14(6):1276-85
7720718
RNA. 2008 Mar;14(3):465-81
18192612
Nature. 2000 Jul 20;406(6793):315-8
10917534
Proc Natl Acad Sci U S A. 1990 Nov;87(21):8467-71
2236056
Mol Biol Evol. 2003 Jul;20(7):1134-42
12777534
J Mol Biol. 2002 Jul 12;320(3):455-74
12096903
RNA. 1995 Apr;1(2):219-22
7585251
J Mol Biol. 2007 Sep 28;372(4):942-957
17707400
Nucleic Acids Res. 1991 Nov 11;19(21):5901-5
1719483
J Bacteriol. 2001 Apr;183(8):2560-9
11274116
RNA. 2001 Aug;7(8):1142-52
11497432