Cited by 165Cancer-related Molecular PathwaysUbiquitin and proteasome pathwaysDNA Repair Mechanisms

ATM activates p53 by regulating MDM2 oligomerization and E3 processivity

Open access
Cheng, Qian, Chen, Lihong, Li, Zhenyu, Lane, William S, Chen, Jiandong·2009·The EMBO Journal

Abstract

Rapid activation of p53 by ionizing irradiation is a classic DNA damage response mediated by the ATM kinase. However, the major signalling target and mechanism that lead to p53 stabilization are unknown. We show in this report that ATM induces p53 accumulation by phosphorylating the ubiquitin E3 ligase MDM2. Multiple ATM target sites near the MDM2 RING domain function in a redundant manner to provide robust DNA damage signalling. In the absence of DNA damage, the MDM2 RING domain forms oligomers that mediate p53 poly ubiquitination and proteasomal degradation. Phosphorylation by ATM inhibits RING domain oligomerization, specifically suppressing p53 poly ubiquitination. Blocking MDM2 phosphorylation by alanine substitution of all six phosphorylation sites results in constitutive degradation of p53 after DNA damage. These observations show that ATM controls p53 stability by regulating MDM2 RING domain oligomerization and E3 ligase processivity. Promoting or disrupting E3 oligomerization may be a general mechanism by which signalling kinases regulate ubiquitination reactions, and a potential target for therapeutic intervention.

AI snapshot

Written from the paper’s full text.

TL;DR

ATM phosphorylates multiple C-terminal sites on MDM2, inhibiting MDM2 RING-domain oligomerization and thereby blocking p53 polyubiquitination and degradation. This provides a mechanism for rapid p53 stabilization after DNA damage and suggests E3 oligomerization as a regulatory target.

Key findings

  • Mass spectrometry identified six MDM2 phosphorylation sites near the RING domain—S386, S395, S407, T419, S425, and S429—with S386 and S429 induced by IR and other DNA-damaging agents; ATM was required for their phosphorylation, and ATM directly phosphorylated S386/S429 in vitro.
  • Phospho-mimic MDM2 mutants were partially defective in p53 degradation, while MDM2-6A (all six sites mutated to alanine) increased p53 degradation; MDM2-6A blocked p53 accumulation for up to 8 h after IR and impaired p21 induction, but did not affect MDMX degradation.
  • MDM2 phosphorylation specifically reduced p53 polyubiquitination while retaining substantial p53 mono/oligo-ubiquitination; in vitro, MDM2-6D mainly induced p53 mono-ubiquitination, whereas MDM2-6A was more active in p53 polyubiquitination.
  • In nonirradiated cells, about 50% of the MDM2 RING domain migrated as oligomers (~200 kDa) and 50% as monomers (~15 kDa); IR inhibited RING oligomerization, and the ATM inhibitor KU55933 restored it. Non-phosphorylated RING bound MDM2 with much higher affinity than phosphorylated RING.

Methods

  • Cell-based assays used 293T, SJSA, ATM-deficient Hs235, normal human foreskin fibroblast, H1299, and U2OS cells; MDM2 point mutants were generated by site-directed mutagenesis, and U2OS lines stably expressing MDM2 mutants were selected with G418.
  • MDM2 phosphorylation sites were mapped by mass spectrometry after 10 Gy IR and MG132; phospho-specific antibodies, in vitro kinase reactions with FLAG-ATM/Chk1/Chk2, in vivo and in vitro ubiquitination assays, caspase-3 cleavage, and gel filtration chromatography were used.
  • Functional consequences were assessed by western blot, immunoprecipitation, autoradiography, densitometry, 3H-thymidine incorporation after 10 Gy IR, and colony formation after 0–7.5 Gy IR over 15 days.

Limitations

  • The paper does not state limitations.
  • Evident from the text: all experiments are in cultured human cell lines, with no in vivo animal models or primary tumor data.
  • Evident from the text: conclusions rely heavily on overexpression and phospho-mimic/alanine MDM2 mutants, and the proposed conformational/steric mechanism in Figure 9 is a model rather than a direct structural demonstration.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1038/emboj.2009.294

Cites

45 of 45 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 25 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    Alanine substitution of all six MDM2 phosphorylation sites causes constitutive p53 degradation after DNA damage.

    “Blocking MDM2 phosphorylation by alanine substitution of all six phosphorylation sites results in constitutive degradation of p53 after DNA damage.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Alanine substitution at the six MDM2 phosphorylation sites prevents their phosphorylation.
  • Findingown data

    S386E and S429D phospho-mimic mutants were partially defective in p53 degradation.

    “However, S386E and S429D phospho-mimic mutants were partially defective in p53 degradation (Figure 3A).”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Phosphomimic substitutions with aspartate or glutamate at ATM target sites functionally mimic phosphorylation of MDM2.
  • Findingown data

    Mass spectrometry identified novel MDM2 phosphorylation sites near the C-terminal RING domain, including S386, T419, S425, and S429, in addition to S395 and S407.

    “The results showed that in addition to previously reported S395 and S407 sites, several novel modifications sites were identified near the C-terminal RING domain, including S386, T419, S425, and S429 (Figure 1A).”
    Quote in the paperSubstantial claim
  • Findingown data

    The MDM2 phosphorylation mutant blocks p53 stabilization.

    “Inhibition of p53 stabilization by MDM2 phosphorylation mutant.”
    Quote in the paperSubstantial claim
  • Findingown data

    MDM2 mutants affect long-term survival after IR.

    “Regulation of cell cycle and long-term survival after IR by MDM2 mutants.”
    Quote in the paperSubstantial claim
  • May combine two claims. 14
  • Classified as probably not a substantial claim. 10
  • The quote only partly states this claim. 2
  • May combine two claims.

    Findingown data

    MDM2 phosphorylation was induced rapidly after IR before significant p53 accumulation and peaked about 2.5 h in SJSA cells.

    “MDM2 phosphorylation was induced rapidly after IR before significant accumulation of p53, and peaked about 2.5 h in SJSA cells (Figure 2A).”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingnone given

    The MDM2 RING fragment runs on SDS-PAGE at about 30 kDa, which is slower than its calculated 15 kDa.

    “Note that the RING fragment migrates on SDS-PAGE as a B30 kDa band, which is slower than its calculated molecular weight of 15 kDa.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    ATM-specific inhibitor KU55933 or ATM/ATR inhibitor caffeine blocked S386 and S429 phosphorylation after IR.

    “Further, treatment of SJSA cells with ATM-specific inhibitor KU55933 (Figure 2C) or the less specific ATM/ATR inhibitor caffeine (not shown) also blocked phosphorylation of S386 and S429 after IR.”
    Quote in the paperSubstantial claim
  • The quote only partly states this claim.

    Findingown data

    MDM2 phosphorylation site mutations change MDMX degradation.

    “Effects of MDM2 phosphorylation site mutation on p53 and MDMX degradation.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    S386 and S429 are directly phosphorylated by ATM in vitro, while kinase-inactive ATM-KD has no effect.

    “The results showed that both S386 and S429 were phosphorylated by ATM in vitro, and the kinase-inactive ATM-KD had no effect (Figure 2D).”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingcitation

    Chk1 and Chk2 failed to phosphorylate S386 and S429 in vitro, but phosphorylated MDMX S367.

    “Furthermore, Chk1 and Chk2 failed to phosphorylate S386 and S429 in vitro, but phosphorylated the positive control site MDMX S367 (Chen et al, 2005).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Chen et al, 2005 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    ATM phosphorylation inhibits MDM2 RING domain oligomerization and specifically suppresses p53 polyubiquitination.

    “Phosphorylation by ATM inhibits RING domain oligomerization, specifically suppressing p53 poly ubiquitination.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Phosphomimic substitutions with aspartate or glutamate at ATM target sites functionally mimic phosphorylation of MDM2.
    • Rests on an assumption: The MDM2 RING domain oligomers observed in vitro correspond to the functional E3 complex that mediates p53 polyubiquitination in cells.
  • May combine two claims.

    Premisecitation

    ATM activates Chk2, which phosphorylates p53 S20, a residue in the MDM2-binding site.

    “ATM also activates Chk2, which in turn phosphorylates p53 on S20, which is a part of the MDM2-binding site (Shieh et al, 1997(Shieh et al, , 2000;;Banin et al, 1998;Chehab et al, 2000).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Shieh et al, 1997 source

      Not checked in the free run.

    • cites Banin et al, 1998 source

      Not checked in the free run.

    • cites Chehab et al, 2000 source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Premisecitation

    S15 and S20 phosphorylation do not prevent MDM2 binding in vitro.

    “However, biochemical analysis using phosphorylated p53 peptide indicated that S15 and S20 phosphorylation do not prevent MDM2 binding in vitro (Bottger et al, 1999).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Bottger et al, 1999 source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    MDM2 binds p53 and acts as an E3 ligase to promote p53 degradation by the proteasome.

    “P53 turnover is regulated by MDM2, which binds p53 and functions as an ubiquitin E3 ligase to promote p53 degradation by the proteasome (Zhang and Xiong, 2001).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Zhang and Xiong, 2001

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). The quote only partly states this claim.

    Study design and conductown data

    E. coli-produced His6-MDM2 was used to rule out cross-reactivity of the phosphorylation-specific antibodies.

    “His6-MDM2 produced in E. coli was used to rule out cross reactivity.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Interpretationown data

    Without DNA damage, MDM2 RING domains oligomerize, recruit several E2s, and thereby make ubiquitin chain elongation more processive.

    “In the absence of DNA damage, MDM2 RING domain forms oligomers that recruit multiple E2s, increasing the processivity of ubiquitin chain elongation.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: High-order E3 structures help expose multiple E2 active sites to the substrate and speed up the reaction.
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    RING domains commonly form high-order oligomers.

    “Formation of high-order oligomers is a common feature of RING domains (Kentsis et al, 2002;Poyurovsky et al, 2007).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Kentsis et al, 2002 source

      Not checked in the free run.

    • cites Poyurovsky et al, 2007 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    RING fragment complex sizes were assigned by comparing their elution profile with a molecular weight standard run under the same conditions.

    “The sizes of RING fragment complexes were determined by comparing the elution profile to a molecular weight standard fractionated under identical conditions.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Study design and conductown data

    The PS386 and PS429 antibodies did not react with non-phosphorylated His6-MDM2 or with S386A and S429A mutants after IR.

    “The specificity of the antibodies was confirmed by lack of reactivity to non-phosphorylated His6-MDM2 purified from Escherichia coli (Figure 1B) or to transfected MDM2-S386A and S429A mutants after IR (Figure 1C).”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    In the SCFcdc4 E3 ligase, assembly of SCF protomers into dimers is required for adding ubiquitin chains to substrates; when dimerization fails, substrates receive only a single ubiquitin.

    “In the multimeric SCFcdc4 E3 ligase complex, dimer formation by SCF protomers is important for poly ubiquitination of substrates, whereas failure to form E3 dimer results in substrate mono ubiquitination (Tang et al, 2007).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Tang et al, 2007 source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Study design and conductown data

    CIP dephosphorylation was done on immobilized MDM2 before capturing p53.

    “Dephosphorylation by CIP was performed on immobilized MDM2 before p53 capture.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    In cancer, failure of SCF(Fbx4) to dimerize blocks ubiquitination of cyclin D1, leading to cyclin D1 accumulation and transformation.

    “Lack of SCF(Fbx4) dimerization in cancer prevents ubiquitination of its substrate cyclin D1, which contributes to cyclin D1 overexpression and transformation (Barbash et al, 2008).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Barbash et al, 2008 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    GST-MDMX-280-490 served as a positive control for Chk2 phosphorylation of S367.

    “GST-MDMX-280-490 was used as a positive control for Chk2 phosphorylation of S367.”
    Quote in the paperNot a substantial claim
  • Classified as probably not a substantial claim.

    Premisecitation

    MDM2 is phosphorylated by ATM, ATR, and C-Abl on sites near its C terminus.

    “MDM2 is phosphorylated by ATM, ATR, and C-Abl on sites near the C terminus (Maya et al, 2001;Sionov et al, 2001;Shinozaki et al, 2003).”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites Maya et al, 2001 source

      Not checked in the free run.

    • cites Sionov et al, 2001 source

      Not checked in the free run.

    • cites Shinozaki et al, 2003 source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Blocking mouse p53 phosphorylation on S18 and S23 only partially reduced p53 stabilization after DNA damage and caused partial defects in apoptosis and tumour suppression.

    “Studies in mouse models showed that blocking mouse p53 phosphorylation on S18 and S23 (equivalents of human p53 S15 and S20) only partially reduced p53 stabilization after DNA damage, and causes partial defects in apoptosis and tumour suppression functions (Chao et al, 2006).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Chao et al, 2006 source

      Not checked in the free run.

  • May combine two claims.

    Premiseown data

    Caspase 3 cuts MDM2 at one site, residue 361, releasing a C-terminal fragment (362-491) that contains the phosphorylation sites and the RING domain.

    “Caspase 3 cleaves MDM2 at a single site (361) and releases the C-terminal fragment 362-491 containing the phosphorylation sites and RING domain.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Chen et al, 1997 source

      Not checked in the free run.

22 of 22
  • The paper relies on this without support.

    Phosphomimic substitutions with aspartate or glutamate at ATM target sites functionally mimic phosphorylation of MDM2.

    “However, S386E and S429D phospho-mimic mutants were partially defective in p53 degradation (Figure 3A).”
  • The paper relies on this without support.

    Alanine substitution at the six MDM2 phosphorylation sites prevents their phosphorylation.

    “Interestingly, substitution of all six phosphorylation sites with alanine (MDM2-6A) significantly increased p53 degradation (Figure 3B and C).”
  • The paper relies on this without support.

    The MDM2 RING domain oligomers observed in vitro correspond to the functional E3 complex that mediates p53 polyubiquitination in cells.

    “In the absence of DNA damage, the MDM2 RING domain forms oligomers that mediate p53 poly ubiquitination and proteasomal degradation.”
  • The paper relies on this without support.

    High-order E3 structures help expose multiple E2 active sites to the substrate and speed up the reaction.

    “Mechanistically, formation of high-order structures by E3 helps to present multiple E2 active sites to the substrate and increase the reaction rate.”
4 of 4

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Phosphorylation of novel sites adjacent to the Mdm2 RING domain upon irradiation prevents Mdm2 oligomerization.

    “The phosphorylation appears to prevent Mdm2 oligomerization, as the Mdm2 RING domain isolated from irradiated cells is unable to interact with non-phosphorylated Mdm2.”

    From The p53 orchestra: Mdm2 and Mdmx set the tone (2010) · cites this paper as [29]

  • In cell lines expressing non-phosphorylatable Mdm2 mutants, p53 stabilization and activation after damage is markedly attenuated.

    “In cell lines expressing non-phosphorylatable Mdm2 mutants, p53 stabilization and activation after damage is markedly attenuated.”

    From The p53 orchestra: Mdm2 and Mdmx set the tone (2010) · cites this paper as [29]

  • Phosphorylated Mdm2 retains the capacity to bind and degrade Mdmx.

    “Cheng et al. also show that phosphorylated Mdm2 retains the capacity to bind and degrade Mdmx.”

    From The p53 orchestra: Mdm2 and Mdmx set the tone (2010) · cites this paper as [29]

  • Control of Mdm2 oligomerization is important for p53 stabilization following DNA damage.

    “However, Cheng and colleagues recently found that control of Mdm2 oligomerization is important for p53 stabilization following DNA damage [29].”

    From The p53 orchestra: Mdm2 and Mdmx set the tone (2010) · cites this paper as [29]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Figure 5C and Methods give different treatment times and antibodies

    Minor

    For the endogenous MDM2 gel-filtration experiment, the Figure 5C caption says cells were collected 2 h after irradiation and MDM2 was immunoprecipitated with 2A9. The Methods describe 1 h after irradiation and immunoprecipitation with 4B2.

1 of 1

Cites

Flagged first, then by citations

2 of the 47 references couldn’t be matched to a known paper.

Cited by

Sorted by citations

Authors
Cheng, Q., Chen, L., Li, Z., Lane, W. S., & Chen, J.
Affiliations
  • Moffitt Cancer Center (US)
  • Harvard University (US)
Corresponding author
Chen, Jiandong
Venue
The EMBO Journal
Published
2009-10-08
Volume
28
Issue
24
Pages
3857-3867
ISSN
  • 0261-4189 (ISSN-L)
  • 1460-2075
OpenAlex
W2052556036
Cited by
165
References
47
Citations by year
2026: 11 · 2025: 3 · 2024: 4 · 2023: 6 · 2022: 10 · 2021: 7 · 2020: 9 · 2019: 4 · 2018: 6 · 2017: 11 · 2016: 8 · 2015: 14 · 2014: 11 · 2013: 12 · 2012: 23
FWCI
8.15
Type
journal article
Language
en
Open access
Locations
  • The EMBO Journal (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • National Institutes of Health
  • National Cancer Institute (R01CA109636, CA 109636, CA118219)
Topics
  • Health Sciences › Medicine › Oncology › Cancer-related Molecular Pathways
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
Keywords
ATM kinase, p53 stabilization, MDM2, proteasomal degradation, DNA damage response, ionizing radiation, kinase phosphorylation
MeSH terms
Amino Acid Sequence, Cell Line, Chromatography, Gel, DNA Damage, DNA-Binding Proteins, Humans, Molecular Sequence Data, Phosphorylation, Signal Transduction, Tumor Suppressor Protein p53, Protein Serine-Threonine Kinases, Cell Cycle Proteins, Tumor Suppressor Proteins, Ubiquitin, Ubiquitin-Protein Ligases, Cell Line, Tumor, Proteasome Endopeptidase Complex, Proto-Oncogene Proteins c-mdm2, Ataxia Telangiectasia Mutated Proteins

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-08.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-08.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review