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.


2qim

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px <!-- The line below this paragraph, containing "STRUCTURE_2qim", creates the "Structure Box" on the page. You may change the PDB parameter (which sets the PD...)
Current revision (09:16, 21 February 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2qim.jpg|left|200px]]
 
-
<!--
+
==Crystal Structure of Pathogenesis-related Protein LlPR-10.2B from yellow lupine in complex with Cytokinin==
-
The line below this paragraph, containing "STRUCTURE_2qim", creates the "Structure Box" on the page.
+
<StructureSection load='2qim' size='340' side='right'caption='[[2qim]], [[Resolution|resolution]] 1.35&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'>[[2qim]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lupinus_luteus Lupinus luteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QIM 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]] 1.35&#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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZEA:(2E)-2-METHYL-4-(9H-PURIN-6-YLAMINO)BUT-2-EN-1-OL'>ZEA</scene></td></tr>
-
{{STRUCTURE_2qim| PDB=2qim | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2qim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qim OCA], [https://pdbe.org/2qim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qim RCSB], [https://www.ebi.ac.uk/pdbsum/2qim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qim ProSAT]</span></td></tr>
-
 
+
</table>
-
'''Crystal Structure of Pathogenesis-related Protein LlPR-10.2B from yellow lupine in complex with Cytokinin'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/P102B_LUPLU P102B_LUPLU] Class II ribonuclease (RNase) (By similarity). Binds to several cytokinins including natural adenine-type (e.g. trans-zeatin and kinetin) and artificial urea-type (e.g. N,N'-diphenylurea and N-phenyl-N'-(2-chloro-4-pyridyl)urea) hormones (PubMed:18406424, PubMed:19220853, PubMed:29630775). Interacts with melatonin (PubMed:29630775).[UniProtKB:P52779]<ref>PMID:18406424</ref> <ref>PMID:19220853</ref> <ref>PMID:29630775</ref>
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
Plant pathogenesis-related (PR) proteins of class 10 (PR-10) are small and cytosolic. The main feature of their three-dimensional structure is a large cavity between a seven-stranded antiparallel beta-sheet and a long C-terminal alpha-helix. Although PR-10 proteins are abundant in plants, their physiological role remains unknown. Recent data have indicated ligand binding as their possible biological function. The article describes the structure of a complex between a classic PR-10 protein (yellow lupine LlPR-10.2B) and the plant hormone, trans-zeatin. Previously, trans-zeatin binding has been reported in a structurally related cytokinin-specific binding protein, which has a distant sequence relation with classic PR-10 proteins. In the present 1.35 A resolution crystallographic model, three perfectly ordered zeatin molecules are found in the binding cavity of the protein. The fact that three zeatin molecules are bound by the protein when only a fourfold molar excess of the ligand was used indicates an unusual type of affinity for this ligand and suggests that LlPR-10.2B, and perhaps other PR-10 proteins as well, acts as a reservoir of cytokinin molecules in the aqueous environment of the cell.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qi/2qim_consurf.spt"</scriptWhenChecked>
-
2QIM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Lupinus_luteus Lupinus luteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QIM OCA].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
Lupinus luteus pathogenesis-related protein as a reservoir for cytokinin., Fernandes H, Pasternak O, Bujacz G, Bujacz A, Sikorski MM, Jaskolski M, J Mol Biol. 2008 May 16;378(5):1040-51. Epub 2008 Mar 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18406424 18406424]
+
</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=2qim ConSurf].
 +
<div style="clear:both"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Lupinus luteus]]
[[Category: Lupinus luteus]]
-
[[Category: Single protein]]
+
[[Category: Bujacz A]]
-
[[Category: Bujacz, A.]]
+
[[Category: Bujacz G]]
-
[[Category: Bujacz, G.]]
+
[[Category: Fernandes HC]]
-
[[Category: Fernandes, H C.]]
+
[[Category: Jaskolski M]]
-
[[Category: Jaskolski, M.]]
+
[[Category: Pasternak O]]
-
[[Category: Pasternak, O.]]
+
[[Category: Sikorski MM]]
-
[[Category: Sikorski, M M.]]
+
-
[[Category: Allergen]]
+
-
[[Category: Cytokinin]]
+
-
[[Category: Pathogenesis-related protein]]
+
-
[[Category: Plant hormone]]
+
-
[[Category: Plant protein]]
+
-
[[Category: Pr-10 protein]]
+
-
[[Category: Trans-zeatin]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 30 13:17:14 2008''
+

Current revision

Crystal Structure of Pathogenesis-related Protein LlPR-10.2B from yellow lupine in complex with Cytokinin

PDB ID 2qim

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/2qim"
Personal tools