5CIQ: Ran Gdp Wild Type Tetragonal Crystal Form

Citation:
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 gamma-phosphate and Gln-69 prevents the optimal positioning of the attacking water molecule by the Gln-69 relative to the gamma-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 alpha-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-A resolution, allowing an improved understanding of catalysis.
PDB ID: 5CIQDownload
MMDB ID: 132492
PDB Deposition Date: 2015/7/13
Updated in MMDB: 2015/11
Experimental Method:
x-ray diffraction
Resolution: 1.65  Å
Source Organism:
Similar Structures:
Biological Unit for 5CIQ: monomeric; determined by author
Molecular Components in 5CIQ
Label Count Molecule
Protein (1 molecule)
1
Gtp-binding Nuclear Protein RAN(Gene symbol: RAN)
Molecule annotation
Chemicals (2 molecules)
1
1
2
1
* Click molecule labels to explore molecular sequence information.

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