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.


2bl0

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:17, 9 May 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2bl0.gif|left|200px]]
 
-
<!--
+
==Physarum polycephalum myosin II regulatory domain==
-
The line below this paragraph, containing "STRUCTURE_2bl0", creates the "Structure Box" on the page.
+
<StructureSection load='2bl0' size='340' side='right'caption='[[2bl0]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[2bl0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Physarum_polycephalum Physarum polycephalum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BL0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BL0 FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-
{{STRUCTURE_2bl0| PDB=2bl0 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bl0 OCA], [https://pdbe.org/2bl0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bl0 RCSB], [https://www.ebi.ac.uk/pdbsum/2bl0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bl0 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q9BJD3_PHYPO Q9BJD3_PHYPO]
 +
== 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/bl/2bl0_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=2bl0 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
We have previously identified a single inhibitory Ca2+-binding site in the first EF-hand of the essential light chain of Physarum conventional myosin (Farkas, L., Malnasi-Csizmadia, A., Nakamura, A., Kohama, K., and Nyitray, L. (2003) J. Biol. Chem. 278, 27399-27405). As a general rule, conformation of the EF-hand-containing domains in the calmodulin family is "closed" in the absence and "open" in the presence of bound cations; a notable exception is the unusual Ca2+-bound closed domain in the essential light chain of the Ca2+-activated scallop muscle myosin. Here we have reported the 1.8 A resolution structure of the regulatory domain (RD) of Physarum myosin II in which Ca2+ is bound to a canonical EF-hand that is also in a closed state. The 12th position of the EF-hand loop, which normally provides a bidentate ligand for Ca2+ in the open state, is too far in the structure to participate in coordination of the ion. The structure includes a second Ca2+ that only mediates crystal contacts. To reveal the mechanism behind the regulatory effect of Ca2+, we compared conformational flexibilities of the liganded and unliganded RD. Our working hypothesis, i.e. the modulatory effect of Ca2+ on conformational flexibility of RD, is in line with the observed suppression of hydrogen-deuterium exchange rate in the Ca2+-bound form, as well as with results of molecular dynamics calculations. Based on this evidence, we concluded that Ca2+-induced change in structural dynamics of RD is a major factor in Ca2+-mediated regulation of Physarum myosin II activity.
-
'''PHYSARUM POLYCEPHALUM MYOSIN II REGULATORY DOMAIN'''
+
Structural evidence for non-canonical binding of Ca2+ to a canonical EF-hand of a conventional myosin.,Debreczeni JE, Farkas L, Harmat V, Hetenyi C, Hajdu I, Zavodszky P, Kohama K, Nyitray L J Biol Chem. 2005 Dec 16;280(50):41458-64. Epub 2005 Oct 13. PMID:16227209<ref>PMID:16227209</ref>
-
 
+
-
 
+
-
==Overview==
+
-
We have previously identified a single inhibitory Ca2+-binding site in the first EF-hand of the essential light chain of Physarum conventional myosin (Farkas, L., Malnasi-Csizmadia, A., Nakamura, A., Kohama, K., and Nyitray, L. (2003) J. Biol. Chem. 278, 27399-27405). As a general rule, conformation of the EF-hand-containing domains in the calmodulin family is "closed" in the absence and "open" in the presence of bound cations; a notable exception is the unusual Ca2+-bound closed domain in the essential light chain of the Ca2+-activated scallop muscle myosin. Here we have reported the 1.8 A resolution structure of the regulatory domain (RD) of Physarum myosin II in which Ca2+ is bound to a canonical EF-hand that is also in a closed state. The 12th position of the EF-hand loop, which normally provides a bidentate ligand for Ca2+ in the open state, is too far in the structure to participate in coordination of the ion. The structure includes a second Ca2+ that only mediates crystal contacts. To reveal the mechanism behind the regulatory effect of Ca2+, we compared conformational flexibilities of the liganded and unliganded RD. Our working hypothesis, i.e. the modulatory effect of Ca2+ on conformational flexibility of RD, is in line with the observed suppression of hydrogen-deuterium exchange rate in the Ca2+-bound form, as well as with results of molecular dynamics calculations. Based on this evidence, we concluded that Ca2+-induced change in structural dynamics of RD is a major factor in Ca2+-mediated regulation of Physarum myosin II activity.
+
-
==About this Structure==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
2BL0 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Physarum_polycephalum Physarum polycephalum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BL0 OCA].
+
</div>
 +
<div class="pdbe-citations 2bl0" style="background-color:#fffaf0;"></div>
-
==Reference==
+
==See Also==
-
Structural evidence for non-canonical binding of Ca2+ to a canonical EF-hand of a conventional myosin., Debreczeni JE, Farkas L, Harmat V, Hetenyi C, Hajdu I, Zavodszky P, Kohama K, Nyitray L, J Biol Chem. 2005 Dec 16;280(50):41458-64. Epub 2005 Oct 13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16227209 16227209]
+
*[[Myosin 3D Structures|Myosin 3D Structures]]
-
[[Category: Myosin ATPase]]
+
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Physarum polycephalum]]
[[Category: Physarum polycephalum]]
-
[[Category: Protein complex]]
+
[[Category: Debreczeni JE]]
-
[[Category: Debreczeni, J E.]]
+
[[Category: Farkas L]]
-
[[Category: Farkas, L.]]
+
[[Category: Harmat V]]
-
[[Category: Harmat, V.]]
+
[[Category: Nyitray L]]
-
[[Category: Nyitray, L.]]
+
-
[[Category: Ef-hand]]
+
-
[[Category: Muscle protein]]
+
-
[[Category: Myosin]]
+
-
[[Category: Slime mould]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 20:26:10 2008''
+

Current revision

Physarum polycephalum myosin II regulatory domain

PDB ID 2bl0

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools