6k4i

From Proteopedia

(Difference between revisions)

Revision as of 10:53, 14 June 2023

The partially disordered conformation of ubiquitin (Q41N variant)

Structural highlights

6k4i is a 1 chain structure with sequence from Homo sapiens. This structure supersedes the now removed PDB entry 6jlt. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UBB_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 PubMed

Nuclear magnetic resonance (NMR) is a powerful tool to study three-dimensional structures as well as protein conformational fluctuations in solution, but it is compromised by increases in peak widths and missing signals. We previously reported that ubiquitin has two folded conformations, N1 and N2 and plus another folded conformation, I, in which some amide group signals of residues 33-41 almost disappeared above 3 kbar at pH 4.5 and 273 K. Thus, well-converged structural models could not be obtained for this region owing to the absence of distance restraints. Here, we reexamine the problem using the ubiquitin Q41N variant as a model for this locally disordered conformation, I. We demonstrate that the variant shows pressure-induced loss of backbone amide group signals at residues 28, 33, 36, and 39-41 like the wild-type, with a similar but smaller effect on CalphaH and CbetaH signals. In order to characterize this I structure, we measured paramagnetic relaxation enhancement (PRE) under high pressure to obtain distance restraints, and calculated the structure assisted by Bayesian inference. We conclude that the more disordered I conformation observed at pH 4.0, 278 K, and 2.5 kbar largely retained the N2 conformation, although the amide groups at residues 33-41 have more heterogeneous conformations and more contact with water, which differ from the N1 and N2 states. The PRE-assisted strategy has the potential to improve structural characterization of proteins that lack NMR signals, especially for relatively more open and hydrated protein conformations.

Paramagnetic relaxation enhancement-assisted structural characterization of a partially disordered conformation of ubiquitin.,Wakamoto T, Ikeya T, Kitazawa S, Baxter NJ, Williamson MP, Kitahara R Protein Sci. 2019 Nov;28(11):1993-2003. doi: 10.1002/pro.3734. PMID:31587403^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Huang F, Kirkpatrick D, Jiang X, Gygi S, Sorkin A. Differential regulation of EGF receptor internalization and degradation by multiubiquitination within the kinase domain. Mol Cell. 2006 Mar 17;21(6):737-48. PMID:16543144 doi:S1097-2765(06)00120-1
↑ Komander D. The emerging complexity of protein ubiquitination. Biochem Soc Trans. 2009 Oct;37(Pt 5):937-53. doi: 10.1042/BST0370937. PMID:19754430 doi:10.1042/BST0370937
↑ Wakamoto T, Ikeya T, Kitazawa S, Baxter NJ, Williamson MP, Kitahara R. Paramagnetic relaxation enhancement-assisted structural characterization of a partially disordered conformation of ubiquitin. Protein Sci. 2019 Nov;28(11):1993-2003. doi: 10.1002/pro.3734. PMID:31587403 doi:http://dx.doi.org/10.1002/pro.3734

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6k4i"

@@ Line 1: / Line 1: @@
 ==The partially disordered conformation of ubiquitin (Q41N variant)==
-<StructureSection load='6k4i' size='340' side='right'caption='[[6k4i]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='6k4i' size='340' side='right'caption='[[6k4i]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6k4i]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6jlt 6jlt]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K4I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K4I FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6k4i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6jlt 6jlt]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K4I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K4I FirstGlance]. <br>
-</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=6k4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4i OCA], [http://pdbe.org/6k4i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k4i RCSB], [http://www.ebi.ac.uk/pdbsum/6k4i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4i ProSAT]</span></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=6k4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4i OCA], [https://pdbe.org/6k4i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k4i RCSB], [https://www.ebi.ac.uk/pdbsum/6k4i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4i ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/UBB_HUMAN UBB_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 ==
@@ Line 15: / Line 17: @@
 </div>
 <div class="pdbe-citations 6k4i" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Baxter, N J]]
+[[Category: Baxter NJ]]
-[[Category: Ikeya, T]]
+[[Category: Ikeya T]]
-[[Category: Kitahara, R]]
+[[Category: Kitahara R]]
-[[Category: Kitazawa, S]]
+[[Category: Kitazawa S]]
-[[Category: Wakamoto, T]]
+[[Category: Wakamoto T]]
-[[Category: Williamson, M P]]
+[[Category: Williamson MP]]
-[[Category: Partially disordered conformation]]
-[[Category: Pressure]]
-[[Category: Structural protein]]

6k4i

From Proteopedia

Revision as of 10:53, 14 June 2023

The partially disordered conformation of ubiquitin (Q41N variant)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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