7OJX

E2 UBE2K covalently linked to donor Ub, acceptor di-Ub, and RING E3 primed for K48-linked Ub chain synthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

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This is version 1.3 of the entry. See complete history


Literature

Structure of UBE2K-Ub/E3/polyUb reveals mechanisms of K48-linked Ub chain extension.

Nakasone, M.A.Majorek, K.A.Gabrielsen, M.Sibbet, G.J.Smith, B.O.Huang, D.T.

(2022) Nat Chem Biol 18: 422-431

  • DOI: 10.1038/s41589-021-00952-x
  • Primary Citation of Related Structures:  
    7OJX

  • PubMed Abstract: 
  • Ubiquitin (Ub) chain types govern distinct biological processes. K48-linked polyUb chains target substrates for proteasomal degradation, but the mechanism of Ub chain synthesis remains elusive due to the transient nature of Ub handover. Here, we present the structure of a chemically trapped complex of the E2 UBE2K covalently linked to donor Ub and acceptor K48-linked di-Ub, primed for K48-linked Ub chain synthesis by a RING E3 ...

    Ubiquitin (Ub) chain types govern distinct biological processes. K48-linked polyUb chains target substrates for proteasomal degradation, but the mechanism of Ub chain synthesis remains elusive due to the transient nature of Ub handover. Here, we present the structure of a chemically trapped complex of the E2 UBE2K covalently linked to donor Ub and acceptor K48-linked di-Ub, primed for K48-linked Ub chain synthesis by a RING E3. The structure reveals the basis for acceptor Ub recognition by UBE2K active site residues and the C-terminal Ub-associated (UBA) domain, to impart K48-linked Ub specificity and catalysis. Furthermore, the structure unveils multiple Ub-binding surfaces on the UBA domain that allow distinct binding modes for K48- and K63-linked Ub chains. This multivalent Ub-binding feature serves to recruit UBE2K to ubiquitinated substrates to overcome weak acceptor Ub affinity and thereby promote chain elongation. These findings elucidate the mechanism of processive K48-linked polyUb chain formation by UBE2K.


    Organizational Affiliation

    Institute of Cancer Sciences, University of Glasgow, Glasgow, UK. d.huang@beatson.gla.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RNF38A79Homo sapiensMutation(s): 0 
Gene Names: RNF38
EC: 2.3.2.27
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PHAROS:  Q9H0F5
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UniProt GroupQ9H0F5
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 KB202Homo sapiensMutation(s): 4 
Gene Names: UBE2KHIP2LIG
EC: 2.3.2.23
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Find proteins for P61086 (Homo sapiens)
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PHAROS:  P61086
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UniProt GroupP61086
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-BC79Homo sapiensMutation(s): 0 
Gene Names: UBB
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Find proteins for P0CG47 (Homo sapiens)
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PHAROS:  P0CG47
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UniProt GroupP0CG47
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-BD76Homo sapiensMutation(s): 1 
Gene Names: UBB
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PHAROS:  P0CG47
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-BE76Homo sapiensMutation(s): 0 
Gene Names: UBB
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Find proteins for P0CG47 (Homo sapiens)
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PHAROS:  P0CG47
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UniProt GroupP0CG47
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ME7
Query on ME7

Download Ideal Coordinates CCD File 
H [auth B]1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione)
C10 H8 N2 O4
PUKLCKVOVCZYKF-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.835α = 90
b = 85.835β = 90
c = 167.354γ = 120
Software Package:
Software NamePurpose
xia2data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union647849
Cancer Research UKUnited KingdomA23278/A29256

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-01-26
    Changes: Database references
  • Version 1.2: 2022-02-23
    Changes: Author supporting evidence
  • Version 1.3: 2022-04-13
    Changes: Database references