PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons
E-Collection

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
Viroporins
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
CXCR4
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
Lysostaphin
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

Peptidoglycan binding: Calcium-free killing

PSI-SGKB [doi:10.1038/fa_psisgkb.2010.22]
Featured Article - June 2010
Short description: NMR spectroscopy reveals the molecular basis for Ca2+-independent recognition by bactericidal Reg family lectins.

Human REG3A (also known as HIP/PAP) is directly bactericidal for Gram-positive bacteria. It is highly expressed in the small intestine and a member of the mammalian Reg (regenerating) family proteins. These proteins contain a C-type lectin-like domain (CTLD) and bind to bacterial cell wall peptidoglycan. Despite having a CTLD, Reg proteins lack the conserved sequences required for Ca2+-dependent carbohydrate binding that are found in other lectins. Lora Hooper and colleagues now identify a motif in Reg proteins that is essential for binding of the peptidoglycan carbohydrate backbone, and propose a model to explain how the bacterial surface is specifically recognised even in the presence of soluble peptidoglycan fragments.

The CTLD of REG3A has a typical structure with two loop regions. In other lectins, a tripeptide EPN motif in Loop 2 contacts 3- and 4-OH groups of mannose or N-acetylglucosamine (GlcNAc) polysaccharides. Although this Loop 2 EPN binding is Ca2+ dependent, REG3A binds mannose and GlcNAc without calcium, and its Loop 2 lacks the EPN motif.

Using solution nuclear magnetic resonance (NMR) spectroscopy, the authors discovered that REG3A contains a Loop 1 EPN sequence, rather than Loop 2. Soluble peptidoglycan was titrated into labelled REG3A, and chemical shift perturbations of backbone amide resonances were measured. These indicate changes in the environment of specific residues, allowing binding sites to be mapped.

Primary sequence alignments showed that the Loop 1 EPN motif is conserved among Ca2+-independent mannose and GlcNAc-binding lectins, and absent in their Ca2+-dependent counterparts. Mutational analysis confirmed that it is critical for peptidoglycan binding activity by REG3A, and for successful bacterial killing.

To investigate the binding preferences of the REG3A EPN motif, the authors used analogs of the peptidoglycan carbohydrate backbone and fractions derived from native peptidoglycan and determined that binding affinity is dictated by polysaccharide chain length. This explains how shorter peptidoglycan fragments, which are constantly shed by intestinal bacteria, do not out-compete REG3A for binding to the bacterial surface. The peptide moiety did not form a significant part of the REG3A–peptidoglycan interaction.

Mucin–binding lectins, which have high affinity for extended rather than monovalent ligands, have been previously shown to 'bind and slide' from sugar to sugar in a manner that relates chain length to binding affinity. The authors propose that REG3A and other mammalian Loop 1 EPN-containing Reg proteins use a similar dynamic recognition process. This enables high-affinity binding to the bacterial cell wall and emphasizes that the clustered in vivo presentation of carbohydrate epitopes is critical for recognition by lectins.

Emma Leah

References

  1. R. E. Lehotzky et al. Molecular basis for peptidoglycan recognition by a bactericidal lectin.
    Proc. Natl Acad. Sci. USA 107, 7722-7727 (2010). doi:10.1073/pnas.0909449107

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