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| | ==Crystal Structure of Medicago truncatula Nodulin 13 (MtN13) in complex with trans-zeatin== | | ==Crystal Structure of Medicago truncatula Nodulin 13 (MtN13) in complex with trans-zeatin== |
| - | <StructureSection load='4jhg' size='340' side='right' caption='[[4jhg]], [[Resolution|resolution]] 1.85Å' scene=''> | + | <StructureSection load='4jhg' size='340' side='right'caption='[[4jhg]], [[Resolution|resolution]] 1.85Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4jhg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Barrel_medic Barrel medic]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3rws 3rws]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JHG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JHG FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4jhg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Medicago_truncatula Medicago truncatula]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3rws 3rws]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JHG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JHG 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=ZEA:(2E)-2-METHYL-4-(9H-PURIN-6-YLAMINO)BUT-2-EN-1-OL'>ZEA</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]] 1.85Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4gy9|4gy9]], [[1icx|1icx]], [[2qim|2qim]], [[3us7|3us7]], [[4jhh|4jhh]], [[4jhi|4jhi]]</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=ZEA:(2E)-2-METHYL-4-(9H-PURIN-6-YLAMINO)BUT-2-EN-1-OL'>ZEA</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=4jhg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jhg OCA], [https://pdbe.org/4jhg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jhg RCSB], [https://www.ebi.ac.uk/pdbsum/4jhg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jhg 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=4jhg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jhg OCA], [http://pdbe.org/4jhg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jhg RCSB], [http://www.ebi.ac.uk/pdbsum/4jhg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jhg ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [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. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Barrel medic]] | + | [[Category: Large Structures]] |
| - | [[Category: Brzezinski, K]] | + | [[Category: Medicago truncatula]] |
| - | [[Category: Ciesielska, A]] | + | [[Category: Brzezinski K]] |
| - | [[Category: Dauter, M]] | + | [[Category: Ciesielska A]] |
| - | [[Category: Dauter, Z]] | + | [[Category: Dauter M]] |
| - | [[Category: Jaskolski, M]] | + | [[Category: Dauter Z]] |
| - | [[Category: Ruszkowski, M]] | + | [[Category: Jaskolski M]] |
| - | [[Category: Sikorski, M]] | + | [[Category: Ruszkowski M]] |
| - | [[Category: Tusnio, K]] | + | [[Category: Sikorski M]] |
| - | [[Category: Cytokinin binding]]
| + | [[Category: Tusnio K]] |
| - | [[Category: Legume-bacteria symbiosis]]
| + | |
| - | [[Category: Nitrogen fixation]]
| + | |
| - | [[Category: Nodulation]]
| + | |
| - | [[Category: Nodulin]]
| + | |
| - | [[Category: Plant protein]]
| + | |
| - | [[Category: Pr-10 fold]]
| + | |
| Structural highlights
Function
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.
Publication Abstract from PubMed
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ruszkowski M, Szpotkowski K, Sikorski M, Jaskolski M. The landscape of cytokinin binding by a plant nodulin. Acta Crystallogr D Biol Crystallogr. 2013 Dec;69(Pt 12):2365-80. doi:, 10.1107/S0907444913021975. Epub 2013 Nov 19. PMID:24311578 doi:http://dx.doi.org/10.1107/S0907444913021975
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