Formation of the Stable Structural Analog of ADP-sensitive Phosphoenzyme of Ca2+-ATPase with Occluded Ca2+ by Beryllium Fluoride

Dankó, Stefánia; Daiho, Takashi; Yamasaki, Kazuo; Liu, Xiaoyu; Suzuki, Hiroshi

doi:10.1074/jbc.m109.029702

Cited by 35 publications

(47 citation statements)

References 72 publications

(68 reference statements)

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“…Even though the side chain of Arg174 on the A domain is fairly free to move, the A domain should be located within a rather restricted range for a hydrogen bond to be formed with the ribose. In fact, addition of TNP-AMP to E1 · BeF 3 − slowly converts it into E1 · 2Ca 2þ , judging from proteolysis patterns (32). Thus, our crystal structures corroborate the idea that the position of the A domain and the structure of the phosphorylation site in E1P are different from those in the E1 · AlF 4 − · ADP crystal structure (32).…”

Section: Discussionsupporting

confidence: 76%

“…In fact, Seebregts and McIntosh (5) Unfortunately, as far as we know, there is no literature that reports on the affinity of all three under the same conditions. The observation that TNP-AMP binds to E2 · AlF 4 − and E2 · BeF 3 − with high affinity (32) suggests that the primary origin of the high affinity of TNP-AxPs is hydrophobic stabilization of the TNP ring. In these two complexes, there is no direct stabilization of the adenine ring (Fig.…”

Section: Discussionmentioning

confidence: 99%

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Trinitrophenyl derivatives bind differently from parent adenine nucleotides to Ca ²⁺ -ATPase in the absence of Ca ²⁺

Toyoshima

Yonekura

Tsueda

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Trinitrophenyl derivatives of adenine nucleotides are widely used for probing ATP-binding sites. Here we describe crystal structures of Ca 2þ -ATPase, a representative P-type ATPase, in the absence of Ca 2þ with bound ATP, trinitrophenyl-ATP, -ADP, and -AMP at better than 2.4-Å resolution, stabilized with thapsigargin, a potent inhibitor. These crystal structures show that the binding mode of the trinitrophenyl derivatives is distinctly different from the parent adenine nucleotides. The adenine binding pocket in the nucleotide binding domain of Ca 2þ -ATPase is now occupied by the trinitrophenyl group, and the side chains of two arginines sandwich the adenine ring, accounting for the much higher affinities of the trinitrophenyl derivatives. Trinitrophenyl nucleotides exhibit a pronounced fluorescence in the E2P ground state but not in the other E2 states. Crystal structures of the E2P and E2 ∼ P analogues of Ca 2þ -ATPase with bound trinitrophenyl-AMP show that different arrangements of the three cytoplasmic domains alter the orientation and water accessibility of the trinitrophenyl group, explaining the origin of "superfluorescence." Thus, the crystal structures demonstrate that ATP and its derivatives are highly adaptable to a wide range of site topologies stabilized by a variety of interactions.crystallography | ion pump | nucleotide derivatives T rinitrophenyl (TNP)-nucleotides (1) are often used for probing the structure of ATP-binding sites and conformational changes arising from nucleotide binding (2, 3), and for measuring the affinity of ATP by competition experiments (2, 4). It is a preferred ATP analogue for photochemical crosslinking with azide derivatives (5). These applications utilize the enhancement of fluorescence or absorption of visible light of the TNP group upon binding to a protein (6). Because of its sensitivity, competition with ATP/ADP has been a valuable means for examining mutational effects on nucleotide affinity (7). Thus, TNP nucleotides have been widely used with F1 (8), myosin (1), and P-type ATPases (2-5, 7, 9, 10), among others.Nonetheless, whether TNP derivatives are good mimics of authentic adenine nucleotides (AxPs) may be questionable. In several proteins TNP nucleotides have much higher affinities than the genuine AxPs. For instance, TNP-ATP is a high affinity (nM) antagonist of P2X receptors, which have IC 50 for ATP (or AMPPCP) in the μM range (11). The affinity is at least one order of magnitude higher in the E2 states of Ca 2þ -ATPase (3, 12) and Na þ , K þ -ATPase (4), representative P-type ATPases. Furthermore, TNP-AMP binds to Ca 2þ -ATPase similarly to or even more strongly than TNP-ATP (12), in marked contrast to AxPs. Thus, a substantially different binding mode of TNP derivatives is suggested. Although more than 20 entries are registered in the Protein Data Bank (PDB) for Ca 2þ -ATPase (reviewed in ref. 13), no structure with a bound TNP nucleotide exists. In fact, only three crystal structures have been published with bound TNP nucleotides. They are a bacterial h...

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Section: Discussionsupporting

confidence: 76%

Section: Discussionmentioning

confidence: 99%

Trinitrophenyl derivatives bind differently from parent adenine nucleotides to Ca ²⁺ -ATPase in the absence of Ca ²⁺

Toyoshima

Yonekura

Tsueda

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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“…Structural analysis of the analog and intermediate states suggests that formation of native E1PCa 2 ⅐Mg 2ϩ results in structural changes in the cytoplasmic and transmembrane domains due to configuration and ligation changes of the phosphate moiety (27). The Mg 2ϩ bound at the catalytic site contributes to these structural changes (27) …”

mentioning

confidence: 99%

“…We have recently developed an E1Ca 2 ⅐BeF 3 Ϫ complex as a stable analog of E1PCa 2 ⅐Mg 2ϩ (E1PCa 2 with bound Mg 2ϩ at the catalytic site) (27). Structural analysis of the analog and intermediate states suggests that formation of native E1PCa 2 ⅐Mg 2ϩ results in structural changes in the cytoplasmic and transmembrane domains due to configuration and ligation changes of the phosphate moiety (27).…”

mentioning

confidence: 99%

Stable Structural Analog of Ca2+-ATPase ADP-insensitive Phosphoenzyme with Occluded Ca2+ Formed by Elongation of A-domain/M1′-linker and Beryllium Fluoride Binding

Daiho

Dankó

Yamasaki

et al. 2010

Journal of Biological Chemistry

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During EP isomerization/Ca 2ϩ -release (E1PCa 2 3 E2P ϩ 2Ca 2ϩ ), the A domain swings around parallel to the membrane plane (i.e. horizontal), whereas the A and P domains and M2 incline and tightly associate (Fig. 2) (15-25). We found that shortening of the A/M1Ј-linker by deletion of any single residue blocks E1PCa 2 3 E2PCa 2 isomerization and E2P hydrolysis (26). On the other hand, its elongation by two or more glycine insertions markedly accelerates the isomerization and blocks Ca 2ϩ deocclusion/release (E2PCa 2 3 E2P ϩ 2Ca 2ϩ ) (14). Thus, elongating the A/M1Ј-linker stabilized the normally transient intermediate state E2PCa 2 (i.e. ADP-insensitive EP with occluded Ca 2ϩ ) and showed that the length of this linker is critical for the structural changes that occur during E1PCa 2 3 E2PCa 2 3 E2P ϩ 2Ca 2ϩ and subsequent E2P hydrolysis (14, 26).We have recently developed an E1Ca 2 ⅐BeF 3 Ϫ complex as a stable analog of E1PCa 2 ⅐Mg 2ϩ (E1PCa 2 with bound Mg 2ϩ at the catalytic site) (27). Structural analysis of the analog and intermediate states suggests that formation of native E1PCa 2 ⅐Mg 2ϩ results in structural changes in the cytoplasmic and transmembrane domains due to configuration and ligation changes of the phosphate moiety (27). The Mg 2ϩ bound at the catalytic site contributes to these structural changes (27)

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“…In E1PCa 2 3 E2P ϩ 2Ca 2ϩ , the A domain rotates parallel to the membrane plane and the P domain inclines to the A domain, thereby associating with each other to produce a compactly organized and inclined headpiece (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27). This tight structure is stabilized by critical interaction networks between the A and P domains at three regions (10 -14) (see Fig.…”

Section: During Camentioning

confidence: 99%

Ca2+ Release to Lumen from ADP-sensitive Phosphoenzyme E1PCa2 without Bound K+ of Sarcoplasmic Reticulum Ca2+-ATPase

Yamasaki

Daiho

Dankó

et al. 2010

Journal of Biological Chemistry

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Formation of the Stable Structural Analog of ADP-sensitive Phosphoenzyme of Ca2+-ATPase with Occluded Ca2+ by Beryllium Fluoride

Cited by 35 publications

References 72 publications

Trinitrophenyl derivatives bind differently from parent adenine nucleotides to Ca ²⁺ -ATPase in the absence of Ca ²⁺

Trinitrophenyl derivatives bind differently from parent adenine nucleotides to Ca ²⁺ -ATPase in the absence of Ca ²⁺

Stable Structural Analog of Ca2+-ATPase ADP-insensitive Phosphoenzyme with Occluded Ca2+ Formed by Elongation of A-domain/M1′-linker and Beryllium Fluoride Binding

Ca2+ Release to Lumen from ADP-sensitive Phosphoenzyme E1PCa2 without Bound K+ of Sarcoplasmic Reticulum Ca2+-ATPase

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Formation of the Stable Structural Analog of ADP-sensitive Phosphoenzyme of Ca2+-ATPase with Occluded Ca2+ by Beryllium Fluoride

Cited by 35 publications

References 72 publications

Trinitrophenyl derivatives bind differently from parent adenine nucleotides to Ca 2+ -ATPase in the absence of Ca 2+

Trinitrophenyl derivatives bind differently from parent adenine nucleotides to Ca 2+ -ATPase in the absence of Ca 2+

Stable Structural Analog of Ca2+-ATPase ADP-insensitive Phosphoenzyme with Occluded Ca2+ Formed by Elongation of A-domain/M1′-linker and Beryllium Fluoride Binding

Ca2+ Release to Lumen from ADP-sensitive Phosphoenzyme E1PCa2 without Bound K+ of Sarcoplasmic Reticulum Ca2+-ATPase

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Trinitrophenyl derivatives bind differently from parent adenine nucleotides to Ca ²⁺ -ATPase in the absence of Ca ²⁺

Trinitrophenyl derivatives bind differently from parent adenine nucleotides to Ca ²⁺ -ATPase in the absence of Ca ²⁺