5zq3

From Proteopedia

(Difference between revisions)

Revision as of 21:23, 28 October 2020

PDE-Ubiquitin

Structural highlights

5zq3 is a 4 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[1] ^[2]

Publication Abstract from PubMed

Ubiquitination constitutes one of the most important signaling mechanisms in eukaryotes. Conventional ubiquitination is catalyzed by the universally conserved E1-E2-E3 three-enzyme cascade in an ATP-dependent manner. The newly identified SidE family effectors of the pathogen Legionella pneumophila ubiquitinate several human proteins by a different mechanism without engaging any of the conventional ubiquitination machinery. We now report the crystal structures of SidE alone and in complex with ubiquitin, NAD, and ADP-ribose, thereby capturing different conformations of SidE before and after ubiquitin and ligand binding. The structures of ubiquitin bound to both mART and PDE domains reveal several unique features of the two reaction steps catalyzed by SidE. Further, the structural and biochemical results demonstrate that SidE family members do not recognize specific structural folds of the substrate proteins. Our studies provide both structural explanations for the functional observations and new insights into the molecular mechanisms of this non-canonical ubiquitination machinery.

Structural Insights into Non-canonical Ubiquitination Catalyzed by SidE.,Wang Y, Shi M, Feng H, Zhu Y, Liu S, Gao A, Gao P Cell. 2018 May 17;173(5):1231-1243.e16. doi: 10.1016/j.cell.2018.04.023. Epub, 2018 May 3. PMID:29731171^[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
↑ Wang Y, Shi M, Feng H, Zhu Y, Liu S, Gao A, Gao P. Structural Insights into Non-canonical Ubiquitination Catalyzed by SidE. Cell. 2018 May 17;173(5):1231-1243.e16. doi: 10.1016/j.cell.2018.04.023. Epub, 2018 May 3. PMID:29731171 doi:http://dx.doi.org/10.1016/j.cell.2018.04.023

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5zq3"

@@ Line 1: / Line 1: @@
 ==PDE-Ubiquitin==
-<StructureSection load='5zq3' size='340' side='right' caption='[[5zq3]], [[Resolution|resolution]] 2.18&Aring;' scene=''>
+<StructureSection load='5zq3' size='340' side='right'caption='[[5zq3]], [[Resolution|resolution]] 2.18&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5zq3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZQ3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5zq3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQ3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZQ3 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=5zq3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zq3 OCA], [http://pdbe.org/5zq3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zq3 RCSB], [http://www.ebi.ac.uk/pdbsum/5zq3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zq3 ProSAT]</span></td></tr>
+</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5zq3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zq3 OCA], [http://pdbe.org/5zq3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zq3 RCSB], [http://www.ebi.ac.uk/pdbsum/5zq3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zq3 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 21: / Line 21: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Gao, A]]
 [[Category: Gao, P]]

5zq3

From Proteopedia

Revision as of 21:23, 28 October 2020

PDE-Ubiquitin

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox