5A3R

Crystal structure of the (SR) Calcium ATPase E2.BeF3- complex bound to TNP-AMPPCP

Summary for 5A3R

• Entry DOI: 10.2210/pdb5a3r/pdb
• Related: 5A3Q 5A3S
• Descriptor: SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1, Spiro(2,4,6-trinitrobenzene[1,2a]-O2',O3'-methylene-adenosine (beta,gamma-methylene)triphosphate, POTASSIUM ION, ... (5 entities in total)
• Functional Keywords: hydrolase, sarco(endo)plasmic, sarco(endo)plasmic reticulum calcium atpase, beryllium fluoride, p-type atpase, serca, trinitrophenyl-nucleotide analoges, tnp-amppcp, calcium transport, inhibition, transition state
• Biological source: ORYCTOLAGUS CUNICULUS (RABBIT)
• Total number of polymer chains: 1
• Total formula weight: 110495.89

Authors

Clausen, J.D.,Bublitz, M.,Arnou, B.,Olesen, C.,Andersen, J.P.,Moller, J.V.,Nissen, P. (deposition date: 2015-06-02, release date: 2016-04-13, Last modification date: 2024-11-06)

Primary citation

Clausen, J.D.,Bublitz, M.,Arnou, B.,Olesen, C.,Andersen, J.P.,Moller, J.V.,Nissen, P.
Crystal Structure of the Vanadate-Inhibited Ca(2+)-ATPase.
Structure, 24:617-, 2016

PubMed Abstract: Vanadate is the hallmark inhibitor of the P-type ATPase family; however, structural details of its inhibitory mechanism have remained unresolved. We have determined the crystal structure of sarcoplasmic reticulum Ca(2+)-ATPase with bound vanadate in the absence of Ca(2+). Vanadate is bound at the catalytic site as a planar VO3(-) in complex with water and Mg(2+) in a dephosphorylation transition-state-like conformation. Validating bound VO3(-) by anomalous difference Fourier maps using long-wavelength data we also identify a hitherto undescribed Cl(-) site near the dephosphorylation site. Crystallization was facilitated by trinitrophenyl (TNP)-derivatized nucleotides that bind with the TNP moiety occupying the binding pocket that normally accommodates the adenine of ATP, rationalizing their remarkably high affinity for E2P-like conformations of the Ca(2+)-ATPase. A comparison of the configurations of bound nucleotide analogs in the E2·VO3(-) structure with that in E2·BeF3(-) (E2P ground state analog) reveals multiple binding modes to the Ca(2+)-ATPase.

PubMed: 27050689
DOI: 10.1016/J.STR.2016.02.018

Experimental method

X-RAY DIFFRACTION (3.05 Å)