A structural database for k-turn motifs in RNA

被引：64

作者：

Schroeder, Kersten T. ^{[1
]}

McPhee, Scott A. ^{[1
]}

Ouellet, Jonathan ^{[1
]}

Lilley, David M. J. ^{[1
]}

机构：

[1] Univ Dundee, Canc Res UK Nucle Acid Struct Res Grp, Dundee DD1 5EH, Scotland

来源：

RNA | 2010年 / 16卷 / 08期

基金：

英国惠康基金;

关键词：

RNA structure; kink turn; motif; BOX C/D RNA; PRERIBOSOMAL RNA; MOLECULAR-BASIS; BINDING MOTIF; L7AE PROTEIN; SITE; LOOP; RECOGNITION; METHYLATION; MUTATIONS;

D O I：

10.1261/rna.2207910

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：

The kink-turn (k-turn) is a common structural motif in RNA that introduces a tight kink into the helical axis. k-turns play an important architectural role in RNA structures and serve as binding sites for a number of proteins. We have created a database of known and postulated k-turn sequences and three-dimensional (3D) structures, available via the internet. This site provides (1) a database of sequence and structure, as a resource for the RNA community, and (2) a tool to enable the manipulation and comparison of 3D structures where known.

引用

页码：1463 / 1468

页数：6

共 43 条

[1] The SBP2 and 15.5 kD/Snu13p proteins share the same RNA binding domain: Identification of SBP2 amino acids important to SECIS RNA binding [J].

Allmang, C ;

Carbon, P ;

Krol, A .

RNA, 2002, 8 (10) :1308-1318

[2] Mutations outside the anisomycin-binding site can make ribosomes drug-resistant [J].

Blaha, Gregor ;

Gurel, Guliz ;

Schroeder, Susan J. ;

Moore, Peter B. ;

Steitz, Thomas A. .

JOURNAL OF MOLECULAR BIOLOGY, 2008, 379 (03) :505-519

[3] A loop-loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control [J].

Blouin, Simon ;

Lafontaine, Daniel A. .

RNA, 2007, 13 (08) :1256-1267

[4] In vitro RNP assembly and methylation guide activity of an unusual box C/D RNA, cis-acting archaeal pre-tRNATrp [J].

Bortolin, ML ;

Bachellerie, JP ;

Clouet-d'Orval, B .

NUCLEIC ACIDS RESEARCH, 2003, 31 (22) :6524-6535

[5] The Comparative RNA Web (CRW) Site:: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs:: Correction (vol 3, pg 2, 2002) -: art. no. 15 [J].

Cannone, JJ ;

Subramanian, S ;

Schnare, MN ;

Collett, JR ;

D'Souza, LM ;

Du, YS ;

Feng, B ;

Lin, N ;

Madabusi, LV ;

Müller, KM ;

Pande, N ;

Shang, ZD ;

Yu, N ;

Gutell, RR .

BMC BIOINFORMATICS, 2002, 3 (1)

[6] Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif [J].

Cojocaru, V ;

Klement, R ;

Jovin, TM .

NUCLEIC ACIDS RESEARCH, 2005, 33 (10) :3435-3446

[7] WebLogo: A sequence logo generator [J].

Crooks, GE ;

Hon, G ;

Chandonia, JM ;

Brenner, SE .

GENOME RESEARCH, 2004, 14 (06) :1188-1190

[8]

DeLano W.L., 2002, The PyMOL molecular graphics system

[9] Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs [J].

Ganot, P ;

Bortolin, ML ;

Kiss, T .

CELL, 1997, 89 (05) :799-809

[10] Rfam: updates to the RNA families database [J].

Gardner, Paul P. ;

Daub, Jennifer ;

Tate, John G. ;

Nawrocki, Eric P. ;

Kolbe, Diana L. ;

Lindgreen, Stinus ;

Wilkinson, Adam C. ;

Finn, Robert D. ;

Griffiths-Jones, Sam ;

Eddy, Sean R. ;

Bateman, Alex .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D136-D140

← 1 2 3 4 5 →