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

Cell wall recycler

SBKB [doi:10.1038/sbkb.2011.16]
Featured Article - May 2011
Short description: The crystal structure of the bacterial cell wall recycling protein Mpl reveals similarities as well as differences compared with functionally related Mur ligases.

Ribbon diagram of PaMpl highlighting the three domains: N-terminal domain (ND), green; middle domain (MD), cyan; C-terminal domain (CD), yellow. [PDB: 3HN7]

Bacterial cell walls contain peptidoglycan (murein), which is synthesized de novo by enzymes of the Mur family. In Gram-negative bacteria, ∼30–60% of the bacterial cell wall is recycled via a process that involves the murein peptide ligase (Mpl), which attaches a breakdown product, the tripeptide L-Ala-γ-Glu-meso-A2pm (it can also attach tetra- and pentapeptides, but less efficiently), to UDP-N-acetylmuramic acid (UDP-MurNAc). Mpl is functionally similar to MurC, as both enzymatic mechanisms involve the ATP-dependent ligation of an amino acid (in the case of MurC) or peptide (in the case of Mpl) to UDP-MurNAc.

Das and colleagues (PSI JCSG) have determined the crystal structure of the first full-length apo Mpl protein from the permafrost bacterium Psychrobacter arcticus 273-4 (PaMpl) at 1.65-Å resolution. PaMpl can be divided into three distinct domains: the N-terminal UDP-MurNAc–binding domain (ND), the middle ATP-binding domain (MD) and the C-terminal tripeptide-binding domain (CD), which are linked contiguously to from a triangular-shaped molecule. Although PaMpl is larger than MurC from Escherichia coli (EcMurC), with major insertions in the MD, they share a common structural core. The largest conformational difference is in the position of the structurally flexible CD in PaMpl, which is rotated 30° relative to ND and MD, compared with MurC. PaMpl is a monomer in the crystal asymmetric unit but is thought to be dimeric in solution. EcMurC is a dimer in the crystal structure, but exists in a dynamic equilibrium between monomers and dimers in solution. The residues involved in dimerization in PaMpl probably differ from those involved in EcMurC dimerization, suggesting that the mode of dimerization might also be different.

Residues in the ND and MD that are important for interaction with UDP-MurNAc, ATP and metal cofactor have been described for Mur enzymes, and many of these residues are structurally conserved in PaMpl. As true for MurC, PaMpl activity is dependent on magnesium, although no Mg2+ is observed in the PaMpl structure. One metal-binding site is conserved, whereas the region comprising a second metal-binding site is disordered—probably owing to the absence of Mg2+. A loop from CD is folded into part of the ATP- and UDP-MurNAc–binding site, and the authors suggest that a significant conformational change is likely to occur in this region upon binding of substrates and cofactors, thereby ordering the second metal-binding site and opening the CD.

CD is the least conserved domain between Mpl and MurC, which probably reflects their different substrate specificities. Conserved, solvent-exposed Mpl-specific residues in the CD are likely to be important for substrate specificity. The authors identified a number of residues that, upon substrate binding, are likely to induce a conformational change of the CD with respect to the ND and MD. This conformational change is thought to allow UDP-MurNAc to bind to the ND and the tripeptide to access and be positioned at the active site.

These data provide the basis for more extensive functional characterization of Mpl proteins. Given the parallels with Mur enzymes, which are established drug discovery targets, this might lead to the design of better Mur inhibitors that could block both the de novo and recycling pathways for cell wall synthesis, and thereby act as effective antimicrobial agents.

Arianne Heinrichs

References

  1. D. Das et al. Structure and function of the first full-length murein peptide ligase (Mpl) cell wall recycling protein.
    PLoS One 6, e17624 (2011). doi:10.1371/journal.pone.0017624

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