Limits...
Orthologous and Paralogous AmpD Peptidoglycan Amidases from Gram-Negative Bacteria

View Article: PubMed Central - PubMed

ABSTRACT

Cell wall recycling and β-lactam antibiotic resistance are linked in Enterobacteriaceae and in Pseudomonas aeruginosa. This process involves a large number of murolytic enzymes, among them a cytoplasmic peptidoglycan amidase AmpD, which plays an essential role by cleaving the peptide stem from key intermediates en route to the β-lactamase production (a resistance mechanism) and cell wall recycling. Uniquely, P. aeruginosa has two additional paralogues of AmpD, designated AmpDh2 and AmpDh3, which are periplasmic enzymes. Despite the fact that AmpDh2 and AmpDh3 share a common motif for their respective catalytic domains, they are each comprised of multidomain architectures and exhibit distinct oligomerization properties. We review herein the structural and biochemical properties of orthologous and paralogous AmpD proteins and discuss their implication in cell wall recycling and antibiotic resistance processes.

No MeSH data available.


Related in: MedlinePlus

Oligomeric state and cell wall binding in AmpD enzymes. The enzyme structures are given as ribbon representation (a–c) and Connolley surface (d–g). The ligands are depicted as capped sticks. (a) Crystal structure of AmpD from Citrobacter freundii (green cartoon) in complex with anhNAM(pentapetide), 2c (PDB code 2Y2B). (b) Combined structures of AmpDh2 from Pseudomonas aeruginosa in complex with 2c and complex with 4 (PDB codes 4BOL and 4BPA, respectively). (c) Crystal structure of the tetramer of AmpDh3 from P. aeruginosa in complex with (NAG-NAM(pentapeptide))2, 5 (PDB code 4BXD). (d) Detail of the active site of AmpD from C. freundii in complex with anhNAM(pentapetide), 2c (depicted as capped sticks). (e) Detail of the active site of AmpDh3 from P. aeruginosa in complex with anhNAM(pentapetide), 2c (PDB code 4BXE). (f) Detail of the active site of AmpDh2 from P. aeruginosa in complex with 2c and with 4 (PDB codes 4BOL and 4BPA, respectively). Surface of monomers colored as in (b). (g) Detail of the active site of AmpDh3 from P. aeruginosa in complex with (NAG-NAM(pentapetide))2, 5. Surface of monomers colored as in (c).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC5036320&req=5

f4: Oligomeric state and cell wall binding in AmpD enzymes. The enzyme structures are given as ribbon representation (a–c) and Connolley surface (d–g). The ligands are depicted as capped sticks. (a) Crystal structure of AmpD from Citrobacter freundii (green cartoon) in complex with anhNAM(pentapetide), 2c (PDB code 2Y2B). (b) Combined structures of AmpDh2 from Pseudomonas aeruginosa in complex with 2c and complex with 4 (PDB codes 4BOL and 4BPA, respectively). (c) Crystal structure of the tetramer of AmpDh3 from P. aeruginosa in complex with (NAG-NAM(pentapeptide))2, 5 (PDB code 4BXD). (d) Detail of the active site of AmpD from C. freundii in complex with anhNAM(pentapetide), 2c (depicted as capped sticks). (e) Detail of the active site of AmpDh3 from P. aeruginosa in complex with anhNAM(pentapetide), 2c (PDB code 4BXE). (f) Detail of the active site of AmpDh2 from P. aeruginosa in complex with 2c and with 4 (PDB codes 4BOL and 4BPA, respectively). Surface of monomers colored as in (b). (g) Detail of the active site of AmpDh3 from P. aeruginosa in complex with (NAG-NAM(pentapetide))2, 5. Surface of monomers colored as in (c).

Mentions: Importantly, the oligomeric state is different for each AmpD paralogue, something that seems to be related to both their specificity for substrates and regulation. Cytoplasmic AmpD presents a globular monomer of around 40 × 49 Å dimensions for the active-site face (Fig. 4a). AmpDh2 is a large homodimer (60 × 69 Å) (Fig. 4b), both in the crystal and in solution.13 The long N-terminal loop allows both the formation of the dimer and the anchoring of the oligomer to the inner leaflet of the bacterial outer membrane. Interestingly (as detailed below) the dimer also provides a more extensive surface for recognition of the cell wall.13 On the other hand, the periplasmic AmpDh3 is soluble and is folded in a very large tetrameric arrangement of around 74 × 87 Å (Fig. 4c). The N-terminal coiled-coil/loop and an extra α helix (α2 in Fig. 3d), not present in homologous AmpDh2, provide a strong network of interactions that allow the formation of the tetramer in AmpDh3. This tetramer displays two active sites in one side of the oligomer and the other two in the back, allowing a multivalent binding of AmpDh3 onto the cell wall, which lends itself to its processive remodeling.12


Orthologous and Paralogous AmpD Peptidoglycan Amidases from Gram-Negative Bacteria
Oligomeric state and cell wall binding in AmpD enzymes. The enzyme structures are given as ribbon representation (a–c) and Connolley surface (d–g). The ligands are depicted as capped sticks. (a) Crystal structure of AmpD from Citrobacter freundii (green cartoon) in complex with anhNAM(pentapetide), 2c (PDB code 2Y2B). (b) Combined structures of AmpDh2 from Pseudomonas aeruginosa in complex with 2c and complex with 4 (PDB codes 4BOL and 4BPA, respectively). (c) Crystal structure of the tetramer of AmpDh3 from P. aeruginosa in complex with (NAG-NAM(pentapeptide))2, 5 (PDB code 4BXD). (d) Detail of the active site of AmpD from C. freundii in complex with anhNAM(pentapetide), 2c (depicted as capped sticks). (e) Detail of the active site of AmpDh3 from P. aeruginosa in complex with anhNAM(pentapetide), 2c (PDB code 4BXE). (f) Detail of the active site of AmpDh2 from P. aeruginosa in complex with 2c and with 4 (PDB codes 4BOL and 4BPA, respectively). Surface of monomers colored as in (b). (g) Detail of the active site of AmpDh3 from P. aeruginosa in complex with (NAG-NAM(pentapetide))2, 5. Surface of monomers colored as in (c).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5036320&req=5

f4: Oligomeric state and cell wall binding in AmpD enzymes. The enzyme structures are given as ribbon representation (a–c) and Connolley surface (d–g). The ligands are depicted as capped sticks. (a) Crystal structure of AmpD from Citrobacter freundii (green cartoon) in complex with anhNAM(pentapetide), 2c (PDB code 2Y2B). (b) Combined structures of AmpDh2 from Pseudomonas aeruginosa in complex with 2c and complex with 4 (PDB codes 4BOL and 4BPA, respectively). (c) Crystal structure of the tetramer of AmpDh3 from P. aeruginosa in complex with (NAG-NAM(pentapeptide))2, 5 (PDB code 4BXD). (d) Detail of the active site of AmpD from C. freundii in complex with anhNAM(pentapetide), 2c (depicted as capped sticks). (e) Detail of the active site of AmpDh3 from P. aeruginosa in complex with anhNAM(pentapetide), 2c (PDB code 4BXE). (f) Detail of the active site of AmpDh2 from P. aeruginosa in complex with 2c and with 4 (PDB codes 4BOL and 4BPA, respectively). Surface of monomers colored as in (b). (g) Detail of the active site of AmpDh3 from P. aeruginosa in complex with (NAG-NAM(pentapetide))2, 5. Surface of monomers colored as in (c).
Mentions: Importantly, the oligomeric state is different for each AmpD paralogue, something that seems to be related to both their specificity for substrates and regulation. Cytoplasmic AmpD presents a globular monomer of around 40 × 49 Å dimensions for the active-site face (Fig. 4a). AmpDh2 is a large homodimer (60 × 69 Å) (Fig. 4b), both in the crystal and in solution.13 The long N-terminal loop allows both the formation of the dimer and the anchoring of the oligomer to the inner leaflet of the bacterial outer membrane. Interestingly (as detailed below) the dimer also provides a more extensive surface for recognition of the cell wall.13 On the other hand, the periplasmic AmpDh3 is soluble and is folded in a very large tetrameric arrangement of around 74 × 87 Å (Fig. 4c). The N-terminal coiled-coil/loop and an extra α helix (α2 in Fig. 3d), not present in homologous AmpDh2, provide a strong network of interactions that allow the formation of the tetramer in AmpDh3. This tetramer displays two active sites in one side of the oligomer and the other two in the back, allowing a multivalent binding of AmpDh3 onto the cell wall, which lends itself to its processive remodeling.12

View Article: PubMed Central - PubMed

ABSTRACT

Cell wall recycling and β-lactam antibiotic resistance are linked in Enterobacteriaceae and in Pseudomonas aeruginosa. This process involves a large number of murolytic enzymes, among them a cytoplasmic peptidoglycan amidase AmpD, which plays an essential role by cleaving the peptide stem from key intermediates en route to the β-lactamase production (a resistance mechanism) and cell wall recycling. Uniquely, P. aeruginosa has two additional paralogues of AmpD, designated AmpDh2 and AmpDh3, which are periplasmic enzymes. Despite the fact that AmpDh2 and AmpDh3 share a common motif for their respective catalytic domains, they are each comprised of multidomain architectures and exhibit distinct oligomerization properties. We review herein the structural and biochemical properties of orthologous and paralogous AmpD proteins and discuss their implication in cell wall recycling and antibiotic resistance processes.

No MeSH data available.


Related in: MedlinePlus