5CIT

Ran GDP wild type monoclinic crystal form

5CIT の概要

• エントリーDOI: 10.2210/pdb5cit/pdb
• 関連するPDBエントリー: 5CIQ
• 分子名称: GTP-binding nuclear protein Ran, GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: gtpase, nuclear transport, transport protein, hydrolase
• 由来する生物種: Homo sapiens (Human)
• 細胞内の位置: Nucleus: P62826
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 49847.22

構造登録者

Vetter, I.R.,Brucker, S. (登録日: 2015-07-13, 公開日: 2015-09-09, 最終更新日: 2024-05-01)

主引用文献

Rudack, T.,Jenrich, S.,Brucker, S.,Vetter, I.R.,Gerwert, K.,Kotting, C.
Catalysis of GTP Hydrolysis by Small GTPases at Atomic Detail by Integration of X-ray Crystallography, Experimental, and Theoretical IR Spectroscopy.
J.Biol.Chem., 290:24079-24090, 2015

PubMed Abstract: Small GTPases regulate key processes in cells. Malfunction of their GTPase reaction by mutations is involved in severe diseases. Here, we compare the GTPase reaction of the slower hydrolyzing GTPase Ran with Ras. By combination of time-resolved FTIR difference spectroscopy and QM/MM simulations we elucidate that the Mg(2+) coordination by the phosphate groups, which varies largely among the x-ray structures, is the same for Ran and Ras. A new x-ray structure of a Ran·RanBD1 complex with improved resolution confirmed this finding and revealed a general problem with the refinement of Mg(2+) in GTPases. The Mg(2+) coordination is not responsible for the much slower GTPase reaction of Ran. Instead, the location of the Tyr-39 side chain of Ran between the γ-phosphate and Gln-69 prevents the optimal positioning of the attacking water molecule by the Gln-69 relative to the γ-phosphate. This is confirmed in the RanY39A·RanBD1 crystal structure. The QM/MM simulations provide IR spectra of the catalytic center, which agree very nicely with the experimental ones. The combination of both methods can correlate spectra with structure at atomic detail. For example the FTIR difference spectra of RasA18T and RanT25A mutants show that spectral differences are mainly due to the hydrogen bond of Thr-25 to the α-phosphate in Ran. By integration of x-ray structure analysis, experimental, and theoretical IR spectroscopy the catalytic center of the x-ray structural models are further refined to sub-Å resolution, allowing an improved understanding of catalysis.

PubMed: 26272610
DOI: 10.1074/jbc.M115.648071

実験手法

X-RAY DIFFRACTION (1.75 Å)