Lee Jung C, Cannone Jamie J, Gutell Robin R
The University of Texas at Austin, College of Pharmacy, 1 University Station, A1900, Austin, TX 78712-0120, USA.
J Mol Biol. 2003 Jan 3;325(1):65-83. doi: 10.1016/s0022-2836(02)01106-3.
The lonepair triloop (LPTL) is an RNA structural motif that contains a single ("lone") base-pair capped by a hairpin loop containing three nucleotides. The two nucleotides immediately outside of this motif (5' and 3' to the lonepair) are not base-paired to one another, restricting the length of this helix to a single base-pair. Four examples of this motif, along with three tentative examples, were initially identified in the 16S and 23S rRNAs with covariation analysis. An evaluation of the recently determined crystal structures of the Thermus thermophilus 30S and Haloarcula marismortui 50S ribosomal subunits revealed the authenticity for all of these proposed interactions and identified 16 more LPTLs in the 5S, 16S and 23S rRNAs. This motif is found in the T loop in the tRNA crystal structures. The lonepairs are positioned, in nearly all examples, immediately 3' to a regular secondary structure helix and are stabilized by coaxial stacking onto this flanking helix. In all but two cases, the nucleotides in the triloop are involved in a tertiary interaction with another section of the rRNA, establishing an overall three-dimensional function for this motif. Of these 24 examples, 14 occur in multi-stem loops, seven in hairpin loops and three in internal loops. While the most common lonepair, U:A, occurs in ten of the 24 LPTLs, the remaining 14 LPTLs contain seven different base-pair types. Only a few of these lonepairs adopt the standard Watson-Crick base-pair conformations, while the majority of the base-pairs have non-standard conformations. While the general three-dimensional conformation is similar for all examples of this motif, characteristic differences lead to several subtypes present in different structural environments. At least one triloop nucleotide in 22 of the 24 LPTLs in the rRNAs and tRNAs forms a tertiary interaction with another part of the RNA. When a LPTL containing the GNR or UYR triloop sequence forms a tertiary interaction with the first (and second) triloop nucleotide, it recruits a fourth nucleotide to mediate stacking and mimic the tetraloop conformation. Approximately half of the LPTL motifs are in close association with proteins. The majority of these LPTLs are positioned at sites in rRNAs that are conserved in the three phylogenetic domains; a few of these occur in regions of the rRNA associated with ribosomal function, including the presumed site of peptidyl transferase activity in the 23S rRNA.
孤对三核苷酸环（LPTL）是一种RNA结构基序，它包含一个由含有三个核苷酸的发夹环封闭的单一（“孤”）碱基对。该基序外侧紧邻的两个核苷酸（孤对的5'和3'端）彼此未配对，将该螺旋的长度限制为一个碱基对。最初通过共变分析在16S和23S rRNA中鉴定出了该基序的四个实例以及三个暂定实例。对嗜热栖热菌30S核糖体亚基和嗜盐栖热放线菌50S核糖体亚基最近确定的晶体结构进行评估，揭示了所有这些推测相互作用的真实性，并在5S、16S和23S rRNA中又鉴定出16个LPTL。在tRNA晶体结构的T环中发现了这种基序。在几乎所有实例中，孤对都位于规则二级结构螺旋的紧邻3'端，并通过同轴堆积到该侧翼螺旋上而得以稳定。除了两个实例外，三核苷酸环中的核苷酸都与rRNA的另一部分发生三级相互作用，为该基序建立了整体三维功能。在这24个实例中，14个出现在多茎环中，7个出现在发夹环中，3个出现在内环中。虽然最常见的孤对是U:A，出现在24个LPTL中的10个中，但其余14个LPTL包含七种不同的碱基对类型。这些孤对中只有少数采用标准的沃森-克里克碱基对构象，而大多数碱基对具有非标准构象。虽然该基序的所有实例的总体三维构象相似，但特征差异导致在不同结构环境中存在几种亚型。rRNA和tRNA中24个LPTL中的22个中至少有一个三核苷酸环核苷酸与RNA的另一部分形成三级相互作用。当含有GNR或UYR三核苷酸环序列的LPTL与第一个（和第二个）三核苷酸环核苷酸形成三级相互作用时，它会招募第四个核苷酸来介导堆积并模拟四环构象。大约一半的LPTL基序与蛋白质紧密相关。这些LPTL中的大多数位于rRNA中在三个系统发育域中保守的位点；其中一些出现在与核糖体功能相关的rRNA区域，包括23S rRNA中假定的肽基转移酶活性位点。
