4ARZ

The crystal structure of Gtr1p-Gtr2p complexed with GTP-GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

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Literature

Crystal Structure of the Gtr1Pgtp-Gtr2Pgdp Complex Reveals Large Structural Rearrangements Triggered by GTP-to-Gdp Conversion

Jeong, J.H.Lee, K.H.Kim, Y.M.Kim, D.H.Oh, B.H.Kim, Y.G.

(2012) J Biol Chem 287: 29648

  • DOI: 10.1074/jbc.C112.384420
  • Primary Citation of Related Structures:  
    4ARZ

  • PubMed Abstract: 
  • The heterodimeric Rag GTPases consisting of RagA (or RagB) and RagC (or RagD) are the key regulator activating the target of rapamycin complex 1 (TORC1) in response to the level of amino acids. The heterodimer between GTP-loaded RagA/B and GDP-loaded RagC/D is the most active form that binds Raptor and leads to the activation of TORC1 ...

    The heterodimeric Rag GTPases consisting of RagA (or RagB) and RagC (or RagD) are the key regulator activating the target of rapamycin complex 1 (TORC1) in response to the level of amino acids. The heterodimer between GTP-loaded RagA/B and GDP-loaded RagC/D is the most active form that binds Raptor and leads to the activation of TORC1. Here, we present the crystal structure of Gtr1p(GTP)-Gtr2p(GDP), the active yeast Rag GTPase heterodimer. The structure reveals that GTP-to-GDP conversion on Gtr2p results in a large conformational transition of this subunit, including a large scale rearrangement of a long segment whose corresponding region in RagA is involved in binding to Raptor. In addition, the two GTPase domains of the heterodimer are brought to contact with each other, but without causing any conformational change of the Gtr1p subunit. These features explain how the nucleotide-bound statuses of the two GTPases subunits switch the Raptor binding affinity on and off.


    Organizational Affiliation

    Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-BINDING PROTEIN GTR1A310Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q00582 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q00582 
Go to UniProtKB:  Q00582
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-BINDING PROTEIN GTR2B341Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P53290 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53290 
Go to UniProtKB:  P53290
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
C [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
E [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.712α = 90
b = 148.897β = 90
c = 117.759γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2012-04-27 
  • Released Date: 2012-07-25 
  • Deposition Author(s): Jeong, J.H., Kim, Y.G.

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2012-09-05
    Changes: Database references