This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2agv

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="2agv" size="450" color="white" frame="true" align="right" spinBox="true" caption="2agv, resolution 2.40&Aring;" /> '''Crystal structure of...)
Current revision (08:17, 25 October 2023) (edit) (undo)
 
(17 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2agv.gif|left|200px]]<br /><applet load="2agv" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2agv, resolution 2.40&Aring;" />
 
-
'''Crystal structure of the SR CA2+-ATPASE with BHQ and TG'''<br />
 
-
==Overview==
+
==Crystal structure of the SR CA2+-ATPASE with BHQ and TG==
-
Ca(2+)-ATPase of sarcoplasmic reticulum is an ATP-powered Ca(2+) pump but, also a H(+) pump in the opposite direction with no demonstrated functional, role. Here, we report a 2.4-A-resolution crystal structure of the, Ca(2+)-ATPase in the absence of Ca(2+) stabilized by two inhibitors, dibutyldihydroxybenzene, which bridges two transmembrane helices, and, thapsigargin, also bound in the membrane region. Now visualized are water, and several phospholipid molecules, one of which occupies a cleft between, two transmembrane helices. Atomic models of the Ca(2+) binding sites with, explicit hydrogens derived by continuum electrostatic calculations show, how water and protons fill the space and compensate charge imbalance, created by Ca(2+)-release. They suggest that H(+) countertransport is a, consequence of a requirement for maintaining structural integrity of the, empty Ca(2+)-binding sites. For this reason, cation countertransport is, probably mandatory for all P-type ATPases and possibly accompanies, transport of water as well.
+
<StructureSection load='2agv' size='340' side='right'caption='[[2agv]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2agv]] is a 2 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=2AGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AGV FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BHQ:2,5-DITERT-BUTYLBENZENE-1,4-DIOL'>BHQ</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></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=2agv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2agv OCA], [https://pdbe.org/2agv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2agv RCSB], [https://www.ebi.ac.uk/pdbsum/2agv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2agv ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[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).
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ag/2agv_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2agv ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Ca(2+)-ATPase of sarcoplasmic reticulum is an ATP-powered Ca(2+) pump but also a H(+) pump in the opposite direction with no demonstrated functional role. Here, we report a 2.4-A-resolution crystal structure of the Ca(2+)-ATPase in the absence of Ca(2+) stabilized by two inhibitors, dibutyldihydroxybenzene, which bridges two transmembrane helices, and thapsigargin, also bound in the membrane region. Now visualized are water and several phospholipid molecules, one of which occupies a cleft between two transmembrane helices. Atomic models of the Ca(2+) binding sites with explicit hydrogens derived by continuum electrostatic calculations show how water and protons fill the space and compensate charge imbalance created by Ca(2+)-release. They suggest that H(+) countertransport is a consequence of a requirement for maintaining structural integrity of the empty Ca(2+)-binding sites. For this reason, cation countertransport is probably mandatory for all P-type ATPases and possibly accompanies transport of water as well.
-
==About this Structure==
+
Structural role of countertransport revealed in Ca(2+) pump crystal structure in the absence of Ca(2+).,Obara K, Miyashita N, Xu C, Toyoshima I, Sugita Y, Inesi G, Toyoshima C Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14489-96. Epub 2005 Sep 6. PMID:16150713<ref>PMID:16150713</ref>
-
2AGV is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus] with NA, TG1, BHQ and PTY as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Calcium-transporting_ATPase Calcium-transporting ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.8 3.6.3.8] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2AGV OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Structural role of countertransport revealed in Ca(2+) pump crystal structure in the absence of Ca(2+)., Obara K, Miyashita N, Xu C, Toyoshima I, Sugita Y, Inesi G, Toyoshima C, Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14489-96. Epub 2005 Sep 6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16150713 16150713]
+
</div>
-
[[Category: Calcium-transporting ATPase]]
+
<div class="pdbe-citations 2agv" style="background-color:#fffaf0;"></div>
-
[[Category: Oryctolagus cuniculus]]
+
-
[[Category: Single protein]]
+
-
[[Category: Norimatsu, Y.]]
+
-
[[Category: Obara, K.]]
+
-
[[Category: Toyoshima, C.]]
+
-
[[Category: BHQ]]
+
-
[[Category: NA]]
+
-
[[Category: PTY]]
+
-
[[Category: TG1]]
+
-
[[Category: had fold]]
+
-
[[Category: membrane protein]]
+
-
[[Category: p-type atpase]]
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 08:06:52 2007''
+
==See Also==
 +
*[[ATPase 3D structures|ATPase 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
 +
[[Category: Oryctolagus cuniculus]]
 +
[[Category: Norimatsu Y]]
 +
[[Category: Obara K]]
 +
[[Category: Toyoshima C]]

Current revision

Crystal structure of the SR CA2+-ATPASE with BHQ and TG

PDB ID 2agv

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2agv"
Personal tools