4IRU

Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3

Summary for 4IRU

• Entry DOI: 10.2210/pdb4iru/pdb
• Descriptor: LepB, Ras-related protein Rab-1A, ACETATE ION, ... (9 entities in total)
• Functional Keywords: arginine finger, glutamate finger, p-loop motif, nucleotide binding, intrinsic gtpase activity, gtp hydrolysis, gtp hydrolysis activator, gtpase activating protein (gap), protein transport, hydrolase-hydrolase complex, hydrolase/hydrolase
• Biological source: Legionella pneumophila; More
• Cellular location: Golgi apparatus: P62820
• Total number of polymer chains: 6
• Total formula weight: 168608.75

Authors

Mishra, A.K.,Delcampo, C.M.,Collins, R.E.,Roy, C.R.,Lambright, D.G. (deposition date: 2013-01-15, release date: 2013-07-10, Last modification date: 2013-09-04)

Primary citation

Mishra, A.K.,Del Campo, C.M.,Collins, R.E.,Roy, C.R.,Lambright, D.G.
The Legionella pneumophila GTPase Activating Protein LepB Accelerates Rab1 Deactivation by a Non-canonical Hydrolytic Mechanism.
J.Biol.Chem., 288:24000-24011, 2013

PubMed Abstract: GTPase activating proteins (GAPs) from pathogenic bacteria and eukaryotic host organisms deactivate Rab GTPases by supplying catalytic arginine and glutamine fingers in trans and utilizing the cis-glutamine in the DXXGQ motif of the GTPase for binding rather than catalysis. Here, we report the transition state mimetic structure of the Legionella pneumophila GAP LepB in complex with Rab1 and describe a comprehensive structure-based mutational analysis of potential catalytic and recognition determinants. The results demonstrate that LepB does not simply mimic other GAPs but instead deploys an expected arginine finger in conjunction with a novel glutamic acid finger, which forms a salt bridge with an indispensible switch II arginine that effectively locks the cis-glutamine in the DXXGQ motif of Rab1 in a catalytically competent though unprecedented transition state configuration. Surprisingly, a heretofore universal transition state interaction with the cis-glutamine is supplanted by an elaborate polar network involving critical P-loop and switch I serines. LepB further employs an unusual tandem domain architecture to clamp a switch I tyrosine in an open conformation that facilitates access of the arginine finger to the hydrolytic site. Intriguingly, the critical P-loop serine corresponds to an oncogenic substitution in Ras and replaces a conserved glycine essential for the canonical transition state stereochemistry. In addition to expanding GTP hydrolytic paradigms, these observations reveal the unconventional dual finger and non-canonical catalytic network mechanisms of Rab GAPs as necessary alternative solutions to a major impediment imposed by substitution of the conserved P-loop glycine.

PubMed: 23821544
DOI: 10.1074/jbc.M113.470625

Experimental method

X-RAY DIFFRACTION (3.2 Å)