Structural insights into the dual nucleotide exchange and GDI displacement activity of SidM/DrrA

• Published in: The EMBO journal 2010-01, Vol.29 (2), p.496-504
• Main Authors: Suh, Hye-Young, Lee, Dong-Won, Lee, Kwang-Hoon, Ku, Bonsu, Choi, Sung-Jin, Woo, Jae-Sung, Kim, Yeon-Gil, Oh, Byung-Ha
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Catalysis; Cellular biology; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; EMBO37; EMBO40; GDF; GDI; GEF; Guanine Nucleotide Dissociation Inhibitors - metabolism; Guanine Nucleotide Exchange Factors - chemistry; Guanine Nucleotide Exchange Factors - genetics; Guanine Nucleotide Exchange Factors - metabolism; Guanosine Diphosphate - metabolism; Guanosine Triphosphate - metabolism; Humans; Inhibitor drugs; Legionella pneumophila; Legionella pneumophila - metabolism; Legionnaires' Disease - metabolism; Liposomes - metabolism; Magnesium - metabolism; Models, Molecular; Molecular biology; Molecular Sequence Data; Mutation; p-Rab1; Point Mutation; Protein Binding; Protein Conformation; rab1 GTP-Binding Proteins - metabolism; rho-Specific Guanine Nucleotide Dissociation Inhibitors; Sequence Alignment; SidM/DrrA; Substrate Specificity
• ISSN: 0261-4189; 1460-2075
• DOI: 10.1038/emboj.2009.347

GDP‐bound prenylated Rabs, sequestered by GDI (GDP dissociation inhibitor) in the cytosol, are delivered to destined sub‐cellular compartment and subsequently activated by GEFs (guanine nucleotide exchange factors) catalysing GDP‐to‐GTP exchange. The dissociation of GDI from Rabs is believed to require a GDF (GDI displacement factor). Only two RabGDFs, human PRA‐1 and Legionella pneumophila SidM/DrrA, have been identified so far and the molecular mechanism of GDF is elusive. Here, we present the structure of a SidM/DrrA fragment possessing dual GEF and GDF activity in complex with Rab1. SidM/DrrA reconfigures the Switch regions of the GTPase domain of Rab1, as eukaryotic GEFs do toward cognate Rabs. Structure‐based mutational analyses show that the surface of SidM/DrrA, catalysing nucleotide exchange, is involved in GDI1 displacement from prenylated Rab1:GDP. In comparison with an eukaryotic GEF TRAPP I, this bacterial GEF/GDF exhibits high binding affinity for Rab1 with GDP retained at the active site, which appears as the key feature for the GDF activity of the protein.