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.


4gy9

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:59, 14 March 2024) (edit) (undo)
 
(One intermediate revision not shown.)
Line 1: Line 1:
==Crystal Structure of Medicago truncatula Nodulin 13 (MtN13) in complex with N6-isopentenyladenine (2iP)==
==Crystal Structure of Medicago truncatula Nodulin 13 (MtN13) in complex with N6-isopentenyladenine (2iP)==
-
<StructureSection load='4gy9' size='340' side='right' caption='[[4gy9]], [[Resolution|resolution]] 2.04&Aring;' scene=''>
+
<StructureSection load='4gy9' size='340' side='right'caption='[[4gy9]], [[Resolution|resolution]] 2.04&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4gy9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Barrel_medic Barrel medic]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GY9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GY9 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4gy9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Medicago_truncatula Medicago truncatula]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GY9 FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZIP:N-(3-METHYLBUT-2-EN-1-YL)-9H-PURIN-6-AMINE'>ZIP</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.04&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3rws|3rws]], [[1icx|1icx]], [[1ifv|1ifv]], [[1xdf|1xdf]], [[2flh|2flh]], [[2qim|2qim]], [[3ei5|3ei5]], [[3us7|3us7]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZIP:N-(3-METHYLBUT-2-EN-1-YL)-9H-PURIN-6-AMINE'>ZIP</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MtN13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3880 Barrel medic])</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=4gy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gy9 OCA], [https://pdbe.org/4gy9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gy9 RCSB], [https://www.ebi.ac.uk/pdbsum/4gy9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gy9 ProSAT]</span></td></tr>
-
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4gy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gy9 OCA], [http://pdbe.org/4gy9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gy9 RCSB], [http://www.ebi.ac.uk/pdbsum/4gy9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gy9 ProSAT]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/NOD13_MEDTR NOD13_MEDTR] May be involved in nodule organogenesis rather in the processes related to nitrogen fixation or interactions with the bacteria. May regulate nodulation by controlling the levels of freely available cytokinins.
-
Nodulation is an extraordinary symbiotic interaction between leguminous plants and nitrogen-fixing bacteria (rhizobia) that assimilate atmospheric nitrogen (in root nodules) and convert it into compounds suitable for the plant host. A class of plant hormones called cytokinins are involved in the nodulation process. In the model legume Medicago truncatula, nodulin 13 (MtN13), which belongs to the pathogenesis-related proteins of class 10 (PR-10), is expressed in the outer cortex of the nodules. In general, PR-10 proteins are small and monomeric and have a characteristic fold with an internal hydrophobic cavity formed between a seven-stranded antiparallel beta-sheet and a C-terminal alpha-helix. Previously, some PR-10 proteins not related to nodulation were found to bind cytokinins such as trans-zeatin. Here, four crystal structures of the MtN13 protein are reported in complexes with several cytokinins, namely trans-zeatin, N(6)-isopentenyladenine, kinetin and N(6)-benzyladenine. All four phytohormones are bound in the hydrophobic cavity in the same manner and have excellent definition in the electron-density maps. The binding of the cytokinins appears to be strong and specific and is reinforced by several hydrogen bonds. Although the binding stoichiometry is 1:1, the complex is actually dimeric, with a cytokinin molecule bound in each subunit. The ligand-binding site in each cavity is formed with the participation of a loop element from the other subunit, which plugs the only entrance to the cavity. Interestingly, a homodimer of MtN13 is also formed in solution, as confirmed by small-angle X-ray scattering (SAXS).
+
-
 
+
-
The landscape of cytokinin binding by a plant nodulin.,Ruszkowski M, Szpotkowski K, Sikorski M, Jaskolski M Acta Crystallogr D Biol Crystallogr. 2013 Dec;69(Pt 12):2365-80. doi:, 10.1107/S0907444913021975. Epub 2013 Nov 19. PMID:24311578<ref>PMID:24311578</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 4gy9" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Barrel medic]]
+
[[Category: Large Structures]]
-
[[Category: Jaskolski, M]]
+
[[Category: Medicago truncatula]]
-
[[Category: Ruszkowski, M]]
+
[[Category: Jaskolski M]]
-
[[Category: Sikorski, M]]
+
[[Category: Ruszkowski M]]
-
[[Category: Cytokinin binding]]
+
[[Category: Sikorski M]]
-
[[Category: Legume plant-rhizobium symbiosis]]
+
-
[[Category: Nodulation]]
+
-
[[Category: Nodulin]]
+
-
[[Category: Plant protein]]
+
-
[[Category: Pr-10 fold]]
+

Current revision

Crystal Structure of Medicago truncatula Nodulin 13 (MtN13) in complex with N6-isopentenyladenine (2iP)

PDB ID 4gy9

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/4gy9"
Personal tools