4P29

Crystal structure of the LpoA N-terminal domain from Haemophilus influenzae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural analyses of theHaemophilus influenzaepeptidoglycan 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:  
    4P29, 5KCN, 5VAT, 5VBG

  • 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 Ha ...

    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 ( Hi LpoA) 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 Hi LpoA 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 Hi LpoA molecules. In contrast to an elongated model previously suggested for E. coli LpoA, each Hi LpoA 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 Hi LpoA 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

    the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-5606 and.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LpoAAB231Haemophilus influenzae Rd KW20Mutation(s): 0 
Gene Names: lpoAHI_1655
Find proteins for P45299 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P45299 
Go to UniProtKB:  P45299
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.03α = 90
b = 51.18β = 90
c = 198.61γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
d*TREKdata scaling
SOLVEphasing
RESOLVEmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21 AI099984
Philip Morris External Research ProgramUnited States--

Revision History 

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-25
    Changes: Database references