4gy9

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==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)==
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<StructureSection load='4gy9' size='340' side='right' caption='[[4gy9]], [[Resolution|resolution]] 2.04&Aring;' scene=''>
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<StructureSection load='4gy9' size='340' side='right'caption='[[4gy9]], [[Resolution|resolution]] 2.04&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<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>
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<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>
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</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>
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</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>
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<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>
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<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>
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<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>
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<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>
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<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>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[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.
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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).
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 4gy9" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Barrel medic]]
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[[Category: Large Structures]]
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[[Category: Jaskolski, M]]
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[[Category: Medicago truncatula]]
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[[Category: Ruszkowski, M]]
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[[Category: Jaskolski M]]
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[[Category: Sikorski, M]]
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[[Category: Ruszkowski M]]
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[[Category: Cytokinin binding]]
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[[Category: Sikorski M]]
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[[Category: Legume plant-rhizobium symbiosis]]
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[[Category: Nodulation]]
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[[Category: Nodulin]]
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[[Category: Plant protein]]
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[[Category: Pr-10 fold]]
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Current revision

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

PDB ID 4gy9

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