PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons

Related Articles
Design and Evolution: Molecular Sleuthing Reveals Drug Selectivity
June 2015
Families in Gene Neighborhoods
June 2015
Ryanodine Receptor
April 2015
CCR5 and HIV Infection
January 2015
Drug Targets: Bile Acids in Motion
September 2014
Drug Targets: S1R's Ligands and Partners
September 2014
P2Y Receptors and Blood Clotting
September 2014
Bacterial CDI Toxins
June 2014
Glucagon Receptor
April 2014
March 2014
Microbial Pathogenesis: Targeting Drug Resistance in Mycobacterium tuberculosis
February 2014
Design and Discovery: Virtual Drug Screening
January 2014
Cancer Networks: IFI16-mediated p53 Activation
November 2013
G Proteins and Cancer
November 2013
Drug Discovery: Antidepressant Potential of 6-NQ SERT Inhibitors
October 2013
Drug Discovery: Finding Druggable Targets
October 2013
Drug Discovery: Identifying Dynamic Networks by CONTACT
October 2013
Drug Discovery: Modeling NET Interactions
October 2013
Membrane Proteome: GPCR Substrate Recognition and Functional Selectivity
August 2013
Infectious Diseases: Determining the Essential Structome
May 2013
NDM-1 and Antibiotics
May 2013
Microbial Pathogenesis: Computational Epitope Prediction
January 2013
Microbial Pathogenesis: Influenza Inhibitor Screen
January 2013
Microbial Pathogenesis: Measles Virus Attachment
January 2013
Cytochrome Oxidase
November 2012
Membrane Proteome: The ABCs of Transport
November 2012
Bacterial Phosphotransferase System
October 2012
Regulatory insights
September 2012
Solute Channels
September 2012
Pocket changes
July 2012
Receptor bias
July 2012
Anthrax Stealth Siderophores
June 2012
G Protein-Coupled Receptors
May 2012
Substrate specificity sleuths
April 2012
Reading out regioselectivity
December 2011
Superbugs and Antibiotic Resistance
December 2011
Terminal activation
December 2011
A change to resistance
November 2011
Docking and rolling
October 2011
Breaking down the defenses
September 2011
A2A Adenosine Receptor
May 2011
Cell wall recycler
May 2011
Subtly different
March 2011
January 2011
Subtle shifts
January 2011
ABA receptor diversity
November 2010
COX inhibition: Naproxen by proxy
November 2010
Zinc Transporter ZntB
July 2010
Peptidoglycan binding: Calcium-free killing
June 2010
Treating sleeping sickness
May 2010
Bacterial spore kinase
April 2010
Antibiotics and Ribosome Function
March 2010
Safer Alzheimer's drugs?
March 2010
Anthrax evasion tactics
September 2009
GPCR subunits: Separate but not equal
September 2009
Antibiotic target
August 2009
Salicylic Acid Binding Protein 2
August 2009
July 2009
Tackling influenza
June 2009
Bacterial Leucine Transporter, LeuT
May 2009
Anthrax stealth molecule
March 2009
Drug targets to aim for
February 2009
High-energy storage system
February 2009
Transporter mechanism in sight
February 2009
Scavenger Decapping Enzyme DcpS
November 2008
Blocking AmtB
September 2008

Research Themes Drug discovery

Anthrax Stealth Siderophores

SBKB [doi:10.3942/psi_sgkb/fm_2012_6]
Featured System - June 2012
Short description: Iron is an essential mineral, used by many enzymes for its ability to trap small molecules like oxygen and to act as a conduit of electron transfer.

Iron is an essential mineral, used by many enzymes for its ability to trap small molecules like oxygen and to act as a conduit of electron transfer. We get our supply of iron from our diet. The bacteria that inhabit our bodies, however, need to steal their iron from us. Our bodies quickly soak up all the iron we eat and sequester it tightly in proteins that store it and deliver it to our cells. The amount of free iron left for bacteria is vanishingly small, and successful bacteria have to find ways to gather it efficiently.


One of the major ways that bacteria gather iron is with siderophores. These are small flexible molecules with a collection of oxygen atoms that surround and trap individual iron atoms. The one shown here is petrobactin. It is built from several small molecules: citrate at the center, two spermidine molecules that form long, flexible linkers, and two unusual molecules of 3,4-dihydroxybenzoic acid (3,4- DHBA) at the two ends of the molecule. Siderophores gather up iron ions when they find them, and specialized transport system delivers the siderophores into the bacterial cells. PSI researchers at MCSG have solved the structure of the part of this transporter that binds to siderophores, shown here from PDB entry 3gfv.

Building Siderophores

Bacteria contain dedicated machinery for building these siderophores. PSI researchers at MCSG have reconstructed this pathway using purified enzymes, and surprisingly shown that the different components may be connected in different orders, all converging to the same petrobactin structure. As part of this work, they have also solved the structure of two of the central enzymes, shown here from PDB entries 3to3 and 3dx5, and clarified how they fit into the entire pathway. AsbB makes one of the connections between citrate and spermidine, using ATP to power the process. The bacterium encodes two enzymes that perform this type of reaction, AsbA and AsbB, but study of the reconstructed pathway has shown that both are needed for full activity. AsbF builds the unusual benzoic acid ring at the two ends of petrobactin, which is one of the features that makes petrobactin so successful in its job.

Stealth Siderophores

The bacteria that cause anthrax build two different siderophores, bacillibactin and petrobactin, but petrobactin is the one that's particularly important in virulent infections. Bacillibactin is less important because we build a special defense protein, siderocalin (shown here from PDB entry 3cmp), that gathers up any bacillibactin that it finds. Petrobactin, on the other hand, has an unusual arrangement of hydroxyl groups on the benzoic acid rings (created by AsbF), and it is not recognized by siderocalin. For this reason, petrobactin is a "stealth" siderophore that evades our defenses, and is an important target when designing drugs to fight anthrax infection.

AsbB in Action

AsbB brings together three molecules: spermidine, an intermediate with citrate connected to one spermidine and sometimes the terminal benzoic acid, and ATP. It performs its reaction in two steps: first, it breaks ATP and adds part of it to an acidic group in the intermediate. This activates the intermediate, allowing it to form a new bond with the spermidine, releasing the fragment of ATP. The MCSG structure has ATP bound in one of the two subunits. They have also created a model of how the spermidine and intermediate molecule bind. To take a closer look at this model, the JSmol tab below displays an interactive JSmol.

AsbB Model with Substrates (based on PDB entry 3to3)

The structure of AsbB includes a magnesium ion (shown in magenta) and ATP (pink) bound in the active site. MCSG researchers have also created a model of the other substrates based on this structure, shown here with spermidine in yellow and the spermidine-citrate intermediate in green. Use the buttons to change the colors and representations of the protein and ligands.


  1. Hotta, K., Kim, C.-Y., Fox, D. T. & Koppisch, A. T. Siderophore-mediated iron acquisition in Bacillus anthracis and related strains. Microbiology 156, 1918-1925 (2010).

References to Structures

  1. 3to3 - Nusca, T. D., et al. Functional and structural analysis of the siderophore synthetase AsbB through reconstruction of the petrobactin biosynthetic pathway from Bacillus anthracis. J. Biol. Chem. in press.

  2. 3gfv - Zawadzka, A. M., et al. Characterization of a Bacillus subtilis transporter for petrobactin, an anthrax stealth siderophore. Proc. Natl. Acad. Sci. USA 106, 21854- 21859 (2009).

  3. 3cmp - DOI: 10.2210/pdb3cmp/pdb

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