3GZN

Structure of NEDD8-activating enzyme in complex with NEDD8 and MLN4924


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Substrate-assisted inhibition of ubiquitin-like protein-activating enzymes: the NEDD8 E1 inhibitor MLN4924 forms a NEDD8-AMP mimetic in situ.

Brownell, J.E.Sintchak, M.D.Gavin, J.M.Liao, H.Bruzzese, F.J.Bump, N.J.Soucy, T.A.Milhollen, M.A.Yang, X.Burkhardt, A.L.Ma, J.Loke, H.K.Lingaraj, T.Wu, D.Hamman, K.B.Spelman, J.J.Cullis, C.A.Langston, S.P.Vyskocil, S.Sells, T.B.Mallender, W.D.Visiers, I.Li, P.Claiborne, C.F.Rolfe, M.Bolen, J.B.Dick, L.R.

(2010) Mol Cell 37: 102-111

  • DOI: 10.1016/j.molcel.2009.12.024
  • Primary Citation of Related Structures:  
    3GZN

  • PubMed Abstract: 
  • The NEDD8-activating enzyme (NAE) initiates a protein homeostatic pathway essential for cancer cell growth and survival. MLN4924 is a selective inhibitor of NAE currently in clinical trials for the treatment of cancer. Here, we show that MLN4924 is a ...

    The NEDD8-activating enzyme (NAE) initiates a protein homeostatic pathway essential for cancer cell growth and survival. MLN4924 is a selective inhibitor of NAE currently in clinical trials for the treatment of cancer. Here, we show that MLN4924 is a mechanism-based inhibitor of NAE and creates a covalent NEDD8-MLN4924 adduct catalyzed by the enzyme. The NEDD8-MLN4924 adduct resembles NEDD8 adenylate, the first intermediate in the NAE reaction cycle, but cannot be further utilized in subsequent intraenzyme reactions. The stability of the NEDD8-MLN4924 adduct within the NAE active site blocks enzyme activity, thereby accounting for the potent inhibition of the NEDD8 pathway by MLN4924. Importantly, we have determined that compounds resembling MLN4924 demonstrate the ability to form analogous adducts with other ubiquitin-like proteins (UBLs) catalyzed by their cognate-activating enzymes. These findings reveal insights into the mechanism of E1s and suggest a general strategy for selective inhibition of UBL conjugation pathways.


    Organizational Affiliation

    Discovery, Millennium Pharmaceuticals, Inc., 40 Landsdowne Street, Cambridge, MA 02139, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NEDD8IJ82Homo sapiensMutation(s): 0 
Gene Names: NEDD8
Find proteins for Q15843 (Homo sapiens)
Explore Q15843 
Go to UniProtKB:  Q15843
NIH Common Fund Data Resources
PHAROS  Q15843
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NEDD8-activating enzyme E1 regulatory subunitAC534Homo sapiensMutation(s): 0 
Gene Names: APPBP1HPP1NAE1
Find proteins for Q13564 (Homo sapiens)
Explore Q13564 
Go to UniProtKB:  Q13564
NIH Common Fund Data Resources
PHAROS  Q13564
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NEDD8-activating enzyme E1 catalytic subunitBD463Homo sapiensMutation(s): 0 
Gene Names: UBA3UBE1C
EC: 6.3.2 (PDB Primary Data), 6.2.1 (UniProt)
Find proteins for Q8TBC4 (Homo sapiens)
Explore Q8TBC4 
Go to UniProtKB:  Q8TBC4
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PHAROS  Q8TBC4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B39
Query on B39

Download CCD File 
I, J
[(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-2-hydroxycyclopentyl]methyl sulfamate
C21 H25 N5 O4 S
MPUQHZXIXSTTDU-QXGSTGNESA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B39IC50 :  10   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.03α = 90
b = 228.715β = 90
c = 229.307γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-04-07 
  • Released Date: 2010-02-02 
  • Deposition Author(s): Sintchak, M.D.

Revision History 

  • Version 1.0: 2010-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Database references