3GP6

Crystal structure of PagP in SDS/MPD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

PagP crystallized from SDS/cosolvent reveals the route for phospholipid access to the hydrocarbon ruler.

Cuesta-Seijo, J.A.Neale, C.Khan, M.A.Moktar, J.Tran, C.D.Bishop, R.E.Pomes, R.Prive, G.G.

(2010) Structure 18: 1210-1219

  • DOI: 10.1016/j.str.2010.06.014

  • PubMed Abstract: 
  • Enzymatic reactions involving bilayer lipids occur in an environment with strict physical and topological constraints. The integral membrane enzyme PagP transfers a palmitoyl group from a phospholipid to lipid A in order to assist Escherichia coli in ...

    Enzymatic reactions involving bilayer lipids occur in an environment with strict physical and topological constraints. The integral membrane enzyme PagP transfers a palmitoyl group from a phospholipid to lipid A in order to assist Escherichia coli in evading host immune defenses during infection. PagP measures the palmitoyl group with an internal hydrocarbon ruler that is formed in the interior of the eight-stranded antiparallel β barrel. The access and egress of the palmitoyl group is thought to take a lateral route from the bilayer phase to the barrel interior. Molecular dynamics, mutagenesis, and a 1.4 A crystal structure of PagP in an SDS / 2-methyl-2,4-pentanediol (MPD) cosolvent system reveal that phospholipid access occurs at the crenel present between strands F and G of PagP. In this way, the phospholipid head group can remain exposed to the cell exterior while the lipid acyl chain remains in a predominantly hydrophobic environment as it translocates to the protein interior.


    Organizational Affiliation

    Division of Cancer Genomics and Proteomics, Ontario Cancer Institute and Campbell Family Cancer Research Institute, 101 College Street, Toronto, ON M5G 1L7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein pagP
A
163Escherichia coli (strain K12)Gene Names: pagP (crcA, ybeG)
EC: 2.3.1.251
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Monomeric/Dimeric
Protein: 
PagP outer membrane palimitoyl transferease
Find proteins for P37001 (Escherichia coli (strain K12))
Go to UniProtKB:  P37001
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LI
Query on LI

Download SDF File 
Download CCD File 
A
LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

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Download CCD File 
A
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
SDS
Query on SDS

Download SDF File 
Download CCD File 
A
DODECYL SULFATE
C12 H26 O4 S
MOTZDAYCYVMXPC-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.171 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 113.228α = 90.00
b = 113.228β = 90.00
c = 55.064γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-3000data collection
EPMRphasing
HKL-3000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance