2pyy

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (11:13, 30 August 2023) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2pyy.jpg|left|200px]]
 
-
{{Structure
+
==Crystal Structure of the GluR0 ligand-binding core from Nostoc punctiforme in complex with (L)-glutamate==
-
|PDB= 2pyy |SIZE=350|CAPTION= <scene name='initialview01'>2pyy</scene>, resolution 2.1&Aring;
+
<StructureSection load='2pyy' size='340' side='right'caption='[[2pyy]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-
|SITE= <scene name='pdbsite=AC1:GLU+Binding+Site+For+Residue+A+1620'>AC1</scene>, <scene name='pdbsite=AC2:GLU+Binding+Site+For+Residue+B+2620'>AC2</scene> and <scene name='pdbsite=AC3:GLU+Binding+Site+For+Residue+C+3620'>AC3</scene>
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>
+
<table><tr><td colspan='2'>[[2pyy]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Nostoc_punctiforme_PCC_73102 Nostoc punctiforme PCC 73102]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PYY FirstGlance]. <br>
-
|ACTIVITY=
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyy OCA], [https://pdbe.org/2pyy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pyy RCSB], [https://www.ebi.ac.uk/pdbsum/2pyy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pyy ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyy OCA], [http://www.ebi.ac.uk/pdbsum/2pyy PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2pyy RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/D0VWX9_NOSP7 D0VWX9_NOSP7]
-
 
+
== Evolutionary Conservation ==
-
'''Crystal Structure of the GluR0 ligand-binding core from Nostoc punctiforme in complex with (L)-glutamate'''
+
[[Image:Consurf_key_small.gif|200px|right]]
-
 
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==Overview==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/2pyy_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=2pyy ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
GluR0 from Nostoc punctiforme (NpGluR0) is a bacterial homologue of the ionotropic glutamate receptor (iGluR). We have solved the crystal structure of the ligand-binding core of NpGluR0 in complex with l-glutamate at a resolution of 2.1 A. The structure exhibits a noncanonical ligand interaction and two distinct subunit interfaces. The side-chain guanidium group of Arg80 forms a salt bridge with the gamma-carboxyl group of bound L-glutamate: in GluR0 from Synechocystis (SGluR0) and other iGluRs, the equivalent residues are Asn or Thr, which cannot form a similar interaction. We suggest that the local positively charged environment and the steric constraint created by Arg80 mediate the selectivity of L-glutamate binding by preventing the binding of positively charged and hydrophobic amino acids. In addition, the NpGluR0 ligand-binding core forms a new subunit interface in which the two protomers are arranged differently than the known iGluR and SGluR0 dimer interfaces. The significance of there being two different dimer interfaces was investigated using analytical ultracentrifugation analysis.
GluR0 from Nostoc punctiforme (NpGluR0) is a bacterial homologue of the ionotropic glutamate receptor (iGluR). We have solved the crystal structure of the ligand-binding core of NpGluR0 in complex with l-glutamate at a resolution of 2.1 A. The structure exhibits a noncanonical ligand interaction and two distinct subunit interfaces. The side-chain guanidium group of Arg80 forms a salt bridge with the gamma-carboxyl group of bound L-glutamate: in GluR0 from Synechocystis (SGluR0) and other iGluRs, the equivalent residues are Asn or Thr, which cannot form a similar interaction. We suggest that the local positively charged environment and the steric constraint created by Arg80 mediate the selectivity of L-glutamate binding by preventing the binding of positively charged and hydrophobic amino acids. In addition, the NpGluR0 ligand-binding core forms a new subunit interface in which the two protomers are arranged differently than the known iGluR and SGluR0 dimer interfaces. The significance of there being two different dimer interfaces was investigated using analytical ultracentrifugation analysis.
-
==About this Structure==
+
Crystal structure of the GluR0 ligand-binding core from Nostoc punctiforme in complex with L-glutamate: structural dissection of the ligand interaction and subunit interface.,Lee JH, Kang GB, Lim HH, Jin KS, Kim SH, Ree M, Park CS, Kim SJ, Eom SH J Mol Biol. 2008 Feb 15;376(2):308-16. Epub 2007 Nov 6. PMID:18164033<ref>PMID:18164033</ref>
-
2PYY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Nostoc_punctiforme Nostoc punctiforme]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYY OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Crystal structure of the GluR0 ligand-binding core from Nostoc punctiforme in complex with L-glutamate: structural dissection of the ligand interaction and subunit interface., Lee JH, Kang GB, Lim HH, Jin KS, Kim SH, Ree M, Park CS, Kim SJ, Eom SH, J Mol Biol. 2008 Feb 15;376(2):308-16. Epub 2007 Nov 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18164033 18164033]
+
</div>
-
[[Category: Nostoc punctiforme]]
+
<div class="pdbe-citations 2pyy" style="background-color:#fffaf0;"></div>
-
[[Category: Single protein]]
+
-
[[Category: Eom, S H.]]
+
-
[[Category: Kang, G B.]]
+
-
[[Category: Lee, J H.]]
+
-
[[Category: Lim, H H.]]
+
-
[[Category: Park, C S.]]
+
-
[[Category: Ree, M.]]
+
-
[[Category: glur0 ligand binding domain]]
+
-
[[Category: transport protein]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:42:31 2008''
+
==See Also==
 +
*[[Glutamate receptor 3D structures|Glutamate receptor 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
 +
[[Category: Nostoc punctiforme PCC 73102]]
 +
[[Category: Eom SH]]
 +
[[Category: Kang GB]]
 +
[[Category: Lee JH]]
 +
[[Category: Lim H-H]]
 +
[[Category: Park C-S]]
 +
[[Category: Ree M]]

Current revision

Crystal Structure of the GluR0 ligand-binding core from Nostoc punctiforme in complex with (L)-glutamate

PDB ID 2pyy

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/2pyy"
Personal tools