Structure of the disordered C Terminus of Rab7 GTPase induced by binding to the Rab Geranylgeranyl Transferase Catalytic Complex reveals the mechanism of Rab Prenylation

Wu, Yao-Wen, Goody, Roger S., Abagyan, Ruben and Alexandrov, Kirill (2009) Structure of the disordered C Terminus of Rab7 GTPase induced by binding to the Rab Geranylgeranyl Transferase Catalytic Complex reveals the mechanism of Rab Prenylation. Journal of Biological Chemistry, 284 19: 13185-13192. doi:10.1074/jbc.M900579200

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Author Wu, Yao-Wen
Goody, Roger S.
Abagyan, Ruben
Alexandrov, Kirill
Title Structure of the disordered C Terminus of Rab7 GTPase induced by binding to the Rab Geranylgeranyl Transferase Catalytic Complex reveals the mechanism of Rab Prenylation
Journal name Journal of Biological Chemistry   Check publisher's open access policy
ISSN 0021-9258
1083-351X
Publication date 2009-05-08
Year available 2009
Sub-type Article (original research)
DOI 10.1074/jbc.M900579200
Open Access Status File (Publisher version)
Volume 284
Issue 19
Start page 13185
End page 13192
Total pages 8
Editor Herbert Tabor
Place of publication Bethesda, MD, U.S.A.
Publisher American Society for Biochemistry and Molecular Biology
Language eng
Subject 06 Biological Sciences
0601 Biochemistry and Cell Biology
C1
970106 Expanding Knowledge in the Biological Sciences
060106 Cellular Interactions (incl. Adhesion, Matrix, Cell Wall)
Abstract Protein prenylation is a widespread process that involves the transfer of either a farnesyl or a geranylgeranyl moiety to one or more C-terminal cysteines of the target protein. Rab geranylgeranyl transferase (RabGGTase) is responsible for the largest number of individual protein prenylation events in the cell. A decade-long effort to crystallize the catalytic ternary complex of RabGGTase has remained fruitless, prompting us to use a computational approach to predict the structure of this 200-kDa assembly. On the basis of high resolution structures of two sub-complexes, we have generated a composite model where the rigid parts of the protein are represented by precomputed grid potentials, whereas the mobile parts are described in atomic details using Internal Coordinate Mechanics. Selection of the best docking solution of the flexible parts on the grid is followed by explicit atomistic refinement of the lowest energy conformations enabling realistic modeling of complex structures. Using this approach we demonstrate that the flexible C terminus of Rab7 substrate forms a series of progressively weaker and less specific interactions that channel it into the active site of RabGGTase. We have validated the computational model through biochemical experiments and demonstrated that to be prenylated RabGTPase must possess at least nine amino acids between the prenylation motif and the hydrophobic sequence anchoring the beginning of the Rab C terminus on the enzyme. This sequence, known as the C-terminal interacting motif is shown to play a dual role in Rab prenylation by contributing a significant fraction of binding energy to the catalytic complex assembly and by orienting the C terminus of RabGTPase in the vicinity of the active site of RabGGTase. This mechanism is unique to RabGGTase when compared with other prenyltransferases, which encode the specificity for their cognate substrates directly at their active site.
Keyword Gdp-Dissociation inhibitor
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID AL 484/7-2
Institutional Status UQ

 
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Created: Thu, 03 Sep 2009, 18:11:44 EST by Mr Andrew Martlew on behalf of Institute for Molecular Bioscience