3FN1

E2-RING expansion of the NEDD8 cascade confers specificity to cullin modification.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

E2-RING expansion of the NEDD8 cascade confers specificity to cullin modification

Huang, D.T.Ayrault, O.Hunt, H.W.Taherbhoy, A.M.Duda, D.M.Scott, D.C.Borg, L.A.Neale, G.Murray, P.J.Roussel, M.F.Schulman, B.A.

(2009) Mol Cell 33: 483-495

  • DOI: 10.1016/j.molcel.2009.01.011
  • Primary Citation of Related Structures:  
    3FN1

  • PubMed Abstract: 
  • Ubiquitin and ubiquitin-like proteins (UBLs) are directed to targets by cascades of E1, E2, and E3 enzymes. The largest ubiquitin E3 subclass consists of cullin-RING ligases (CRLs), which contain one each of several cullins (CUL1, -2, -3, -4, or -5) and RING proteins (RBX1 or -2) ...

    Ubiquitin and ubiquitin-like proteins (UBLs) are directed to targets by cascades of E1, E2, and E3 enzymes. The largest ubiquitin E3 subclass consists of cullin-RING ligases (CRLs), which contain one each of several cullins (CUL1, -2, -3, -4, or -5) and RING proteins (RBX1 or -2). CRLs are activated by ligation of the UBL NEDD8 to a conserved cullin lysine. How is cullin NEDD8ylation specificity established? Here we report that, like UBE2M (also known as UBC12), the previously uncharacterized E2 UBE2F is a NEDD8-conjugating enzyme in vitro and in vivo. Biochemical and structural analyses indicate how plasticity of hydrophobic E1-E2 interactions and E1 conformational flexibility allow one E1 to charge multiple E2s. The E2s have distinct functions, with UBE2M/RBX1 and UBE2F/RBX2 displaying different target cullin specificities. Together, these studies reveal the molecular basis for and functional importance of hierarchical expansion of the NEDD8 conjugation system in establishing selective CRL activation.


    Organizational Affiliation

    Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NEDD8-activating enzyme E1 catalytic subunitA98Homo sapiensMutation(s): 1 
Gene Names: E1CUBA3UBE1C
EC: 6.3.2 (PDB Primary Data), 6.2.1.64 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TBC4 (Homo sapiens)
Explore Q8TBC4 
Go to UniProtKB:  Q8TBC4
PHAROS:  Q8TBC4
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NEDD8-conjugating enzyme UBE2FB167Homo sapiensMutation(s): 0 
Gene Names: NCE2UBE2F
EC: 6.3.2 (PDB Primary Data), 2.3.2.32 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q969M7 (Homo sapiens)
Explore Q969M7 
Go to UniProtKB:  Q969M7
PHAROS:  Q969M7
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.171α = 90
b = 81.171β = 90
c = 212.755γ = 120
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary