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Conformational rearrangement of gastric H(+),K(+)-ATPase induced by an acid suppressant.

Abe K, Tani K, Fujiyoshi Y - Nat Commun (2011)

Bottom Line: The density of the bound SCH28080 is found near transmembrane (TM) helices 4, 5 and 6, in the luminal cavity.The SCH28080-binding site is formed by the rearrangement of TM helices, which is in turn transmitted to the cytoplasmic domains, resulting in a luminal-open conformation.These results represent the first structural evidence for a binding site of an acid suppressant on H(+),K(+)-ATPase, and the conformational change induced by this class of drugs.

View Article: PubMed Central - PubMed

Affiliation: Department of Biophysics, Faculty of Science, Kyoto University, Oiwake, Kitashirakawa, Sakyo-ku, Kyoto 606-0852, Japan.

ABSTRACT
Acid-related gastric diseases are associated with disorder of digestive tract acidification. The gastric proton pump, H(+),K(+)-ATPase, exports H(+) in exchange for luminal K(+) to generate a highly acidic environment in the stomach, and is a main target for acid suppressants. Here, we report the three-dimensional structure of gastric H(+),K(+)-ATPase with bound SCH28080, a representative K(+)-competitive acid blocker, at 7 Å resolution based on electron crystallography of two-dimensional crystals. The density of the bound SCH28080 is found near transmembrane (TM) helices 4, 5 and 6, in the luminal cavity. The SCH28080-binding site is formed by the rearrangement of TM helices, which is in turn transmitted to the cytoplasmic domains, resulting in a luminal-open conformation. These results represent the first structural evidence for a binding site of an acid suppressant on H(+),K(+)-ATPase, and the conformational change induced by this class of drugs.

No MeSH data available.


Related in: MedlinePlus

SCH28080-binding site.(a) Predicted binding mode of SCH28080 (blue stick with transparent surface rendering) to the homology model (spheres) determined by docking simulations. The green mesh shows the subtracted density and amino acids important for the SCH28080-binding are highlighted in red or orange (as shown in Fig. 1b). The calculated binding site of SCH28080 fits well into the homology model as well as the experimentally determined density (green mesh), supporting the reliability of the proposed (b) Comparison between SCH28080- (red stick) and ouabain (white stick)-binding sites. The ribbon models represent the homology model of H+,K+-ATPase (SCH)E2BeF (colour as in Fig. 1a, positions for several important amino acids are marked in red or orange as in Fig. 1b) and the X-ray structure of ouabain-bound Na+,K+-ATPase (grey)20. Indicated in green (ball and stick representation) are side chains, which must be mutated for the formation of an ouabain-sensitive H+,K+-ATPase19. White spheres represent bound K+ ions in the Na+,K+-ATPase structure. The overlap between these two specific inhibitors seems to be consistent with their similar modes of inhibition. In both figure panels, helices M1 and M2 were omitted for clarity.
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f2: SCH28080-binding site.(a) Predicted binding mode of SCH28080 (blue stick with transparent surface rendering) to the homology model (spheres) determined by docking simulations. The green mesh shows the subtracted density and amino acids important for the SCH28080-binding are highlighted in red or orange (as shown in Fig. 1b). The calculated binding site of SCH28080 fits well into the homology model as well as the experimentally determined density (green mesh), supporting the reliability of the proposed (b) Comparison between SCH28080- (red stick) and ouabain (white stick)-binding sites. The ribbon models represent the homology model of H+,K+-ATPase (SCH)E2BeF (colour as in Fig. 1a, positions for several important amino acids are marked in red or orange as in Fig. 1b) and the X-ray structure of ouabain-bound Na+,K+-ATPase (grey)20. Indicated in green (ball and stick representation) are side chains, which must be mutated for the formation of an ouabain-sensitive H+,K+-ATPase19. White spheres represent bound K+ ions in the Na+,K+-ATPase structure. The overlap between these two specific inhibitors seems to be consistent with their similar modes of inhibition. In both figure panels, helices M1 and M2 were omitted for clarity.

Mentions: As predicted by earlier homology modelling of H+,K+-ATPase2526272829 together with mutagenesis studies, the density responsible for bound SCH28080 was found in the luminal cavity (Fig. 1b). The subtraction map (that is, [EM density map]−[homology model], green mesh in Fig. 1b, Fig. 2a,b) clearly shows an excess density in the centre of the luminal cavity. The density is located near the luminal part of M4, M5 and M6 in the luminal ion entry path ∼12 Å from the ion-binding site (Fig. 1c), consistent with the K+-competitive inhibition mode of SCH28080 (refs 3, 17). The density is also predicted to be surrounded by several important amino acids262728 for SCH28080 affinity, including F332, A335, Y799, L809 and C813 (Fig. 1b,c). Molecular docking simulation of SCH28080 to the H+,K+-ATPase homology model suggested that its potential binding site is close to the observed density (Fig. 2a), consistent with many of the earlier studies described above.


Conformational rearrangement of gastric H(+),K(+)-ATPase induced by an acid suppressant.

Abe K, Tani K, Fujiyoshi Y - Nat Commun (2011)

SCH28080-binding site.(a) Predicted binding mode of SCH28080 (blue stick with transparent surface rendering) to the homology model (spheres) determined by docking simulations. The green mesh shows the subtracted density and amino acids important for the SCH28080-binding are highlighted in red or orange (as shown in Fig. 1b). The calculated binding site of SCH28080 fits well into the homology model as well as the experimentally determined density (green mesh), supporting the reliability of the proposed (b) Comparison between SCH28080- (red stick) and ouabain (white stick)-binding sites. The ribbon models represent the homology model of H+,K+-ATPase (SCH)E2BeF (colour as in Fig. 1a, positions for several important amino acids are marked in red or orange as in Fig. 1b) and the X-ray structure of ouabain-bound Na+,K+-ATPase (grey)20. Indicated in green (ball and stick representation) are side chains, which must be mutated for the formation of an ouabain-sensitive H+,K+-ATPase19. White spheres represent bound K+ ions in the Na+,K+-ATPase structure. The overlap between these two specific inhibitors seems to be consistent with their similar modes of inhibition. In both figure panels, helices M1 and M2 were omitted for clarity.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105306&req=5

f2: SCH28080-binding site.(a) Predicted binding mode of SCH28080 (blue stick with transparent surface rendering) to the homology model (spheres) determined by docking simulations. The green mesh shows the subtracted density and amino acids important for the SCH28080-binding are highlighted in red or orange (as shown in Fig. 1b). The calculated binding site of SCH28080 fits well into the homology model as well as the experimentally determined density (green mesh), supporting the reliability of the proposed (b) Comparison between SCH28080- (red stick) and ouabain (white stick)-binding sites. The ribbon models represent the homology model of H+,K+-ATPase (SCH)E2BeF (colour as in Fig. 1a, positions for several important amino acids are marked in red or orange as in Fig. 1b) and the X-ray structure of ouabain-bound Na+,K+-ATPase (grey)20. Indicated in green (ball and stick representation) are side chains, which must be mutated for the formation of an ouabain-sensitive H+,K+-ATPase19. White spheres represent bound K+ ions in the Na+,K+-ATPase structure. The overlap between these two specific inhibitors seems to be consistent with their similar modes of inhibition. In both figure panels, helices M1 and M2 were omitted for clarity.
Mentions: As predicted by earlier homology modelling of H+,K+-ATPase2526272829 together with mutagenesis studies, the density responsible for bound SCH28080 was found in the luminal cavity (Fig. 1b). The subtraction map (that is, [EM density map]−[homology model], green mesh in Fig. 1b, Fig. 2a,b) clearly shows an excess density in the centre of the luminal cavity. The density is located near the luminal part of M4, M5 and M6 in the luminal ion entry path ∼12 Å from the ion-binding site (Fig. 1c), consistent with the K+-competitive inhibition mode of SCH28080 (refs 3, 17). The density is also predicted to be surrounded by several important amino acids262728 for SCH28080 affinity, including F332, A335, Y799, L809 and C813 (Fig. 1b,c). Molecular docking simulation of SCH28080 to the H+,K+-ATPase homology model suggested that its potential binding site is close to the observed density (Fig. 2a), consistent with many of the earlier studies described above.

Bottom Line: The density of the bound SCH28080 is found near transmembrane (TM) helices 4, 5 and 6, in the luminal cavity.The SCH28080-binding site is formed by the rearrangement of TM helices, which is in turn transmitted to the cytoplasmic domains, resulting in a luminal-open conformation.These results represent the first structural evidence for a binding site of an acid suppressant on H(+),K(+)-ATPase, and the conformational change induced by this class of drugs.

View Article: PubMed Central - PubMed

Affiliation: Department of Biophysics, Faculty of Science, Kyoto University, Oiwake, Kitashirakawa, Sakyo-ku, Kyoto 606-0852, Japan.

ABSTRACT
Acid-related gastric diseases are associated with disorder of digestive tract acidification. The gastric proton pump, H(+),K(+)-ATPase, exports H(+) in exchange for luminal K(+) to generate a highly acidic environment in the stomach, and is a main target for acid suppressants. Here, we report the three-dimensional structure of gastric H(+),K(+)-ATPase with bound SCH28080, a representative K(+)-competitive acid blocker, at 7 Å resolution based on electron crystallography of two-dimensional crystals. The density of the bound SCH28080 is found near transmembrane (TM) helices 4, 5 and 6, in the luminal cavity. The SCH28080-binding site is formed by the rearrangement of TM helices, which is in turn transmitted to the cytoplasmic domains, resulting in a luminal-open conformation. These results represent the first structural evidence for a binding site of an acid suppressant on H(+),K(+)-ATPase, and the conformational change induced by this class of drugs.

No MeSH data available.


Related in: MedlinePlus