5VAT

Haemophilus influenzae LpoA: Monoclinic form (Mon2) with 2 molecules per a.u.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analyses of the Haemophilus influenzae peptidoglycan synthase activator LpoA suggest multiple conformations in solution.

Sathiyamoorthy, K.Vijayalakshmi, J.Tirupati, B.Fan, L.Saper, M.A.

(2017) J. Biol. Chem. 292: 17626-17642

  • DOI: 10.1074/jbc.M117.804997
  • Primary Citation of Related Structures:  
  • Also Cited By: 3CKM

  • PubMed Abstract: 
  • In many Gram-negative bacteria, the peptidoglycan synthase PBP1A requires the outer membrane lipoprotein LpoA for constructing a functional peptidoglycan required for bacterial viability. Previously, we have shown that the C-terminal domain of Haemop ...

    In many Gram-negative bacteria, the peptidoglycan synthase PBP1A requires the outer membrane lipoprotein LpoA for constructing a functional peptidoglycan required for bacterial viability. Previously, we have shown that the C-terminal domain of Haemophilus influenzae LpoA (HiLpoA) has a highly conserved, putative substrate-binding cleft between two α/β lobes. Here, we report a 2.0 Å resolution crystal structure of the HiLpoA N-terminal domain. Two subdomains contain tetratricopeptide-like motifs that form a concave groove, but their relative orientation differs by ∼45° from that observed in an NMR structure of the Escherichia coli LpoA N domain. We also determined three 2.0-2.8 Å resolution crystal structures containing four independent full-length HiLpoA molecules. In contrast to an elongated model previously suggested for E. coli LpoA, each HiLpoA formed a U-shaped structure with a different C-domain orientation. This resulted from both N-domain twisting and rotation of the C domain (up to 30°) at the end of the relatively immobile interdomain linker. Moreover, a previously predicted hinge between the lobes of the LpoA C domain exhibited variations of up to 12°. Small-angle X-ray scattering data revealed excellent agreement with a model calculated by normal mode analysis from one of the full-length HiLpoA molecules but even better agreement with an ensemble of this molecule and two of the partially extended normal mode analysis-predicted models. The different LpoA structures helped explain how an outer membrane-anchored LpoA can either withdraw from or extend toward the inner membrane-bound PBP1A through peptidoglycan gaps and hence regulate the synthesis of peptidoglycan necessary for bacterial viability.


    Related Citations: 
    • Structure of YraM, a protein essential for growth of Haemophilus influenzae.
      Vijayalakshmi, J.,Akerley, B.J.,Saper, M.A.
      (2008) Proteins 73: 204


    Organizational Affiliation

    From the Program in Biophysics and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Penicillin-binding protein activator LpoA
A, B
543Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)Mutation(s): 0 
Gene Names: lpoA
Find proteins for P45299 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Go to UniProtKB:  P45299
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 84.935α = 90.00
b = 72.695β = 94.42
c = 120.572γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR21 AI099984

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Database references