酵母苯丙氨酸tRNA在1.93埃分辨率下的晶体结构：重温经典结构
The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited.
作者信息
Shi H, Moore P B
机构信息
Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA.
出版信息
RNA. 2000 Aug;6(8):1091-105. doi: 10.1017/s1355838200000364.
Abstract
The crystal structure of the monoclinic form of yeast phenylalanine tRNA has been redetermined at a resolution of 1.93 A. The structure of yeast tRNAphe described here is more accurate than its predecessors not only because it incorporates higher resolution data, but also because it has been refined using techniques that had not been developed when its predecessors were determined more than 20 years ago. The 1.93 A resolution version of this structure differs interestingly from its predecessors in its details. In loop regions particularly, the backbone torsion angles in the new structure are not the same as those reported earlier. Several new divalent cation binding sites have been identified, and the water structure that has emerged is also different.
摘要
酵母苯丙氨酸tRNA单斜晶系形式的晶体结构已在1.93埃的分辨率下重新测定。这里描述的酵母tRNAphe结构比其先前的结构更精确，这不仅是因为它纳入了更高分辨率的数据，还因为它是使用20多年前测定其先前结构时尚未开发的技术进行精修的。该结构1.93埃分辨率版本在细节上与其先前版本有趣地不同。特别是在环区域，新结构中的主链扭转角与先前报道的不同。已鉴定出几个新的二价阳离子结合位点，并且呈现出的水结构也不同。
相似文献
1
The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited.
RNA. 2000 Aug;6(8):1091-105. doi: 10.1017/s1355838200000364.
2
The crystal structure of yeast phenylalanine tRNA at 2.0 A resolution: cleavage by Mg(2+) in 15-year old crystals.
J Mol Biol. 2000 Aug 11;301(2):401-14. doi: 10.1006/jmbi.2000.3950.
3
Mg(2+) binding to tRNA revisited: the nonlinear Poisson-Boltzmann model.
J Mol Biol. 2000 Jun 9;299(3):813-25. doi: 10.1006/jmbi.2000.3769.
4
Correlation between three-dimensional structure and chemical reactivity of transfer RNA.
Nucleic Acids Res. 1974 Jul;1(7):927-32. doi: 10.1093/nar/1.7.927.
5
A distinctive RNA fold: the solution structure of an analogue of the yeast tRNAPhe T Psi C domain.
Biochemistry. 1999 Jul 6;38(27):8647-56. doi: 10.1021/bi990118w.
6
Structure of the yeast tRNA m7G methylation complex.
Structure. 2008 Jan;16(1):52-61. doi: 10.1016/j.str.2007.10.025.
7
Site-specific hydrolysis of yeast tRNAPhe by anthraquinone-glycine and anthraquinone-iminodiacetate conjugates.
Nucleic Acids Symp Ser. 1995(34):109-10.
8
Altering the intermediate in the equilibrium folding of unmodified yeast tRNAPhe with monovalent and divalent cations.
Biochemistry. 2001 Mar 27;40(12):3629-38. doi: 10.1021/bi002646+.
9
Aminoglycoside binding displaces a divalent metal ion in a tRNA-neomycin B complex.
Nat Struct Biol. 2001 Jun;8(6):510-4. doi: 10.1038/88569.
10
Specific RNA cleavages induced by manganese ions.
FEBS Lett. 1995 Oct 23;374(1):62-8. doi: 10.1016/0014-5793(95)01077-r.
引用本文的文献
1
A pseudouridine synthase shapes tRNA structural dynamics through both catalysis and remodeling.
bioRxiv. 2025 May 9:2025.05.06.652307. doi: 10.1101/2025.05.06.652307.
2
Structure of fungal tRNA ligase Trl1 with RNA reveals conserved substrate-binding principles.
Nat Struct Mol Biol. 2025 Jun 25. doi: 10.1038/s41594-025-01589-3.
3
Top-Down Characterization of Yeast tRNA by Gas-Phase Fractionation and Collisionally Activated Dissociation Informed by Electron Photodetachment Charge Reduction Mass Spectrometry.
Anal Chem. 2025 Jun 24;97(24):12746-12754. doi: 10.1021/acs.analchem.5c01561. Epub 2025 Jun 9.
4
The highly conserved intron of tyrosine tRNA is critical for A58 modification and controls the integrated stress response.
Proc Natl Acad Sci U S A. 2025 Jun 10;122(23):e2502364122. doi: 10.1073/pnas.2502364122. Epub 2025 Jun 6.
5
Armless hairpin-like tRNAs in Romanomermis culicivorax: Evolutionary adaptation of a mitochondrial elongation factor EF-Tu.
J Biol Chem. 2025 May 24;301(7):110294. doi: 10.1016/j.jbc.2025.110294.
6
Structural Impact of 3-methylcytosine Modification on the Anticodon Stem-loop of a Neuronally-enriched Arginine tRNA.
J Mol Biol. 2025 Aug 15;437(16):169096. doi: 10.1016/j.jmb.2025.169096. Epub 2025 Mar 29.
7
tRNA pseudouridine synthase D (TruD) from modifies U13 in tRNA, tRNA, and tRNA and U35 in tRNA.
RNA. 2025 May 16;31(6):850-867. doi: 10.1261/rna.080405.125.
8
An alternative adaptation strategy of the CCA-adding enzyme to accept noncanonical tRNA substrates in Ascaris suum.
J Biol Chem. 2025 Apr;301(4):108414. doi: 10.1016/j.jbc.2025.108414. Epub 2025 Mar 17.
9
Chemical Evolution of Life on Earth.
Genes (Basel). 2025 Feb 13;16(2):220. doi: 10.3390/genes16020220.
10
Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure - Part I: Mg2.
Nucleic Acids Res. 2025 Jan 7;53(1). doi: 10.1093/nar/gkae1148.
本文引用的文献
1
Crystal structures of two plasmid copy control related RNA duplexes: An 18 base pair duplex at 1.20 A resolution and a 19 base pair duplex at 1.55 A resolution.
Biochemistry. 1999 Nov 9;38(45):14784-92. doi: 10.1021/bi9912793.
2
Crystal structure of the ribosomal RNA domain essential for binding elongation factors.
Proc Natl Acad Sci U S A. 1998 Nov 10;95(23):13436-41. doi: 10.1073/pnas.95.23.13436.
3
Crystallography & NMR system: A new software suite for macromolecular structure determination.
Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21. doi: 10.1107/s0907444998003254.
4
Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain.
Cell. 1997 Nov 28;91(5):705-12. doi: 10.1016/s0092-8674(00)80457-2.
5
RNA hydration: a detailed look.
Biochemistry. 1996 Jul 2;35(26):8489-94. doi: 10.1021/bi9607214.
6
Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement.
Proteins. 1994 Aug;19(4):277-90. doi: 10.1002/prot.340190403.
7
Three-dimensional structure of a hammerhead ribozyme.
Nature. 1994 Nov 3;372(6501):68-74. doi: 10.1038/372068a0.
8
Crystal and molecular structure of r(CGCGAAUUAGCG): an RNA duplex containing two G(anti).A(anti) base pairs.
Structure. 1994 Jun 15;2(6):483-94. doi: 10.1016/S0969-2126(00)00049-6.
9
X-ray diffraction study of the zinc(II) binding sites in yeast phenylalanine transfer RNA. Preferential binding of zinc to guanines in purine-purine sequences.
Biochim Biophys Acta. 1983 Mar 15;756(1):111-8. doi: 10.1016/0304-4165(83)90030-2.
10
Structure of yeast phenylalanine tRNA at 3 A resolution.
Nature. 1974 Aug 16;250(467):546-51. doi: 10.1038/250546a0.
Zotero 插件