Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 168.61 kDa 
• Atom Count: 11410 
• Modelled Residue Count: 1397 
• Deposited Residue Count: 1449 
• Unique protein chains: 2

4IRU

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

• PDB DOI: 10.2210/pdb4IRU/pdb

• Classification: HYDROLASE/HYDROLASE
• Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-01-15 Released: 2013-07-10 
• Deposition Author(s): Mishra, A.K., Delcampo, C.M., Collins, R.E., Roy, C.R., Lambright, D.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.288 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 

Literature

The Legionella pneumophila GTPase Activating Protein LepB Accelerates Rab1 Deactivation by a Non-canonical Hydrolytic Mechanism.

Mishra, A.K., Del Campo, C.M., Collins, R.E., Roy, C.R., Lambright, D.G.

(2013) J Biol Chem 288: 24000-24011

• PubMed: 23821544 
• DOI: 10.1074/jbc.M113.470625
• Primary Citation of Related Structures:  
  4IRU


• 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.

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Organizational Affiliation: 

Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LepB	A, C, E	299	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0  Gene Names: lepB, lpg2490 EC: 3.6.5.2
UniProt
Find proteins for Q5ZSM7 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZSM7  Go to UniProtKB:  Q5ZSM7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-1A	B, D, F	184	Homo sapiens	Mutation(s): 0  Gene Names: RAB1, RAB1A EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P62820 (Homo sapiens) Explore P62820  Go to UniProtKB:  P62820
PHAROS:  P62820

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	IA [auth D], NA [auth F], T [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
GOL	FA [auth C], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], X [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
AF3	JA [auth D], OA [auth F], U [auth B]	ALUMINUM FLUORIDE Al F3 KLZUFWVZNOTSEM-UHFFFAOYSA-K
ACT	AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth C], G [auth A], H [auth A], KA [auth D], LA [auth D], V [auth B], W [auth B], Z [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
K	GA [auth C], O [auth A], P [auth A], Q [auth A], R [auth A], Y [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	HA [auth D], MA [auth F], S [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, C, E	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.288 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.404	α = 90
b = 139.404	β = 90
c = 384.519	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AutoSol	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-01-15 
• Released Date: 2013-07-10 
Deposition Author(s): Mishra, A.K., Delcampo, C.M., Collins, R.E., Roy, C.R., Lambright, D.G.

Revision History  

• Version 1.0: 2013-07-10
  Type: Initial release
  
• Version 1.1: 2013-07-17
  Changes: Database references
• Version 1.2: 2013-09-04
  Changes: Database references