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5CJ2

Ran GDP Y39A mutant triclinic crystal form

Summary for 5CJ2
Entry DOI10.2210/pdb5cj2/pdb
Related5CIW
DescriptorGTP-binding nuclear protein Ran, GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... (5 entities in total)
Functional Keywordsgtpase, nuclear transport, transport protein, hydrolase
Biological sourceHomo sapiens (Human)
Cellular locationNucleus: P62826
Total number of polymer chains8
Total formula weight198939.27
Authors
Vetter, I.R.,Brucker, S. (deposition date: 2015-07-13, release date: 2015-09-09, Last modification date: 2024-05-01)
Primary citationRudack, 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
Cited by
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
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.75 Å)
Structure validation

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