4P31

Crystal structure of a selenomethionine derivative of E. coli LptB in complex with ADP-Magensium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Decoupling catalytic activity from biological function of the ATPase that powers lipopolysaccharide transport.

Sherman, D.J.Lazarus, M.B.Murphy, L.Liu, C.Walker, S.Ruiz, N.Kahne, D.

(2014) Proc Natl Acad Sci U S A 111: 4982-4987

  • DOI: 10.1073/pnas.1323516111
  • Primary Citation of Related Structures:  
    4P31, 4P32, 4P33

  • PubMed Abstract: 
  • The cell surface of Gram-negative bacteria contains lipopolysaccharides (LPS), which provide a barrier against the entry of many antibiotics. LPS assembly involves a multiprotein LPS transport (Lpt) complex that spans from the cytoplasm to the outer ...

    The cell surface of Gram-negative bacteria contains lipopolysaccharides (LPS), which provide a barrier against the entry of many antibiotics. LPS assembly involves a multiprotein LPS transport (Lpt) complex that spans from the cytoplasm to the outer membrane. In this complex, an unusual ATP-binding cassette transporter is thought to power the extraction of LPS from the outer leaflet of the cytoplasmic membrane and its transport across the cell envelope. We introduce changes into the nucleotide-binding domain, LptB, that inactivate transporter function in vivo. We characterize these residues using biochemical experiments combined with high-resolution crystal structures of LptB pre- and post-ATP hydrolysis and suggest a role for an active site residue in phosphate exit. We also identify a conserved residue that is not required for ATPase activity but is essential for interaction with the transmembrane components. Our studies establish the essentiality of ATP hydrolysis by LptB to power LPS transport in cells and suggest strategies to inhibit transporter function away from the LptB active site.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lipopolysaccharide export system ATP-binding protein LptBAB249Escherichia coli K-12Mutation(s): 0 
Gene Names: lptByhbGb3201JW3168
EC: 3.6.3 (PDB Primary Data), 7.5.2 (UniProt)
Find proteins for P0A9V1 (Escherichia coli (strain K12))
Explore P0A9V1 
Go to UniProtKB:  P0A9V1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 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: 2.05 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 192.6α = 90
b = 35.88β = 95.83
c = 64.34γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
ADSC Quantumdata collection
SCALAdata scaling
SHARPphasing
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
CNSrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI081059
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM066174
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM094263
Harvard UniversityUnited States--

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2015-02-04
    Changes: Derived calculations
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence