The crystal structure of yeast phenylalanine tRNA at 2.0 Å resolution:: Cleavage by Mg2+ in 15-year old crystals

被引:119
作者
Jovine, L [1 ]
Djordjevic, S [1 ]
Rhodes, D [1 ]
机构
[1] MRC, Mol Biol Lab, Cambridge CB2 2QH, England
关键词
tRNA(Phe); crystal structure; Mg2+; spermine; RNA hydrolysis;
D O I
10.1006/jmbi.2000.3950
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
We have re-determined the crystal structure of yeast tRNA(Phe) to 2.0 Angstrom resolution using 15 year old crystals. The accuracy of the new structure, due both to higher resolution data and formerly unavailable refinement methods, consolidates the previous structural information, but also reveals novel details. Ln particular, the water structure around the tightly bound Mg2+ is now clearly resolved, and hence provides more accurate information on the geometry of the magnesium-binding sites and the role of water molecules in coordinating the metal ions to the tRNA. We have assigned a total of ten magnesium ions and identified a partly conserved geometry for high-affinity Mg2+ binding. In the electron density map there is also clear density for a spermine molecule binding in the major groove of the T Psi C arm and also contacting a symmetry-related tRNA molecule. Interestingly, we have also found that two specific regions of the tRNA in the crystals are partially cleaved. The sites of hydrolysis are within the D and anticodon loops in the vicinity of Mg2+. (C) 2000 Academic Press.
引用
收藏
页码:401 / 414
页数:14
相关论文
共 42 条
[1]   RNA hydration: Three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin [J].
Auffinger, P ;
Westhof, E .
JOURNAL OF MOLECULAR BIOLOGY, 1997, 269 (03) :326-341
[2]   PB(II)-CATALYSED CLEAVAGE OF THE SUGAR-PHOSPHATE BACKBONE OF YEAST TRANSFER RNAPHE - IMPLICATIONS FOR LEAD TOXICITY AND SELF-SPLICING RNA [J].
BROWN, RS ;
HINGERTY, BE ;
DEWAN, JC ;
KLUG, A .
NATURE, 1983, 303 (5917) :543-546
[3]   CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRANSFER-RNA [J].
BROWN, RS ;
DEWAN, JC ;
KLUG, A .
BIOCHEMISTRY, 1985, 24 (18) :4785-4801
[4]   New applications of simulated annealing in X-ray crystallography and solution NMR [J].
Brunger, AT ;
Adams, PD ;
Rice, LM .
STRUCTURE, 1997, 5 (03) :325-336
[5]   Crystallography & NMR system:: A new software suite for macromolecular structure determination [J].
Brunger, AT ;
Adams, PD ;
Clore, GM ;
DeLano, WL ;
Gros, P ;
Grosse-Kunstleve, RW ;
Jiang, JS ;
Kuszewski, J ;
Nilges, M ;
Pannu, NS ;
Read, RJ ;
Rice, LM ;
Simonson, T ;
Warren, GL .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1998, 54 :905-921
[6]   Ribbons [J].
Carson, M .
MACROMOLECULAR CRYSTALLOGRAPHY, PT B, 1997, 277 :493-505
[7]   A magnesium ion core at the heart of a ribozyme domain [J].
Cate, JH ;
Hanna, RL ;
Doudna, JA .
NATURE STRUCTURAL BIOLOGY, 1997, 4 (07) :553-558
[8]   Crystal structure of a group I ribozyme domain: Principles of RNA packing [J].
Cate, JH ;
Gooding, AR ;
Podell, E ;
Zhou, KH ;
Golden, BL ;
Kundrot, CE ;
Cech, TR ;
Doudna, JA .
SCIENCE, 1996, 273 (5282) :1678-1685
[9]   RIBOZYMES - HAMMERHEAD NAILED DOWN [J].
CECH, TR ;
UHLENBECK, OC .
NATURE, 1994, 372 (6501) :39-40
[10]   Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain [J].
Correll, CC ;
Freeborn, B ;
Moore, PB ;
Steitz, TA .
CELL, 1997, 91 (05) :705-712