6MG3

V285A Mutant of the C-terminal bZIP domain of human C/EBPbeta with 16bp Methylated Oligonucleotide Containing Consensus Recognition Sequence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.5 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
  • Structures With Same Primary Citation

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CCAAT/enhancer-binding protein betaA, B78Homo sapiensMutation(s): 1 
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
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  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
16-bp methylated oligonucleotideC, D16Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.43α = 90
b = 114.042β = 90
c = 75.444γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata reduction
CrysalisProdata 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 

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Derived calculations
  • Version 1.2: 2019-01-16
    Changes: Data collection, Database references
  • Version 1.3: 2019-01-30
    Changes: Data collection, Derived calculations
  • Version 1.4: 2019-08-28
    Changes: Data collection, Database references
  • Version 1.5: 2020-01-01
    Changes: Author supporting evidence