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| | ==Nodularin from Nodularia spumigena== | | ==Nodularin from Nodularia spumigena== |
| - | <StructureSection load='1ay3' size='340' side='right' caption='[[1ay3]], [[NMR_Ensembles_of_Models | 27 NMR models]]' scene=''> | + | <StructureSection load='1ay3' size='340' side='right'caption='[[1ay3]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1ay3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Nodularia_spumigena Nodularia spumigena]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AY3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AY3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1ay3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Nodularia_spumigena_BY1 Nodularia spumigena BY1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AY3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AY3 FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1ZN:(2S,3S,4E,6E,8S,9S)-3-AMINO-9-METHOXY-2,6,8-TRIMETHYL-10-PHENYLDECA-4,6-DIENOIC+ACID'>1ZN</scene>, <scene name='pdbligand=ACB:3-METHYL-BETA-D-ASPARTIC+ACID'>ACB</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene>, <scene name='pdbligand=MDH:N-METHYLDEHYDROBUTYRINE'>MDH</scene>, <scene name='pdbligand=MFD:(2S,3S,8S,9S)-3-AMINO-9-METHOXY-2,6,8-TRIMETHYL-10-PHENYLDECA-4,6-DIENOIC+ACID'>MFD</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1ay3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ay3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ay3 RCSB], [http://www.ebi.ac.uk/pdbsum/1ay3 PDBsum]</span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACB:3-METHYL-BETA-D-ASPARTIC+ACID'>ACB</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene>, <scene name='pdbligand=MDH:N-METHYLDEHYDROBUTYRINE'>MDH</scene>, <scene name='pdbligand=MFD:(2S,3S,8S,9S)-3-AMINO-9-METHOXY-2,6,8-TRIMETHYL-10-PHENYLDECA-4,6-DIENOIC+ACID'>MFD</scene></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=1ay3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ay3 OCA], [https://pdbe.org/1ay3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ay3 RCSB], [https://www.ebi.ac.uk/pdbsum/1ay3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ay3 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 1ay3" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Nodularia spumigena]] | + | [[Category: Large Structures]] |
| - | [[Category: Annila, A J]] | + | [[Category: Nodularia spumigena BY1]] |
| - | [[Category: Hepatotoxin]] | + | [[Category: Annila AJ]] |
| - | [[Category: Inhibitor of ser/thr-specific protein phosphatase]]
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| - | [[Category: Toxin]]
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| Structural highlights
Publication Abstract from PubMed
The three-dimensional solution structure of nodularin was studied by NMR and molecular dynamics simulations. The conformation in water was determined from the distance and dihedral data by distance geometry and refined by iterative relaxation matrix analysis. The cyclic backbone adopts a well defined conformation but the remote parts of the side chains of arginine as well as the amino acid derivative Adda have a large spatial dispersion. For the unusual amino acids the partial charges were calculated and nodularin was subjected to molecular dynamic simulations in water. A good agreement was found between experimental and computational data with hydrogen bonds, solvent accessibility, molecular motion, and conformational exchange. The three-dimensional structure resembles very closely that of microcystin-LR in the chemically equivalent segment. Therefore, it is expected that the binding of both microcystins and nodularins to serine/threonine-specific protein phosphatases is similar on an atomic level.
Solution structure of nodularin. An inhibitor of serine/threonine-specific protein phosphatases.,Annila A, Lehtimaki J, Mattila K, Eriksson JE, Sivonen K, Rantala TT, Drakenberg T J Biol Chem. 1996 Jul 12;271(28):16695-702. PMID:8663277[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Annila A, Lehtimaki J, Mattila K, Eriksson JE, Sivonen K, Rantala TT, Drakenberg T. Solution structure of nodularin. An inhibitor of serine/threonine-specific protein phosphatases. J Biol Chem. 1996 Jul 12;271(28):16695-702. PMID:8663277
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