3u30: Difference between revisions
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==Crystal structure of a linear-specific Ubiquitin fab bound to linear ubiquitin== | ==Crystal structure of a linear-specific Ubiquitin fab bound to linear ubiquitin== | ||
<StructureSection load='3u30' size='340' side='right' caption='[[3u30]], [[Resolution|resolution]] 2.43Å' scene=''> | <StructureSection load='3u30' size='340' side='right'caption='[[3u30]], [[Resolution|resolution]] 2.43Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3u30]] is a 6 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3u30]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U30 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U30 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.428Å</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=3u30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u30 OCA], [https://pdbe.org/3u30 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u30 RCSB], [https://www.ebi.ac.uk/pdbsum/3u30 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u30 ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</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;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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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 3u30" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[ | *[[3D structures of ubiquitin|3D structures of ubiquitin]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
[[Category: Dixit | [[Category: Large Structures]] | ||
[[Category: Dong | [[Category: Dixit VM]] | ||
[[Category: Gao | [[Category: Dong KC]] | ||
[[Category: Hannoush | [[Category: Gao X]] | ||
[[Category: Hymowitz | [[Category: Hannoush RN]] | ||
[[Category: Kelley | [[Category: Hymowitz SG]] | ||
[[Category: Kirkpatrick | [[Category: Kelley RF]] | ||
[[Category: Matsumoto | [[Category: Kirkpatrick DS]] | ||
[[Category: Phu | [[Category: Matsumoto ML]] | ||
[[Category: Yu | [[Category: Phu L]] | ||
[[Category: Yu C]] | |||
Latest revision as of 13:30, 6 November 2024
Crystal structure of a linear-specific Ubiquitin fab bound to linear ubiquitinCrystal structure of a linear-specific Ubiquitin fab bound to linear ubiquitin
Structural highlights
FunctionUBC_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.[1] [2] Publication Abstract from PubMedPolyubiquitination is an essential posttranslational modification that plays critical roles in cellular signaling. PolyUb (polyubiquitin) chains are formed by linking the carboxyl-terminus of one Ub (ubiquitin) subunit to either a lysine residue or the amino-terminus of an adjacent Ub. Linkage through the amino-terminus results in linear polyubiquitination that has recently been demonstrated to be a key step in nuclear factor kappaB activation; however, tools to study linear chains have been lacking. We therefore engineered a linear-linkage-specific antibody that is functional in Western blot, immunoprecipitation, and immunofluorescence applications. A crystal structure of the linear-linkage-specific antibody Fab fragment in complex with linear diubiquitin provides molecular insight into the nature of linear chain specificity. We use the antibody to demonstrate that linear polyUb is up-regulated upon tumor necrosis factor alpha stimulation of cells, consistent with a critical role in nuclear factor kappaB signaling. This antibody provides an essential tool for further investigation of the function of linear chains. Engineering and structural characterization of a linear polyubiquitin-specific antibody.,Matsumoto ML, Dong KC, Yu C, Phu L, Gao X, Hannoush RN, Hymowitz SG, Kirkpatrick DS, Dixit VM, Kelley RF J Mol Biol. 2012 May 4;418(3-4):134-44. doi: 10.1016/j.jmb.2011.12.053. Epub 2011, Dec 29. PMID:22227388[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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