6MG2

C-terminal bZIP domain of human C/EBPbeta with 16bp Methylated Oligonucleotide Containing Consensus Recognition Sequence-C2221 Crystal Form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for effects of CpA modifications on C/EBP beta binding of DNA.

Yang, J.Horton, J.R.Wang, D.Ren, R.Li, J.Sun, D.Huang, Y.Zhang, X.Blumenthal, R.M.Cheng, X.

(2019) Nucleic Acids Res 47: 1774-1785

  • DOI: 10.1093/nar/gky1264
  • Primary Citation of Related Structures:  
    6MG1, 6MG3, 6MG2

  • PubMed Abstract: 
  • CCAAT/enhancer binding proteins (C/EBPs) regulate gene expression in a variety of cells/tissues/organs, during a range of developmental stages, under both physiological and pathological conditions. C/EBP-related transcription factors have a consensus binding specificity of 5'-TTG-CG-CAA-3', with a central CpG/CpG and two outer CpA/TpG dinucleotides ...

    CCAAT/enhancer binding proteins (C/EBPs) regulate gene expression in a variety of cells/tissues/organs, during a range of developmental stages, under both physiological and pathological conditions. C/EBP-related transcription factors have a consensus binding specificity of 5'-TTG-CG-CAA-3', with a central CpG/CpG and two outer CpA/TpG dinucleotides. Methylation of the CpG and CpA sites generates a DNA element with every pyrimidine having a methyl group in the 5-carbon position (thymine or 5-methylcytosine (5mC)). To understand the effects of both CpG and CpA modification on a centrally-important transcription factor, we show that C/EBPβ binds the methylated 8-bp element with modestly-increased (2.4-fold) binding affinity relative to the unmodified cognate sequence, while cytosine hydroxymethylation (particularly at the CpA sites) substantially decreased binding affinity (36-fold). The structure of C/EBPβ DNA binding domain in complex with methylated DNA revealed that the methyl groups of the 5mCpA/TpG make van der Waals contacts with Val285 in C/EBPβ. Arg289 recognizes the central 5mCpG by forming a methyl-Arg-G triad, and its conformation is constrained by Val285 and the 5mCpG methyl group. We substituted Val285 with Ala (V285A) in an Ala-Val dipeptide, to mimic the conserved Ala-Ala in many members of the basic leucine-zipper family of transcription factors, important in gene regulation, cell proliferation and oncogenesis. The V285A variant demonstrated a 90-fold binding preference for methylated DNA (particularly 5mCpA methylation) over the unmodified sequence. The smaller side chain of Ala285 permits Arg289 to adopt two alternative conformations, to interact in a similar fashion with either the central 5mCpG or the TpG of the opposite strand. Significantly, the best-studied cis-regulatory elements in RNA polymerase II promoters and enhancers have variable sequences corresponding to the central CpG or reduced to a single G:C base pair, but retain a conserved outer CpA sequence. Our analyses suggest an important modification-dependent CpA recognition by basic leucine-zipper transcription factors.


    Organizational Affiliation

    Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CCAAT/enhancer-binding protein beta AB78Homo sapiensMutation(s): 0 
Gene Names: CEBPBTCF5PP9092
Find proteins for P17676 (Homo sapiens)
Explore P17676 
Go to UniProtKB:  P17676
NIH Common Fund Data Resources
PHAROS:  P17676
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    16-bp methylated oligonucleotideC, D16Homo sapiens
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    EDO
    Query on EDO

    Download Ideal Coordinates CCD File 
    A, D
    1,2-ETHANEDIOL
    C2 H6 O2
    LYCAIKOWRPUZTN-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.93 Å
    • R-Value Free: 0.210 
    • R-Value Work: 0.175 
    • R-Value Observed: 0.177 
    • Space Group: C 2 2 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 101.854α = 90
    b = 113.648β = 90
    c = 75.653γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data reduction
    HKL-2000data 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 StatesGM049245-23

    Revision History  (Full details and data files)

    • Version 1.0: 2018-12-12
      Type: Initial release
    • Version 1.1: 2019-01-16
      Changes: Data collection, Database references
    • Version 1.2: 2019-08-28
      Changes: Data collection, Database references
    • Version 1.3: 2020-01-01
      Changes: Author supporting evidence