5EYO

The crystal structure of the Max bHLH domain in complex with 5-carboxyl cytosine DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

MAX is an epigenetic sensor of 5-carboxylcytosine and is altered in multiple myeloma.

Wang, D.Hashimoto, H.Zhang, X.Barwick, B.G.Lonial, S.Boise, L.H.Vertino, P.M.Cheng, X.

(2017) Nucleic Acids Res 45: 2396-2407

  • DOI: 10.1093/nar/gkw1184
  • Primary Citation of Related Structures:  
    5EYO

  • PubMed Abstract: 
  • The oncogenic transcription factor MYC and its binding partner MAX regulate gene expression by binding to DNA at enhancer-box (E-box) elements 5΄-CACGTG-3΄. In mammalian genomes, the central E-box CpG has the potential to be methylated at the 5-position of cytosine (5mC), or to undergo further oxidation to the 5-hydroxymethyl (5hmC), 5-formyl (5fC), or 5-carboxyl (5caC) forms ...

    The oncogenic transcription factor MYC and its binding partner MAX regulate gene expression by binding to DNA at enhancer-box (E-box) elements 5΄-CACGTG-3΄. In mammalian genomes, the central E-box CpG has the potential to be methylated at the 5-position of cytosine (5mC), or to undergo further oxidation to the 5-hydroxymethyl (5hmC), 5-formyl (5fC), or 5-carboxyl (5caC) forms. We find that MAX exhibits the greatest affinity for a 5caC or unmodified C-containing E-box, and much reduced affinities for the corresponding 5mC, 5hmC or 5fC forms. Crystallization of MAX with a 5caC modified E-box oligonucleotide revealed that MAX Arg36 recognizes 5caC using a 5caC-Arg-Guanine triad, with the next nearest residue to the carboxylate group being Arg60. In an analysis of >800 primary multiple myelomas, MAX alterations occurred at a frequency of ∼3%, more than half of which were single nucleotide substitutions affecting a basic clamp-like interface important for DNA interaction. Among these, arginines 35, 36 and 60 were the most frequently altered. In vitro binding studies showed that whereas mutation of Arg36 (R36W) or Arg35 (R35H/L) completely abolished DNA binding, mutation of Arg60 (R60Q) significantly reduced DNA binding, but retained a preference for the 5caC modified E-box. Interestingly, MAX alterations define a subset of myeloma patients with lower MYC expression and a better overall prognosis. Together these data indicate that MAX can act as a direct epigenetic sensor of E-box cytosine modification states and that local CpG modification and MAX variants converge to modulate the MAX-MYC transcriptional network.


    Organizational Affiliation

    The Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein maxA, C88Homo sapiensMutation(s): 0 
Gene Names: MAXBHLHD4
UniProt & NIH Common Fund Data Resources
Find proteins for P61244 (Homo sapiens)
Explore P61244 
Go to UniProtKB:  P61244
PHAROS:  P61244
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*GP*TP*AP*GP*CP*AP*(1CC)P*GP*TP*GP*CP*TP*AP*CP*T)-3')B, D16synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.39 Å
    • R-Value Free: 0.229 
    • R-Value Work: 0.203 
    • R-Value Observed: 0.204 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 32.75α = 90
    b = 306.16β = 103.79
    c = 49.06γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    XDSdata reduction
    XDSdata scaling
    PHENIXphasing

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM049245

    Revision History  (Full details and data files)

    • Version 1.0: 2016-12-14
      Type: Initial release
    • Version 1.1: 2017-05-03
      Changes: Database references
    • Version 1.2: 2017-09-13
      Changes: Author supporting evidence
    • Version 1.3: 2019-12-25
      Changes: Author supporting evidence