4IHH

Chasing Acyl Carrier Protein Through a Catalytic Cycle of Lipid A Production

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.132 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

Chasing acyl carrier protein through a catalytic cycle of lipid A production.

Masoudi, A., Raetz, C.R., Zhou, P., Pemble, C.W.

(2014) Nature 505: 422-426

  • DOI: 10.1038/nature12679
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Acyl carrier protein represents one of the most highly conserved proteins across all domains of life and is nature's way of transporting hydrocarbon chains in vivo. Notably, type II acyl carrier proteins serve as a crucial interaction hub in primary ...

    Acyl carrier protein represents one of the most highly conserved proteins across all domains of life and is nature's way of transporting hydrocarbon chains in vivo. Notably, type II acyl carrier proteins serve as a crucial interaction hub in primary cellular metabolism by communicating transiently between partner enzymes of the numerous biosynthetic pathways. However, the highly transient nature of such interactions and the inherent conformational mobility of acyl carrier protein have stymied previous attempts to visualize structurally acyl carrier protein tied to an overall catalytic cycle. This is essential to understanding a fundamental aspect of cellular metabolism leading to compounds that are not only useful to the cell, but also of therapeutic value. For example, acyl carrier protein is central to the biosynthesis of the lipid A (endotoxin) component of lipopolysaccharides in Gram-negative microorganisms, which is required for their growth and survival, and is an activator of the mammalian host's immune system, thus emerging as an important therapeutic target. During lipid A synthesis (Raetz pathway), acyl carrier protein shuttles acyl intermediates linked to its prosthetic 4'-phosphopantetheine group among four acyltransferases, including LpxD. Here we report the crystal structures of three forms of Escherichia coli acyl carrier protein engaging LpxD, which represent stalled substrate and liberated products along the reaction coordinate. The structures show the intricate interactions at the interface that optimally position acyl carrier protein for acyl delivery and that directly involve the pantetheinyl group. Conformational differences among the stalled acyl carrier proteins provide the molecular basis for the association-dissociation process. An unanticipated conformational shift of 4'-phosphopantetheine groups within the LpxD catalytic chamber shows an unprecedented role of acyl carrier protein in product release.

    Organizational Affiliation: 

    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
A, B, C, D, E, F
348Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: lpxD (firA, omsA)
EC: 2.3.1.191
Find proteins for P21645 (Escherichia coli (strain K12))
Go to UniProtKB:  P21645
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Acyl carrier protein
G, H, I, J, K, L
80N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PNS
Query on PNS
Download SDF File 
Download CCD File 
G, H, I, J, K, L
4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
 Ligand Interaction
MES
Query on MES
Download SDF File 
Download CCD File 
A, B, C, D, E, F
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.132 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.177 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 89.470α = 75.93
b = 93.225β = 73.81
c = 114.300γ = 58.95
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
SERGUIdata collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2013-11-20
    Type: Database references
  • Version 1.2: 2014-01-22
    Type: Database references
  • Version 1.3: 2014-01-29
    Type: Database references
  • Version 1.4: 2017-11-15
    Type: Advisory, Refinement description