2q6a: Difference between revisions

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-[[Image:2q6a.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2q6a", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_2q6a|  PDB=2q6a  |  SCENE=  }}
-'''Crystal Structure of Nak channel D66E mutant'''
+==Crystal Structure of Nak channel D66E mutant==
+<StructureSection load='2q6a' size='340' side='right'caption='[[2q6a]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2q6a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q6A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q6A 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]] 2.6&#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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=2q6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q6a OCA], [https://pdbe.org/2q6a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q6a RCSB], [https://www.ebi.ac.uk/pdbsum/2q6a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q6a ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q81HW2_BACCR Q81HW2_BACCR]
+== 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/q6/2q6a_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=2q6a ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Apparent blockage of monovalent cation currents by the permeating blocker Ca(2+) is a physiologically essential phenomenon relevant to cyclic nucleotide-gated (CNG) channels. The recently determined crystal structure of a bacterial homolog of CNG channel pores, the NaK channel, revealed a Ca(2+) binding site at the extracellular entrance to the selectivity filter. This site is not formed by the side-chain carboxylate groups from the conserved acidic residue, Asp-66 in NaK, conventionally thought to directly chelate Ca(2+) in CNG channels, but rather by the backbone carbonyl groups of residue Gly-67. Here we present a detailed structural analysis of the NaK channel with a focus on Ca(2+) permeability and blockage. Our results confirm that the Asp-66 residue, although not involved in direct chelation of Ca(2+), plays an essential role in external Ca(2+) binding. Furthermore, we give evidence for the presence of a second Ca(2+) binding site within the NaK selectivity filter where monovalent cations also bind, providing a structural basis for Ca(2+) permeation through the NaK pore. Compared with other Ca(2+)-binding proteins, both sites in NaK present a novel mode of Ca(2+) chelation, using only backbone carbonyl oxygen atoms from residues in the selectivity filter. The external site is under indirect control by an acidic residue (Asp-66), making it Ca(2+)-specific. These findings give us a glimpse of the possible underlying mechanisms allowing Ca(2+) to act both as a permeating ion and blocker of CNG channels and raise the possibility of a similar chemistry governing Ca(2+) chelation in Ca(2+) channels.
-==Overview==
+Structural insight into Ca2+ specificity in tetrameric cation channels.,Alam A, Shi N, Jiang Y Proc Natl Acad Sci U S A. 2007 Sep 25;104(39):15334-9. Epub 2007 Sep 18. PMID:17878296<ref>PMID:17878296</ref>
-Apparent blockage of monovalent cation currents by the permeating blocker Ca(2+) is a physiologically essential phenomenon relevant to cyclic nucleotide-gated (CNG) channels. The recently determined crystal structure of a bacterial homolog of CNG channel pores, the NaK channel, revealed a Ca(2+) binding site at the extracellular entrance to the selectivity filter. This site is not formed by the side-chain carboxylate groups from the conserved acidic residue, Asp-66 in NaK, conventionally thought to directly chelate Ca(2+) in CNG channels, but rather by the backbone carbonyl groups of residue Gly-67. Here we present a detailed structural analysis of the NaK channel with a focus on Ca(2+) permeability and blockage. Our results confirm that the Asp-66 residue, although not involved in direct chelation of Ca(2+), plays an essential role in external Ca(2+) binding. Furthermore, we give evidence for the presence of a second Ca(2+) binding site within the NaK selectivity filter where monovalent cations also bind, providing a structural basis for Ca(2+) permeation through the NaK pore. Compared with other Ca(2+)-binding proteins, both sites in NaK present a novel mode of Ca(2+) chelation, using only backbone carbonyl oxygen atoms from residues in the selectivity filter. The external site is under indirect control by an acidic residue (Asp-66), making it Ca(2+)-specific. These findings give us a glimpse of the possible underlying mechanisms allowing Ca(2+) to act both as a permeating ion and blocker of CNG channels and raise the possibility of a similar chemistry governing Ca(2+) chelation in Ca(2+) channels.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Q6A is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q6A OCA].
+</div>
+<div class="pdbe-citations 2q6a" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structural insight into Ca2+ specificity in tetrameric cation channels., Alam A, Shi N, Jiang Y, Proc Natl Acad Sci U S A. 2007 Sep 25;104(39):15334-9. Epub 2007 Sep 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17878296 17878296]
+*[[Potassium channel 3D structures|Potassium channel 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Bacillus cereus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Alam, A.]]
+[[Category: Alam A]]
-[[Category: Jiang, Y.]]
+[[Category: Jiang Y]]
-[[Category: Shi, N.]]
+[[Category: Shi N]]
-[[Category: Central cavity]]
-[[Category: Helix bundle]]
-[[Category: Inverted teepee]]
-[[Category: Ion binding]]
-[[Category: Membrane protein]]
-[[Category: Metal transport]]
-[[Category: Tetramer]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 14:25:38 2008''