5A3Q

Crystal structure of the (SR) Calcium ATPase E2-vanadate complex bound to thapsigargin and TNP-AMPPCP

Summary for 5A3Q

• Entry DOI: 10.2210/pdb5a3q/pdb
• Related: 5A3R 5A3S
• Descriptor: SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1, 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, oxido(dioxo)vanadium, ... (8 entities in total)
• Functional Keywords: hydrolase, sarco(endo)plasmic reticulum calcium atpase, vanadate, p-type atpase, serca, trinitrophenyl-nucleotide analoges, calcium transport, inhibition, transition state
• Biological source: ORYCTOLAGUS CUNICULUS (RABBIT)
• Total number of polymer chains: 1
• Total formula weight: 111217.77

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.,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)