PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons
E-Collection

Related Articles
Drug Discovery: Solving the Structure of an Anti-hypertension Drug Target
July 2015
Retrospective: 7,000 Structures Closer to Understanding Biology
July 2015
Families in Gene Neighborhoods
June 2015
Channels and Transporters: BEST in Show
April 2015
Channels and Transporters: Reorienting a Peptide in the Pocket
April 2015
Ryanodine Receptor
April 2015
Protein Folding and Misfolding: It's the Journey, Not the Destination
March 2015
Protein Folding and Misfolding: Refolding in Membrane Mimetic
March 2015
Nuclear Pore Complex: A Flexible Transporter
February 2015
Nuclear Pore Complex: Higher Resolution of Macromolecules
February 2015
Nuclear Pore Complex: Integrative Approach to Probe Nup133
February 2015
Piecing Together the Nuclear Pore Complex
February 2015
Mitochondrion: Flipping for UCP2
December 2014
Transmembrane Spans
December 2014
Glucagon Receptor
April 2014
Membrane Proteome: A Cap on Transport
April 2014
Membrane Proteome: Microcrystals Yield Big Data
April 2014
Membrane Proteome: Pumping Out Heavy Metal
April 2014
Design and Discovery: Virtual Drug Screening
January 2014
G Proteins and Cancer
November 2013
Drug Discovery: Antidepressant Potential of 6-NQ SERT Inhibitors
October 2013
Drug Discovery: Modeling NET Interactions
October 2013
Microbiome: Solid-State NMR, Crystallized
September 2013
CAAX Endoproteases
August 2013
Membrane Proteome: A Funnel-like Viroporin
August 2013
Membrane Proteome: GPCR Substrate Recognition and Functional Selectivity
August 2013
Membrane Proteome: Making DNA Nanotubes for NMR Structure Determination
August 2013
Membrane Proteome: Unveiling the Human α-helical Membrane Proteome
August 2013
Cell-Cell Interaction: Magic Structure from Microcrystals
March 2013
Cell-Cell Interaction: Nanoparticles in Cell Camouflage
March 2013
Membrane Proteome: Capturing Multiple Conformations
December 2012
Membrane Proteome: Soft Sampling
December 2012
Membrane Proteome: Sphingolipid Synthesis Selectivity
December 2012
Membrane Proteome: Tuning Membrane Protein Expression
December 2012
Cytochrome Oxidase
November 2012
Membrane Proteome: Building a Carrier
November 2012
Membrane Proteome: Every Protein Has Its Tag
November 2012
Membrane Proteome: Specific vs. Non-specific weak interactions
November 2012
Membrane Proteome: The ABCs of Transport
November 2012
Bacterial Phosphotransferase System
October 2012
Insert Here
October 2012
Solute Channels
September 2012
To structure, faster
August 2012
Pocket changes
July 2012
Predictive protein origami
July 2012
G Protein-Coupled Receptors
May 2012
Twist to open
March 2012
Anchoring's the way
February 2012
Overexpressed problems
February 2012
Gentle membrane protein extraction
January 2012
Docking and rolling
October 2011
A fragmented approach to membrane protein structures
September 2011
Raising a glass to GLIC
August 2011
Sugar transport
June 2011
A2A Adenosine Receptor
May 2011
TrkH Potassium Ion Transporter
April 2011
Subtly different
March 2011
A new amphiphile for crystallizing membrane proteins
January 2011
CXCR4
January 2011
Guard cells pick up the SLAC
December 2010
ABA receptor diversity
November 2010
COX inhibition: Naproxen by proxy
November 2010
Zinc Transporter ZntB
July 2010
Formate transporter or channel?
March 2010
Tips for crystallizing membrane proteins in lipidic mesophases
February 2010
Urea transporter
February 2010
Five good reasons to use single protein production for membrane proteins
January 2010
Membrane proteins spotted in their native habitat
January 2010
Spot the pore
January 2010
Get3 into the groove
October 2009
GPCR subunits: Separate but not equal
September 2009
GPCR modeling: any good?
August 2009
Surviving in an acid environment
August 2009
Tips for crystallizing membrane proteins
June 2009
You look familiar: the Type VI secretion system
June 2009
Bacterial Leucine Transporter, LeuT
May 2009
Aquaglyceroporin
March 2009
Death clusters
March 2009
Protein nanopores
March 2009
Transporter mechanism in sight
February 2009
A pocket guide to GPCRs
December 2008
Tuning membrane protein overexpression
October 2008
Blocking AmtB
September 2008

Research Themes Membrane proteins

Surviving in an acid environment

PSI-SGKB [doi:10.1038/fa_psisgkb.2009.34]
Featured Article - August 2009
Short description: The Escherichia coli O157:H7 amino acid antiporter structure reveals clues to how this bacterium survives in the harsh stomach environment.Science 324, 1565-1568 (2009)

Escherichia coli O157 colonies. Source: Centers for Disease Control and Prevention.

Escherichia coli O157:H7 is a virulent strain that can cause severe stomach cramps, diarrhea and vomiting. Although most people recover within a short time, some cases are life-threatening.

E. coli O157:H7 is particularly effective because can survive in the acidic environment of the stomach, where the pH is between 2 and 3. It achieves this by using acid-resistance systems, termed AR2 and AR3, that exchange one substrate for another. In the case of AR2, transport of glutamate is linked to that of agmatine (Agm, the decarboxylated form of arginine) through the antiporter AdiC. This process results in a net expulsion of one proton for each transport cycle.

A previous low-resolution electron crystallographic study of AdiC provided a broad outline of the antiporter structure but could not elucidate the details of mechanism. Now, Gao et al. reveal the X-ray crystallographic structure of AdiC to a resolution of 3.6 Å. Overall, the structure is similar to that of the sodium-coupled symporters such as LeuT, with each molecule of AdiC having 12 transmembrane segments arranged in two layers. The inner layer is surrounded by the outer layer.

When Gao et al. compared the amino-acid sequence of AdiC with those of other related antiporters they found that a third of the conserved residues are in the central cavity, suggesting that it is a substrate-binding site. Of particular note were the four polar or charged residues located at the bottom of the cavity: Asn22, Tyr93, Glu208 and another tyrosine, Tyr365. By mutating these residues the team confirmed that these four are crucial for substrate binding.

Using this information they propose a four-step model to explain how this antiporter works. They suggest that the structure they have solved is of the initial state with the antiporter in an open, outward-facing conformation. The first step is for Arg to bind within the cavity, away from the periplasm. The second is a change in the antiporter to an open conformation, in which Arg is competitively displaced by Agm, the secondary substrate. For the third step, the antiporter bound to Agm closes, removing Agm from the cytoplasm. For the final step, the antiporter opens up to the periplasm to release Agm.

The key residue appears to be Glu208, which is most probably the pH sensor. In the stomach, at pH 2, Glu is mainly protonated and thus attracts the mainly deprotonated substrate amino acids. Once the antiporter changes conformation, Glu faces the intracellular environment, where Glu is deprotonated to produce a binding cavity with a net negative charge that favors the Agm binding.

Although the overall structure of sodium-coupled symporters and AdiC are similar, the newly revealed structure shows that AdiC and the symporters bind substrates differently.

Maria Hodges

References

  1. X. Gao et al. Structure and mechanism of an amino acid antiporter.
    Science 324, 1565-1568 (2009), doi: 10.1126/science.1173654.

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