PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons

Related Articles
Community-Nominated Targets
July 2015
Drug Discovery: Solving the Structure of an Anti-hypertension Drug Target
July 2015
Retrospective: 7,000 Structures Closer to Understanding Biology
July 2015
Design and Evolution: Unveiling Translocator Proteins
June 2015
Signaling with DivL
May 2015
Signaling: A Platform for Opposing Functions
May 2015
Signaling: Securing Lipid-Protein Partnership
May 2015
Dynamic DnaK
March 2015
Iron-Sulfur Cluster Biosynthesis
December 2014
Mitochondrion: Flipping for UCP2
December 2014
Mitochondrion: Setting a New TRAP1
December 2014
Power in Numbers
August 2014
Quorum Sensing: A Groovy New Component
August 2014
Quorum Sensing: E. coli Gets Involved
August 2014
iTRAQing the Ubiquitinome
July 2014
Microbiome: The Dynamics of Infection
September 2013
Protein-Nucleic Acid Interaction: A Modified SAM to Modify tRNA
July 2013
Protein-Nucleic Acid Interaction: Versatile Glutamate
July 2013
PDZ Domains
April 2013
Alpha-Catenin Connections
March 2013
Cell-Cell Interaction: A FERM Connection
March 2013
Cell-Cell Interaction: Magic Structure from Microcrystals
March 2013
Cell-Cell Interaction: Modulating Self Recognition Affinity
March 2013
Bacterial Hemophores
January 2013
Archaeal Lipids
December 2012
Membrane Proteome: Capturing Multiple Conformations
December 2012
Lethal Tendencies
October 2012
Symmetry from Asymmetry
October 2012
A signal sensing switch
September 2012
Regulatory insights
September 2012
AlkB Homologs
August 2012
Budding ensemble
August 2012
Targeting Enzyme Function with Structural Genomics
July 2012
The machines behind the spindle assembly checkpoint
June 2012
Chaperone interactions
April 2012
Pilus Assembly Protein TadZ
April 2012
Revealing the Nuclear Pore Complex
March 2012
Topping off the proteasome
March 2012
Twist to open
March 2012
Disordered Proteins
February 2012
Analyzing an allergen
January 2012
Making Lipopolysaccharide
January 2012
Pulling on loose ends
January 2012
Terminal activation
December 2011
The Perils of Protein Secretion
November 2011
Bacterial Armor
October 2011
TLR4 regulation: heads or tails?
October 2011
Ribose production on demand
September 2011
Moving some metal
August 2011
Looking for lipids
July 2011
Ribofuranosyl Binding Protein
June 2011
A molecular switch for neuronal growth
May 2011
Cell wall recycler
May 2011
Added benefits
April 2011
NMR challenges current protein hydration dogma
March 2011
Nitrile Reductase QueF
March 2011
Tip formin
March 2011
Inhibiting factor
February 2011
PASK staying active
February 2011
Tryptophanyl-tRNA Synthetase
February 2011
Regulating nitrogen assimilation
January 2011
Subtle shifts
January 2011
December 2010
Function following form
October 2010
tRNA Isopentenyltransferase MiaA
August 2010
Importance of extension for integrin
June 2010
April 2010
Alg13 Subunit of N-Acetylglucosamine Transferase
February 2010
Hemolysin BL
January 2010
December 2009
Two-component signaling
December 2009
Network coverage
November 2009
Pseudouridine Synthase TruA
November 2009
Unusual cell division
October 2009
Toxin-antitoxin VapBC-5
September 2009
Salicylic Acid Binding Protein 2
August 2009
Proofreading RNA
July 2009
Ykul structure solves bacterial signaling puzzle
July 2009
Hda and DNA Replication
June 2009
Controlling p53
May 2009
Mitotic checkpoint control
May 2009
Ribonuclease and Ribonuclease Inhibitor
April 2009
The elusive helicase
April 2009
March 2009
High-energy storage system
February 2009
A new class of bacterial E3 ubiquitination enzymes
January 2009
Poly(A) RNA recognition
January 2009
Activating BAX
December 2008
Scavenger Decapping Enzyme DcpS
November 2008
Bacteriophage Lambda cII Protein
October 2008
New metal-binding domain
October 2008
Blocking AmtB
September 2008
September 2008
Aspartate Dehydrogenase
August 2008
RNase T
July 2008
May 2008

Research Themes Cell biology

Making Lipopolysaccharide

SBKB [doi:10.3942/psi_sgkb/fm_2012_1]
Featured System - January 2012
Short description: Many bacteria surround themselves with a protective coat, to resist attack from antibiotics, predators, and the immune system.

Many bacteria surround themselves with a protective coat, to resist attack from antibiotics, predators, and the immune system. In gram-negative bacteria like Escherichia coli, this protective coat is built primarily of lipopolysaccharides (shown here from PDB entry 1fcp), hybrid molecules with a complex carbohydrate anchored to the cell membrane with an array of lipids. These lipopolysaccharides cover roughly 3/4 of the surface of the cell and are the major barrier between the bacterium and its environment. They are also one of the major molecules recognized by our immune system: we have a dedicated system of Toll-like receptors that sense picomolar amounts of lipopolysaccharides, and mount an immediate defensive response.

Lipid Carrier

Lipopolysaccharides are built in many steps, constructing a "Lipid A" core, composed of several lipid chains attached to a few sugars, and attaching a variety of carbohydrates to it, depending on the particular strain of the bacterium. The protein shown here, solved by NESG, is thought to be involved in delivery of the lipid chains to enzymes that construct the core. It is an acyl-carrier protein (ACP), which has a covalently-attached cofactor (shown in green) that holds lipid chains (PDB entry 2kwm). Many bacteria have a single ACP that performs all of their lipid-carrying tasks. The ACP shown here, however, is a specialized protein that may play a role in delivering unusual lipids to the odd lipopolysaccharides made by the bacterium Geobacter metallireducens.

Metal Remediation

Geobacter metallireducens is one of the few bacteria that can reduce insoluble metal oxides, turning them into soluble salts. For this reason, it is being explored as a biological agent for cleaning up sites that are poisoned by toxic metals, and PSI researchers have chosen it as one of their targets, to help understand the molecular basis of its unusual abilities. Lipopolysaccharides may play a role in the bioremediation: they are important for attaching the bacterium to minerals, and may also bind to individual metal ions.

ACP in Action

The Geobacter ACP is similar to the more typical ACP made by other bacteria. They all have a deep hydrophobic pocket that holds the attached lipid while it is transported from one enzyme to another. Then, the lipid flips out of the binding pocket and inserts into the enzyme's active site. Three structures available in the PDB capture several steps in this process. The Geobacter structure (PDB entry 2kwm) shows ACP before a lipid is bound. PDB entry 2fad is the ACP from E. coli with a short 7-carbon lipid bound. In PDB entry 3ejb (shown here), E. coli ACP (blue) is delivering a longer lipid (yellow) to an enzyme that makes biotin (red). The JSmol tab below displays an interactive JSmol that shows all three of these structures.

Acyl-carrier proteins (PDB entries 2kwm, 2fad and 3ejb)

Three structures of acyl-carrier proteins are overlapped in this Jmol: one before lipid is bound (PDB entry 2kwm), one with a small lipid bound (PDB entry 2fad), and one that is delivering the lipid to an enzyme (PDB entry 3ejb). In each case, acyl-carrier protein is shown in blue with the pantetheine cofactor in green, the lipid is in yellow, and the enzyme is in red. Use the buttons to switch between the three structures, and to change the representation.


  1. Ramelot, T. A. et al. Solution structure of 4'-phosphopantetheine - GmACP3 from Geobacter metallireducens: a specialized acyl-carrier protein with atypical structural features and a putative role in lipopolysaccharide biosynthesis. Biochemistry 50, 1442-1453 (2011).

  2. Raetz, C. R. H. & Whitfield, C. Lipopolysaccharide endotoxins. Annual Review of Biochemistry 71, 635-700 (2002).

  3. Mahadevan, R., Palsson, B. O. & Lovley, D. R. In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling. Nature Reviews Microbiology 9, 39-50 (2011).

  4. Barkleit, A. Foerstendorf, H., Li, B., Rossberg, A., Moll, H. & Bernhard, G. Coordination of uranium(VI) with functional groups of bacterial lipopolysaccharide studied by EXAFS and FT-IR spectroscopy. Dalton Transactions 40, 9868-9876 (2011).

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health