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 evasion tactics

PSI-SGKB [doi:10.1038/fa_psisgkb.2009.38]
Featured Article - September 2009
Short description: The crystal structure of a crucial anthrax capsule enzyme will aid the search for new therapies.

Ribbon diagram of the CapD transpeptidase from Bacillus anthracis cap operon in complex with non-hydrolyzable substrate analogue. The enzyme attaches poly-γ-D-glutamic acid to peptidoglycan and forms a protective capsule on the surface of germinating bacilli. The capsule is essential for virulence during anthrax infection and can be visualized by India ink staining.

The bacterium responsible for the disease anthrax, Bacillus anthracis, is highly virulent and is often deadly. Various countries have tested and deployed this pathogen as a weapon throughout the twentieth century, and more recently it has been used for bioterrorism, with spores being sent through the US postal system.

When the bacterium exists as a spore it is incredibly difficult to destroy and it can persist for decades or even centuries. Once the spore enters the bloodstream, it germinates, replicates and spreads to every tissue in the body, thanks to its ability to evade detection by macrophages and granulocytes.

Bacillus anthracis outwits the immune system by using a thick capsule in which it encases itself in. This capsule is unusual in that it is not formed of polysaccharides, which are found on the surface of most bacterial pathogens, but is instead formed from a peptide poly-γ-D-glutamic acid or PDGA. This peptide is itself unusual in that it is a D isoform rather the L form found in most proteins.

Several genes are needed for capsule biogenesis, but the one that caught the eye of Wu et al. from the PSI MCSG and the University of Chicago was CapD, which sits on the surface of the cell. CapD interacts with PDGA and attaches this compound to the bacteria's cell wall through a transpeptidation reaction.

The sequence of CapD is similar to those of members of the γ-glutamyl transpeptidase (GGT) family, which catalyse the first step in glutathione degradation. However, CapD is specific for PDGA and does not catalyze reactions with the smaller glutathione substrate.

In their report, Wu et al. 1 describe the crystal structure of CapD with and without glutamate dipeptide, a non-hydrolysable analogue of its natural substrate, and compare it with CapD from other bacteria and other GGT family members to discover how it performs this unique reaction.

The overall structure of CapD contains two central β-sheets stacked with cluster of ten α-helices above it and eight α-helices below it. Together it forms a six-layer alpha/alpha/beta/beta/alpha/alpha sandwich, similar to the four-layer alpha/beta/beta/alpha sandwich seen in Ntn hydrolases. CapD has a large solvent-accessible groove in the middle of the molecule between the lower and upper domains. It has a remarkable, extended Y-shaped positive charge on the surface of the structure with the active site threonine 352 at the bottom of this cleft.

The differences in the ligand-bound and ligand-free forms suggest that upon substrate binding several α-helices move towards the Y-shaped groove, making the overall CapD structure more compact. Also, a loop region, Pro494 to Phe497, near the active site becomes more structured and becomes a single-turn helix upon substrate binding. Several side chains also change conformation.

In common with Ntn hydrolases, CapD undergoes self cleavage to form an acyl–enzyme intermediate; without cleavage a part of the amino acid sequence, known as the P segment, blocks the active site. In the CapD structure, a water molecule is visible within the active site, and this would be crucial for cleavage of an internal CapD peptide bond, lending support to the autocatalysis hypothesis of CapD activation.

CapD's substrate, PDGA, is larger than those of other members of the GGT family, and comparison of the CapD structure with other GGT family members suggest that they cannot accommodate PDGA because they have a longer loop that blocks access to the active site.

Surprisingly, CapD's active site is exposed and yet it cannot hydrolyse glutathione. This is likely to be because the Y-shaped cleft mediates substrate recognition. From the structure and from site-directed mutations, Wu et al. suggest that Thr372, Pro427, Gly428 and Gly429 activate Thr352 and stabilize an oxyanion hole. Modeling of the natural substrate, PDGA, within the active site suggests that Asn431, Arg432 and Arg520 position PDGA for catalysis.

Armed with this information, the search for inhibitors of CapD is underway 2 .

Related articles

Anthrax stealth molecule

YukI structure solves bacterial signalling puzzle

Tackling influenza's endonuclease

Unique SARS

Maria Hodges


  1. R. Wu et al. Crystal structure of Bacillus anthracis transpeptidase enzyme CapD.
    J. Biol. Chem. (2009). doi:10.1074/jbc.M109.019034

  2. S. Richter et al. Capsule anchoring in Bacillus anthracis occurs by a transpeptidation reaction that is inhibited by capsidin.
    Mol. Microbiol. 71, 404-420 (2009). doi:10.1111/j.1365-2958.2008.06533.x

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