5CLQ

Ran Y39A in complex with GPPNHP and RanBD1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Catalysis of GTP Hydrolysis by Small GTPases at Atomic Detail by Integration of X-ray Crystallography, Experimental, and Theoretical IR Spectroscopy.

Rudack, T., Jenrich, S., Brucker, S., Vetter, I.R., Gerwert, K., Kotting, C.

(2015) J Biol Chem 290: 24079-24090

  • DOI: 10.1074/jbc.M115.648071
  • Primary Citation of Related Structures:  
    5CIT, 5CIW, 5CIQ, 5CJ2, 5CLQ, 5CLL

  • 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 diff ...

    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.

    Organizational Affiliation: 

    From the Department of Biophysics, University of Bochum, Universitaetstrasse 150, 44780 Bochum, Germany, carsten.koetting@rub.de.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-binding nuclear protein Ran A, C216Homo sapiensMutation(s): 1 
Gene Names: RAN, ARA24, OK/SW-cl.81
Find proteins for P62826 (Homo sapiens)
Explore P62826 
Go to UniProtKB:  P62826
NIH Common Fund Data Resources
PHAROS:  P62826
GTEx:  ENSG00000132341
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
E3 SUMO-protein ligase RanBP2 B, D167Homo sapiensMutation(s): 0 
Gene Names: RANBP2, NUP358
EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
Find proteins for P49792 (Homo sapiens)
Explore P49792 
Go to UniProtKB:  P49792
NIH Common Fund Data Resources
PHAROS:  P49792
GTEx:  ENSG00000153201
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.53α = 90
b = 170.92β = 90
c = 135.65γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-10-14
    Changes: Database references