5V86

Structure of DCN1 bound to NAcM-OPT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.374 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Blocking an N-terminal acetylation-dependent protein interaction inhibits an E3 ligase.

Scott, D.C.Hammill, J.T.Min, J.Rhee, D.Y.Connelly, M.Sviderskiy, V.O.Bhasin, D.Chen, Y.Ong, S.S.Chai, S.C.Goktug, A.N.Huang, G.Monda, J.K.Low, J.Kim, H.S.Paulo, J.A.Cannon, J.R.Shelat, A.A.Chen, T.Kelsall, I.R.Alpi, A.F.Pagala, V.Wang, X.Peng, J.Singh, B.Harper, J.W.Schulman, B.A.Guy, R.K.

(2017) Nat. Chem. Biol. 13: 850-857

  • DOI: 10.1038/nchembio.2386
  • Primary Citation of Related Structures:  5V83, 5V88, 5V89

  • PubMed Abstract: 
  • N-terminal acetylation is an abundant modification influencing protein functions. Because ∼80% of mammalian cytosolic proteins are N-terminally acetylated, this modification is potentially an untapped target for chemical control of their functions. S ...

    N-terminal acetylation is an abundant modification influencing protein functions. Because ∼80% of mammalian cytosolic proteins are N-terminally acetylated, this modification is potentially an untapped target for chemical control of their functions. Structural studies have revealed that, like lysine acetylation, N-terminal acetylation converts a positively charged amine into a hydrophobic handle that mediates protein interactions; hence, this modification may be a druggable target. We report the development of chemical probes targeting the N-terminal acetylation-dependent interaction between an E2 conjugating enzyme (UBE2M or UBC12) and DCN1 (DCUN1D1), a subunit of a multiprotein E3 ligase for the ubiquitin-like protein NEDD8. The inhibitors are highly selective with respect to other protein acetyl-amide-binding sites, inhibit NEDD8 ligation in vitro and in cells, and suppress anchorage-independent growth of a cell line with DCN1 amplification. Overall, our data demonstrate that N-terminal acetyl-dependent protein interactions are druggable targets and provide insights into targeting multiprotein E2-E3 ligases.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme,DCN1-like protein 1
A
384Enterobacteria phage T4Homo sapiens
This entity is chimeric
Gene Names: E, DCUN1D1 (DCUN1L1, RP42, SCCRO)
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Find proteins for Q96GG9 (Homo sapiens)
Go to Gene View: DCUN1D1
Go to UniProtKB:  Q96GG9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8ZA
Query on 8ZA

Download SDF File 
Download CCD File 
A
N-benzyl-N-(1-butylpiperidin-4-yl)-N'-(3,4-dichlorophenyl)urea
C23 H29 Cl2 N3 O
VPHJABWIKCBGMC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.374 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.155 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 35.045α = 90.00
b = 96.849β = 105.83
c = 59.302γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
HKL-2000data collection
PHENIXrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR37GM069530

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-06-21
    Type: Database references, Refinement description
  • Version 1.2: 2017-09-06
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence