5CJ2

Ran GDP Y39A mutant triclinic crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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

  • 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.


  • Organizational Affiliation

    From the Department of Biophysics, University of Bochum, Universitaetstrasse 150, 44780 Bochum, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding nuclear protein Ran
A, B, C, D, E
A, B, C, D, E, F, G, H
216Homo sapiensMutation(s): 1 
Gene Names: RANARA24OK/SW-cl.81
UniProt & NIH Common Fund Data Resources
Find proteins for P62826 (Homo sapiens)
Explore P62826 
Go to UniProtKB:  P62826
PHAROS:  P62826
GTEx:  ENSG00000132341 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62826
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
AA [auth G]
CA [auth H]
I [auth A]
K [auth B]
P [auth C]
AA [auth G],
CA [auth H],
I [auth A],
K [auth B],
P [auth C],
U [auth D],
W [auth E],
Y [auth F]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
N [auth B],
S [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth G]
DA [auth H]
J [auth A]
L [auth B]
M [auth B]
BA [auth G],
DA [auth H],
J [auth A],
L [auth B],
M [auth B],
O [auth B],
Q [auth C],
R [auth C],
T [auth C],
V [auth D],
X [auth E],
Z [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.19α = 97.66
b = 80.73β = 90
c = 91.65γ = 90.01
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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