4GAO

DCNL complex with N-terminally acetylated NEDD8 E2 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Conservation of Distinctive N-terminal Acetylation-Dependent Interactions across a Family of Mammalian NEDD8 Ligation Enzymes.

Monda, J.K.Scott, D.C.Miller, D.J.Lydeard, J.King, D.Harper, J.W.Bennett, E.J.Schulman, B.A.

(2013) Structure 21: 42-53

  • DOI: 10.1016/j.str.2012.10.013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Little is known about molecular recognition of acetylated N termini, despite prevalence of this modification among eukaryotic cytosolic proteins. We report that the family of human DCN-like (DCNL) co-E3s, which promote ligation of the ubiquitin-like ...

    Little is known about molecular recognition of acetylated N termini, despite prevalence of this modification among eukaryotic cytosolic proteins. We report that the family of human DCN-like (DCNL) co-E3s, which promote ligation of the ubiquitin-like protein NEDD8 to cullin targets, recognizes acetylated N termini of the E2 enzymes UBC12 and UBE2F. Systematic biochemical and biophysical analyses reveal 40- and 10-fold variations in affinities among different DCNL-cullin and DCNL-E2 complexes, contributing to varying efficiencies of different NEDD8 ligation cascades. Structures of DCNL2 and DCNL3 complexes with N-terminally acetylated peptides from UBC12 and UBE2F illuminate a common mechanism by which DCNL proteins recognize N-terminally acetylated E2s and how selectivity for interactions dependent on N-acetyl-methionine are established through side chains recognizing distal residues. Distinct preferences of UBC12 and UBE2F peptides for inhibiting different DCNLs, including the oncogenic DCNL1 protein, suggest it may be possible to develop small molecules blocking specific N-acetyl-methionine-dependent protein interactions.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DCN1-like protein 2
A, B, D, G
200Homo sapiensMutation(s): 0 
Gene Names: DCUN1D2 (C13orf17, DCUN1L2)
Find proteins for Q6PH85 (Homo sapiens)
Go to Gene View: DCUN1D2
Go to UniProtKB:  Q6PH85
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NEDD8-conjugating enzyme Ubc12
C, E, F, H
12Homo sapiensMutation(s): 0 
Gene Names: UBE2M (UBC12)
EC: 2.3.2.-
Find proteins for P61081 (Homo sapiens)
Go to Gene View: UBE2M
Go to UniProtKB:  P61081
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR

Download SDF File 
Download CCD File 
A, B
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AME
Query on AME
C, E, F, H
NON-POLYMERC7 H13 N O3 S

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.252 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.567α = 90.00
b = 190.151β = 101.75
c = 49.072γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
ADSCdata collection
PHASERphasing
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2012-12-19
    Type: Database references
  • Version 1.2: 2013-01-30
    Type: Database references