2ld9
From Proteopedia
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==Backbone Structure of Ubiquitin determined using Backbone amide NOEs and Backbone N-H and N-C RDCs== | ==Backbone Structure of Ubiquitin determined using Backbone amide NOEs and Backbone N-H and N-C RDCs== | ||
| - | <StructureSection load='2ld9' size='340' side='right'caption='[[2ld9 | + | <StructureSection load='2ld9' size='340' side='right'caption='[[2ld9]]' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[2ld9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/ | + | <table><tr><td colspan='2'>[[2ld9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LD9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LD9 FirstGlance]. <br> |
| - | </td></tr> | + | </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=2ld9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ld9 OCA], [https://pdbe.org/2ld9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ld9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ld9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ld9 ProSAT]</span></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=2ld9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ld9 OCA], [https://pdbe.org/2ld9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ld9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ld9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ld9 ProSAT]</span></td></tr> | + | |
</table> | </table> | ||
== Function == | == Function == | ||
| - | + | [https://www.uniprot.org/uniprot/UBC_HUMAN UBC_HUMAN] 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.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref> | |
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Development of efficient strategies and automation represent important milestones of progress in rapid structure determination efforts in proteomics research. In this context, we present here an efficient algorithm named as AUTOBA (Automatic Backbone Assignment) designed to automate the assignment protocol based on HN(C)N suite of experiments. Depending upon the spectral dispersion, the user can record 2D or 3D versions of the experiments for assignment. The algorithm uses as inputs: (i) protein primary sequence and (ii) peak-lists from user defined HN(C)N suite of experiments. In the end, one gets H(N), (15)N, C(alpha) and C' assignments (in common BMRB format) for the individual residues along the polypeptide chain. The success of the algorithm has been demonstrated, not only with experimental spectra recorded on two small globular proteins: ubiquitin (76 aa) and M-crystallin (85 aa), but also with simulated spectra of 27 other proteins using assignment data from the BMRB. | ||
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| + | AUTOBA: automation of backbone assignment from HN(C)N suite of experiments.,Borkar A, Kumar D, Hosur RV J Biomol NMR. 2011 Jul;50(3):285-97. doi: 10.1007/s10858-011-9518-0. Epub 2011 , May 29. PMID:21626212<ref>PMID:21626212</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 2ld9" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Homo sapiens]] |
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Hosur | + | [[Category: Hosur R]] |
| - | [[Category: Kumar | + | [[Category: Kumar D]] |
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Revision as of 10:53, 15 February 2023
Backbone Structure of Ubiquitin determined using Backbone amide NOEs and Backbone N-H and N-C RDCs
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