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Systematic comparison of molecular conformations of H+,K+-ATPase reveals an important contribution of the A-M2 linker for the luminal gating.

Abe K, Tani K, Fujiyoshi Y - J. Biol. Chem. (2014)

Bottom Line: The molecular conformation of the (SCH)E2·MgF state thus represents a mixed overall structure in which its cytoplasmic and luminal half appear to be independently modulated by a phosphate analog and an antagonist bound to the respective parts of the enzyme.Comparison of the molecular conformations revealed that the linker region connecting the A domain and the transmembrane helix 2 (A-M2 linker) mediates the regulation of luminal gating.The mechanistic rationale underlying luminal gating observed in H(+),K(+)-ATPase is consistent with that observed in sarcoplasmic reticulum Ca(2+)-ATPase and other P-type ATPases and is most likely conserved for the P-type ATPase family in general.

View Article: PubMed Central - PubMed

Affiliation: From the Cellular and Structural Physiology Institute and Graduate School of Pharmaceutical Science, Nagoya University, Nagoya 464-8601, Japan kabe@cespi.nagoya-u.ac.jp.

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Rotation of the A domain in response to bound XF. Comparisons of the relative orientations of the cytoplasmic domains in the EM density maps of H+,K+-ATPase between the (SCH)E2·BeF (pink surface) versus (SCH)E2·MgF (A and B, yellow mesh), E2·AlF (C and D, green mesh), and (Rb+)E2·AlF (E and F, blue mesh) states superimposed with their respective homology models (ribbons, drawn in same color). Black arrows indicate the different (20°) azimuthal positions of the A domain between the (SCH)E2·BeF state versus other indicated states. The dotted arrow indicates a 5° inclination of the A domain during transition from the (SCH)E2·MgF state to the (Rb+)E2·AlF state. Molecules are aligned by superpositioning of the P domain and viewed from the cytoplasmic side in A, C, and E or from parallel to the membrane plane in (B, D, and F). Schematic representations of their conformational states are shown on the right (see Fig. 9 for details).
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Figure 3: Rotation of the A domain in response to bound XF. Comparisons of the relative orientations of the cytoplasmic domains in the EM density maps of H+,K+-ATPase between the (SCH)E2·BeF (pink surface) versus (SCH)E2·MgF (A and B, yellow mesh), E2·AlF (C and D, green mesh), and (Rb+)E2·AlF (E and F, blue mesh) states superimposed with their respective homology models (ribbons, drawn in same color). Black arrows indicate the different (20°) azimuthal positions of the A domain between the (SCH)E2·BeF state versus other indicated states. The dotted arrow indicates a 5° inclination of the A domain during transition from the (SCH)E2·MgF state to the (Rb+)E2·AlF state. Molecules are aligned by superpositioning of the P domain and viewed from the cytoplasmic side in A, C, and E or from parallel to the membrane plane in (B, D, and F). Schematic representations of their conformational states are shown on the right (see Fig. 9 for details).

Mentions: To compare the relative orientation of the cytoplasmic domains, the EM density map and homology models were aligned based on the superpositioning of the molecules on their P domain (see Fig. 3). To compare other structural parts, including the A-M2 linker and TM helices, the molecules were aligned by superpositioning of the TM segments M7-M10 and βM, which are the least variable of the reported SERCA structures.


Systematic comparison of molecular conformations of H+,K+-ATPase reveals an important contribution of the A-M2 linker for the luminal gating.

Abe K, Tani K, Fujiyoshi Y - J. Biol. Chem. (2014)

Rotation of the A domain in response to bound XF. Comparisons of the relative orientations of the cytoplasmic domains in the EM density maps of H+,K+-ATPase between the (SCH)E2·BeF (pink surface) versus (SCH)E2·MgF (A and B, yellow mesh), E2·AlF (C and D, green mesh), and (Rb+)E2·AlF (E and F, blue mesh) states superimposed with their respective homology models (ribbons, drawn in same color). Black arrows indicate the different (20°) azimuthal positions of the A domain between the (SCH)E2·BeF state versus other indicated states. The dotted arrow indicates a 5° inclination of the A domain during transition from the (SCH)E2·MgF state to the (Rb+)E2·AlF state. Molecules are aligned by superpositioning of the P domain and viewed from the cytoplasmic side in A, C, and E or from parallel to the membrane plane in (B, D, and F). Schematic representations of their conformational states are shown on the right (see Fig. 9 for details).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
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Figure 3: Rotation of the A domain in response to bound XF. Comparisons of the relative orientations of the cytoplasmic domains in the EM density maps of H+,K+-ATPase between the (SCH)E2·BeF (pink surface) versus (SCH)E2·MgF (A and B, yellow mesh), E2·AlF (C and D, green mesh), and (Rb+)E2·AlF (E and F, blue mesh) states superimposed with their respective homology models (ribbons, drawn in same color). Black arrows indicate the different (20°) azimuthal positions of the A domain between the (SCH)E2·BeF state versus other indicated states. The dotted arrow indicates a 5° inclination of the A domain during transition from the (SCH)E2·MgF state to the (Rb+)E2·AlF state. Molecules are aligned by superpositioning of the P domain and viewed from the cytoplasmic side in A, C, and E or from parallel to the membrane plane in (B, D, and F). Schematic representations of their conformational states are shown on the right (see Fig. 9 for details).
Mentions: To compare the relative orientation of the cytoplasmic domains, the EM density map and homology models were aligned based on the superpositioning of the molecules on their P domain (see Fig. 3). To compare other structural parts, including the A-M2 linker and TM helices, the molecules were aligned by superpositioning of the TM segments M7-M10 and βM, which are the least variable of the reported SERCA structures.

Bottom Line: The molecular conformation of the (SCH)E2·MgF state thus represents a mixed overall structure in which its cytoplasmic and luminal half appear to be independently modulated by a phosphate analog and an antagonist bound to the respective parts of the enzyme.Comparison of the molecular conformations revealed that the linker region connecting the A domain and the transmembrane helix 2 (A-M2 linker) mediates the regulation of luminal gating.The mechanistic rationale underlying luminal gating observed in H(+),K(+)-ATPase is consistent with that observed in sarcoplasmic reticulum Ca(2+)-ATPase and other P-type ATPases and is most likely conserved for the P-type ATPase family in general.

View Article: PubMed Central - PubMed

Affiliation: From the Cellular and Structural Physiology Institute and Graduate School of Pharmaceutical Science, Nagoya University, Nagoya 464-8601, Japan kabe@cespi.nagoya-u.ac.jp.

Show MeSH