3AR5

Calcium pump crystal structure with bound TNP-AMP and TG

Summary for 3AR5

• Entry DOI: 10.2210/pdb3ar5/pdb
• Related: 2AGV 2DQS 2ZBD 3AR2 3AR3 3AR4 3AR6 3AR7 3AR8 3AR9
• Descriptor: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1, SODIUM ION, OCTANOIC ACID [3S-[3ALPHA, 3ABETA, 4ALPHA, 6BETA, 6ABETA, 7BETA, 8ALPHA(Z), 9BALPHA]]-6-(ACETYLOXY)-2,3,-3A,4,5,6,6A,7,8,9B-DECAHYDRO-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-[(2-METHYL-1-OXO-2-BUTENYL)OX Y]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL ESTER, ... (6 entities in total)
• Functional Keywords: p-type atpase, hydrolase, calcium transport, calcium binding, atp binding, endoplasmic reticulum, sarcoplasmic reticulum, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Oryctolagus cuniculus (rabbits)
• Cellular location: Endoplasmic reticulum membrane; Multi-pass membrane protein: P04191
• Total number of polymer chains: 1
• Total formula weight: 113062.79

Authors

Toyoshima, C.,Yonekura, S.,Tsueda, J.,Iwasawa, S. (deposition date: 2010-11-24, release date: 2011-02-02, Last modification date: 2024-10-23)

Primary citation

Toyoshima, C.,Yonekura, S.,Tsueda, J.,Iwasawa, S.
Trinitrophenyl derivatives bind differently from parent adenine nucleotides to Ca2+-ATPase in the absence of Ca2+
Proc.Natl.Acad.Sci.USA, 108:1833-1838, 2011

PubMed Abstract: Trinitrophenyl derivatives of adenine nucleotides are widely used for probing ATP-binding sites. Here we describe crystal structures of Ca(2+)-ATPase, a representative P-type ATPase, in the absence of Ca(2+) 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(2+)-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(2+)-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.

PubMed: 21239683
DOI: 10.1073/pnas.1017659108

Experimental method

X-RAY DIFFRACTION (2.2 Å)