6SQR

Crystal structure of Cat MDM2-S429E RING domain bound to UbcH5B-Ub

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural basis for DNA damage-induced phosphoregulation of MDM2 RING domain.

Magnussen, H.M., Ahmed, S.F., Sibbet, G.J., Hristova, V.A., Nomura, K., Hock, A.K., Archibald, L.J., Jamieson, A.G., Fushman, D., Vousden, K.H., Weissman, A.M., Huang, D.T.

(2020) Nat Commun 11: 2094-2094

  • DOI: 10.1038/s41467-020-15783-y
  • Primary Citation of Related Structures:  
    6SQO, 6SQP, 6SQR, 6SQS

  • PubMed Abstract: 

    • Phosphorylation of MDM2 by ATM upon DNA damage is an important mechanism for deregulating MDM2, thereby leading to p53 activation. ATM phosphorylates multiple residues near the RING domain of MDM2, but the underlying molecular basis for deregulation remains elusive ...

    Phosphorylation of MDM2 by ATM upon DNA damage is an important mechanism for deregulating MDM2, thereby leading to p53 activation. ATM phosphorylates multiple residues near the RING domain of MDM2, but the underlying molecular basis for deregulation remains elusive. Here we show that Ser429 phosphorylation selectively enhances the ubiquitin ligase activity of MDM2 homodimer but not MDM2-MDMX heterodimer. A crystal structure of phospho-Ser429 (pS429)-MDM2 bound to E2-ubiquitin reveals a unique 3 10 -helical feature present in MDM2 homodimer that allows pS429 to stabilize the closed E2-ubiquitin conformation and thereby enhancing ubiquitin transfer. In cells Ser429 phosphorylation increases MDM2 autoubiquitination and degradation upon DNA damage, whereas S429A substitution protects MDM2 from auto-degradation. Our results demonstrate that Ser429 phosphorylation serves as a switch to boost the activity of MDM2 homodimer and promote its self-destruction to enable rapid p53 stabilization and resolve a long-standing controversy surrounding MDM2 auto-degradation in response to DNA damage.

    Organizational Affiliation: 

    Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK. d.huang@beatson.gla.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2A69Felis catusMutation(s): 2 
Gene Names: MDM2
EC: 2.3.2.27
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D2B, E, H, K146Homo sapiensMutation(s): 2 
Gene Names: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B
EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P62837 (Homo sapiens)
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PHAROS:  P62837
GTEx:  ENSG00000131508
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aC, F, L77Homo sapiensMutation(s): 0 
Gene Names: RPS27A, UBA80, UBCEP1
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PHAROS:  P62979
GTEx:  ENSG00000143947
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2D, J64Felis catusMutation(s): 2 
Gene Names: MDM2
EC: 2.3.2.27
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2G63Felis catusMutation(s): 2 
Gene Names: MDM2
EC: 2.3.2.27
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-CI76Homo sapiensMutation(s): 0 
Gene Names: UBC
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
EA [auth J], FA [auth J], N [auth A], O [auth A], T [auth D], U [auth D], X [auth G], Y [auth G]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AA [auth I] , CA [auth J] , DA [auth J] , GA [auth K] , HA [auth K] , IA [auth K] , M [auth A] , P [auth B] , 
AA [auth I], CA [auth J], DA [auth J], GA [auth K], HA [auth K], IA [auth K], M [auth A], P [auth B], Q [auth D], R [auth D], V [auth G], W [auth G]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
NO3
Query on NO3
Download Ideal Coordinates CCD File 
BA [auth I], S [auth D], Z [auth H]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.51α = 90
b = 163.88β = 96.03
c = 70.6γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomA23278
European Research CouncilBelgium647849

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Database references