2k39
From Proteopedia
(Difference between revisions)
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==Recognition dynamics up to microseconds revealed from RDC derived ubiquitin ensemble in solution== | ==Recognition dynamics up to microseconds revealed from RDC derived ubiquitin ensemble in solution== | ||
| - | <StructureSection load='2k39' size='340' side='right'caption='[[2k39 | + | <StructureSection load='2k39' size='340' side='right'caption='[[2k39]]' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[2k39]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/ | + | <table><tr><td colspan='2'>[[2k39]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K39 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K39 FirstGlance]. <br> |
| - | </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=2k39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k39 OCA], [https://pdbe.org/2k39 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k39 RCSB], [https://www.ebi.ac.uk/pdbsum/2k39 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k39 ProSAT]</span></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'>[https://proteopedia.org/fgij/fg.htm?mol=2k39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k39 OCA], [https://pdbe.org/2k39 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k39 RCSB], [https://www.ebi.ac.uk/pdbsum/2k39 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k39 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
| - | + | [https://www.uniprot.org/uniprot/UBIQP_XENLA UBIQP_XENLA] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity). | |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</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=2k39 ConSurf]. | </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=2k39 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | Protein dynamics are essential for protein function, and yet it has been challenging to access the underlying atomic motions in solution on nanosecond-to-microsecond time scales. We present a structural ensemble of ubiquitin, refined against residual dipolar couplings (RDCs), comprising solution dynamics up to microseconds. The ensemble covers the complete structural heterogeneity observed in 46 ubiquitin crystal structures, most of which are complexes with other proteins. Conformational selection, rather than induced-fit motion, thus suffices to explain the molecular recognition dynamics of ubiquitin. Marked correlations are seen between the flexibility of the ensemble and contacts formed in ubiquitin complexes. A large part of the solution dynamics is concentrated in one concerted mode, which accounts for most of ubiquitin's molecular recognition heterogeneity and ensures a low entropic complex formation cost. | ||
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| - | Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution.,Lange OF, Lakomek NA, Fares C, Schroder GF, Walter KF, Becker S, Meiler J, Grubmuller H, Griesinger C, de Groot BL Science. 2008 Jun 13;320(5882):1471-5. PMID:18556554<ref>PMID:18556554</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 2k39" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[3D structures of ubiquitin|3D structures of ubiquitin]] | *[[3D structures of ubiquitin|3D structures of ubiquitin]] | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: African clawed frog]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: | + | [[Category: Xenopus laevis]] |
| - | [[Category: | + | [[Category: Becker S]] |
| - | [[Category: | + | [[Category: Fares C]] |
| - | [[Category: | + | [[Category: Griesinger C]] |
| - | [[Category: Grubmuller | + | [[Category: Grubmuller H]] |
| - | [[Category: Lakomek | + | [[Category: Lakomek NA]] |
| - | [[Category: Lange | + | [[Category: Lange OF]] |
| - | [[Category: Meiler | + | [[Category: Meiler J]] |
| - | [[Category: Schroder | + | [[Category: Schroder G]] |
| - | [[Category: Walter | + | [[Category: Walter K]] |
| - | [[Category: | + | [[Category: De Groot BL]] |
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Current revision
Recognition dynamics up to microseconds revealed from RDC derived ubiquitin ensemble in solution
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Categories: Large Structures | Xenopus laevis | Becker S | Fares C | Griesinger C | Grubmuller H | Lakomek NA | Lange OF | Meiler J | Schroder G | Walter K | De Groot BL
