1LTX

Structure of Rab Escort Protein-1 in complex with Rab geranylgeranyl transferase and isoprenoid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of Rab Escort Protein-1 in Complex with Rab Geranylgeranyltransferase

Pylypenko, O.Rak, A.Reents, R.Niculae, A.Sidorovitch, V.Cioaca, M.D.Bessolitsyna, E.Thoma, N.H.Waldmann, H.Schlichting, I.Goody, R.S.Alexandrov, K.

(2003) Mol.Cell 11: 483-494


  • PubMed Abstract: 
  • Posttranslational geranylgeranylation of Rab GTPases is catalyzed by Rab geranylgeranyltransferase (RabGGTase), which consists of a catalytic alpha/beta heterodimer and an accessory Rab escort protein (REP). The crystal structure of isoprenoid-bound ...

    Posttranslational geranylgeranylation of Rab GTPases is catalyzed by Rab geranylgeranyltransferase (RabGGTase), which consists of a catalytic alpha/beta heterodimer and an accessory Rab escort protein (REP). The crystal structure of isoprenoid-bound RabGGTase complexed to REP-1 has been solved to 2.7 A resolution. The complex interface buries a surprisingly small surface area of ca. 680 A and is unexpectedly formed by helices 8, 10, and 12 of the RabGGTase alpha subunit and helices D and E of REP-1. We demonstrate that the affinity of RabGGTase for REP-1 is allosterically regulated by phosphoisoprenoid via a long-range trans-domain signal transduction event. Comparing the structure of REP-1 with the closely related RabGDI, we conclude that the specificity of the REP:RabGGTase interaction is defined by differently positioned phenylalanine residues conserved in the REP and GDI subfamilies.


    Related Citations: 
    • Crystallization and Preliminary X-ray Diffraction Analysis of the Rab Escort Protein-1 in Complex with Rab Geranylgeranyltransferase
      Rak, A.,Reents, R.,Pylypenko, O.,Niculae, A.,Sidorovitch, V.,Thoma, N.H.,Waldmann, H.,Schlichting, I.,Goody, R.S.,Alexandrov, K.
      (2001) J.STRUCT.BIOL. 136: 158


    Organizational Affiliation

    Department of Biomolecular Mechanisms, Max-Planck-Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT
A
567Rattus norvegicusGene Names: Rabggta (Ggta)
EC: 2.5.1.60
Find proteins for Q08602 (Rattus norvegicus)
Go to UniProtKB:  Q08602
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT
B
331Rattus norvegicusGene Names: Rabggtb (Ggtb)
EC: 2.5.1.60
Find proteins for Q08603 (Rattus norvegicus)
Go to UniProtKB:  Q08603
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Rab Escort Protein 1
R
650Rattus norvegicusGene Names: Chm (Rep1)
Find proteins for P37727 (Rattus norvegicus)
Go to UniProtKB:  P37727
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
AAAA
P
4N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAR
Query on FAR

Download SDF File 
Download CCD File 
P
FARNESYL
C15 H26
JXBSHSBNOVLGHF-BUJBXKITSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
R
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 68.700α = 90.00
b = 197.300β = 112.80
c = 85.300γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing
ProDCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-21
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description