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Crystal structures of the UDP-diacylglucosamine pyrophosphohydrase LpxH from Pseudomonas aeruginosa

View Article: PubMed Central - PubMed

ABSTRACT

Lipid A (also known as endotoxin) is the hydrophobic portion of lipopolysaccharides. It is an essential membrane component required for the viability of gram-negative bacteria. The enzymes involved in its biosynthesis are attractive targets for the development of novel antibiotics. LpxH catalyzes the fourth step of the lipid A biosynthesis pathway and cleaves the pyrophosphate bond of UDP-2,3-diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate (lipid X) and UMP. Here we present the structures of LpxH from Pseudomonas aeruginosa (PaLpxH). PaLpxH consists of two domains: a catalytic domain that is homologous to the metallophosphoesterases and a helical insertion domain. Lipid X was captured in the crevice between these two domains, with its phosphate group facing the dinuclear metal (Mn2+) center and two acyl chains buried in the hydrophobic cavity. The structures reveal that a large conformational change occurs at the lipid X binding site surface upon the binding/release of the product molecule. Based on these observations, we propose a novel model for lipid X embedding, which involves the scissor-like movement of helix α6, resulting in the release of lipid X into the lipid bilayer.

No MeSH data available.


Detailed representation of Mn2+ and lipid X recognition by PaLpxH.(a) Residues involved in Mn2+ coordination and the binding of the glucosamine-1-phosphate moiety of lipid X are shown. Mn2+ coordination is depicted with yellow bonds and polar interactions are depicted with light blue dotted lines. Mn1 is in octahedral coordination with six ligands, whereas Mn2 has five ligands with one open site facing the phosphate group of lipid X. Water molecules (W1 and W2) are shown as red spheres. (b) Schematic overview of Mn2+ and lipid X binding. Residues in the catalytic domain are shown in red and those in the HI domain are shown in blue. Residues whose structures change upon lipid X binding are highlighted in squares, whereas residues whose structures are unchanged are underlined. Coordination bonds are indicated with solid yellow lines, bidentate salt bridges are indicated with light blue solid lines, and hydrogen bonds are indicated with light blue dotted lines. Apolar interactions are shown with pink shading.
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f3: Detailed representation of Mn2+ and lipid X recognition by PaLpxH.(a) Residues involved in Mn2+ coordination and the binding of the glucosamine-1-phosphate moiety of lipid X are shown. Mn2+ coordination is depicted with yellow bonds and polar interactions are depicted with light blue dotted lines. Mn1 is in octahedral coordination with six ligands, whereas Mn2 has five ligands with one open site facing the phosphate group of lipid X. Water molecules (W1 and W2) are shown as red spheres. (b) Schematic overview of Mn2+ and lipid X binding. Residues in the catalytic domain are shown in red and those in the HI domain are shown in blue. Residues whose structures change upon lipid X binding are highlighted in squares, whereas residues whose structures are unchanged are underlined. Coordination bonds are indicated with solid yellow lines, bidentate salt bridges are indicated with light blue solid lines, and hydrogen bonds are indicated with light blue dotted lines. Apolar interactions are shown with pink shading.

Mentions: PaLpxH consists of two domains: a catalytic domain homologous to metallophosphoesterases (MPEs) and a helical insertion domain (HI domain) inserted in the middle of the catalytic domain. The catalytic domain of approximately 180 residues (Met1–Leu118 and Val174–Leu240) is composed of two facing β sheets (a six-stranded β sheet that includes β1–β4 and β10–β11 and a five-stranded β sheet that includes β5–β9) and four peripheral α helices (α1–α3 and α8). The HI domain is composed of four α helices (α4–α7), and no similar structure was found in the PDB. At the boundary between the catalytic and HI domains, invariant residues and two Mn2+ ions form a dinuclear metal center (Fig. 3a).


Crystal structures of the UDP-diacylglucosamine pyrophosphohydrase LpxH from Pseudomonas aeruginosa
Detailed representation of Mn2+ and lipid X recognition by PaLpxH.(a) Residues involved in Mn2+ coordination and the binding of the glucosamine-1-phosphate moiety of lipid X are shown. Mn2+ coordination is depicted with yellow bonds and polar interactions are depicted with light blue dotted lines. Mn1 is in octahedral coordination with six ligands, whereas Mn2 has five ligands with one open site facing the phosphate group of lipid X. Water molecules (W1 and W2) are shown as red spheres. (b) Schematic overview of Mn2+ and lipid X binding. Residues in the catalytic domain are shown in red and those in the HI domain are shown in blue. Residues whose structures change upon lipid X binding are highlighted in squares, whereas residues whose structures are unchanged are underlined. Coordination bonds are indicated with solid yellow lines, bidentate salt bridges are indicated with light blue solid lines, and hydrogen bonds are indicated with light blue dotted lines. Apolar interactions are shown with pink shading.
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Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC5016852&req=5

f3: Detailed representation of Mn2+ and lipid X recognition by PaLpxH.(a) Residues involved in Mn2+ coordination and the binding of the glucosamine-1-phosphate moiety of lipid X are shown. Mn2+ coordination is depicted with yellow bonds and polar interactions are depicted with light blue dotted lines. Mn1 is in octahedral coordination with six ligands, whereas Mn2 has five ligands with one open site facing the phosphate group of lipid X. Water molecules (W1 and W2) are shown as red spheres. (b) Schematic overview of Mn2+ and lipid X binding. Residues in the catalytic domain are shown in red and those in the HI domain are shown in blue. Residues whose structures change upon lipid X binding are highlighted in squares, whereas residues whose structures are unchanged are underlined. Coordination bonds are indicated with solid yellow lines, bidentate salt bridges are indicated with light blue solid lines, and hydrogen bonds are indicated with light blue dotted lines. Apolar interactions are shown with pink shading.
Mentions: PaLpxH consists of two domains: a catalytic domain homologous to metallophosphoesterases (MPEs) and a helical insertion domain (HI domain) inserted in the middle of the catalytic domain. The catalytic domain of approximately 180 residues (Met1–Leu118 and Val174–Leu240) is composed of two facing β sheets (a six-stranded β sheet that includes β1–β4 and β10–β11 and a five-stranded β sheet that includes β5–β9) and four peripheral α helices (α1–α3 and α8). The HI domain is composed of four α helices (α4–α7), and no similar structure was found in the PDB. At the boundary between the catalytic and HI domains, invariant residues and two Mn2+ ions form a dinuclear metal center (Fig. 3a).

View Article: PubMed Central - PubMed

ABSTRACT

Lipid A (also known as endotoxin) is the hydrophobic portion of lipopolysaccharides. It is an essential membrane component required for the viability of gram-negative bacteria. The enzymes involved in its biosynthesis are attractive targets for the development of novel antibiotics. LpxH catalyzes the fourth step of the lipid A biosynthesis pathway and cleaves the pyrophosphate bond of UDP-2,3-diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate (lipid X) and UMP. Here we present the structures of LpxH from Pseudomonas aeruginosa (PaLpxH). PaLpxH consists of two domains: a catalytic domain that is homologous to the metallophosphoesterases and a helical insertion domain. Lipid X was captured in the crevice between these two domains, with its phosphate group facing the dinuclear metal (Mn2+) center and two acyl chains buried in the hydrophobic cavity. The structures reveal that a large conformational change occurs at the lipid X binding site surface upon the binding/release of the product molecule. Based on these observations, we propose a novel model for lipid X embedding, which involves the scissor-like movement of helix α6, resulting in the release of lipid X into the lipid bilayer.

No MeSH data available.