5BTX

Structure of the N-terminal domain of lpg1496 from Legionella pneumophila in complex with nucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Structure of the Legionella Effector, lpg1496, Suggests a Role in Nucleotide Metabolism.

Wong, K.Kozlov, G.Zhang, Y.Gehring, K.

(2015) J Biol Chem 290: 24727-24737

  • DOI: https://doi.org/10.1074/jbc.M115.671263
  • Primary Citation of Related Structures:  
    5BTW, 5BTX, 5BTY, 5BTZ, 5BU0, 5BU1, 5BU2

  • PubMed Abstract: 

    Pathogenic Gram-negative bacteria use specialized secretion systems that translocate bacterial proteins, termed effectors, directly into host cells where they interact with host proteins and biochemical processes for the benefit of the pathogen. lpg1496 is a previously uncharacterized effector of Legionella pneumophila, the causative agent of Legionnaires disease. Here, we crystallized three nucleotide binding domains from lpg1496. The C-terminal domain, which is conserved among the SidE family of effectors, is formed of two largely α-helical lobes with a nucleotide binding cleft. A structural homology search has shown similarity to phosphodiesterases involved in cleavage of cyclic nucleotides. We have also crystallized a novel domain that occurs twice in the N-terminal half of the protein that we term the KLAMP domain due to the presence of homologous domains in bacterial histidine kinase-like ATP binding region-containing proteins and S-adenosylmethionine-dependent methyltransferase proteins. Both KLAMP structures are very similar but selectively bind 3',5'-cAMP and ADP. A co-crystal of the KLAMP1 domain with 3',5'-cAMP reveals the contribution of Tyr-61 and Tyr-69 that produces π-stacking interactions with the adenine ring of the nucleotide. Our study provides the first structural insights into two novel nucleotide binding domains associated with bacterial virulence.


  • Organizational Affiliation

    From the Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec H3G 0B1, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
lpg1496
A, B
146Legionella pneumophila subsp. pneumophila ATCC 43290Mutation(s): 0 
Gene Names: lp12_1434
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CMP
Query on CMP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
C10 H12 N5 O6 P
IVOMOUWHDPKRLL-KQYNXXCUSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CMP Binding MOAD:  5BTX Kd: 2.80e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.622α = 90
b = 57.446β = 93.32
c = 63.779γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaGSP-48370

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-09-02
    Changes: Database references
  • Version 1.2: 2015-10-21
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description