3ar5

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ar5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AR5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AR5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ar5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AR5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AR5 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PTY:PHOSPHATIDYLETHANOLAMINE'>PTY</scene>, <scene name='pdbligand=TG1: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)OXY]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL+ESTER'>TG1</scene>, <scene name='pdbligand=TM1:2,3-O-[(1R)-2,4,6-TRINITROCYCLOHEXA-2,5-DIENE-1,1-DIYL]ADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>TM1</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PTY:PHOSPHATIDYLETHANOLAMINE'>PTY</scene>, <scene name='pdbligand=TG1: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'>TG1</scene>, <scene name='pdbligand=TM1:2,3-O-[(1R)-2,4,6-TRINITROCYCLOHEXA-2,5-DIENE-1,1-DIYL]ADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>TM1</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2agv|2agv]], [[2dqs|2dqs]], [[2zbd|2zbd]], [[3ar2|3ar2]], [[3ar3|3ar3]], [[3ar4|3ar4]], [[3ar6|3ar6]], [[3ar7|3ar7]], [[3ar8|3ar8]], [[3ar9|3ar9]]</div></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Calcium-transporting_ATPase Calcium-transporting ATPase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.8 3.6.3.8] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ar5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ar5 OCA], [https://pdbe.org/3ar5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ar5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ar5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ar5 ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ar5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ar5 OCA], [https://pdbe.org/3ar5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ar5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ar5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ar5 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/AT2A1_RABIT AT2A1_RABIT]] This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the translocation of calcium from the cytosol to the sarcoplasmic reticulum lumen. Contributes to calcium sequestration involved in muscular excitation/contraction (By similarity).
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[https://www.uniprot.org/uniprot/AT2A1_RABIT AT2A1_RABIT] This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the translocation of calcium from the cytosol to the sarcoplasmic reticulum lumen. Contributes to calcium sequestration involved in muscular excitation/contraction (By similarity).
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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-A 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 approximately 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.
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Trinitrophenyl derivatives bind differently from parent adenine nucleotides to Ca2+-ATPase in the absence of Ca2+,Toyoshima C, Yonekura SI, Tsueda J, Iwasawa S Proc Natl Acad Sci U S A. 2011 Jan 14. PMID:21239683<ref>PMID:21239683</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3ar5" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[ATPase 3D structures|ATPase 3D structures]]
*[[ATPase 3D structures|ATPase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Calcium-transporting ATPase]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Oryctolagus cuniculus]]
[[Category: Oryctolagus cuniculus]]
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[[Category: Iwasawa, S]]
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[[Category: Iwasawa S]]
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[[Category: Toyoshima, C]]
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[[Category: Toyoshima C]]
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[[Category: Tsueda, J]]
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[[Category: Tsueda J]]
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[[Category: Yonekura, S]]
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[[Category: Yonekura S]]
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[[Category: Atp binding]]
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[[Category: Calcium binding]]
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[[Category: Calcium transport]]
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[[Category: Endoplasmic reticulum]]
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[[Category: Hydrolase]]
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[[Category: Hydrolase-hydrolase inhibitor complex]]
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[[Category: P-type atpase]]
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[[Category: Sarcoplasmic reticulum]]
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Revision as of 08:40, 7 February 2024

Calcium pump crystal structure with bound TNP-AMP and TG

PDB ID 3ar5

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