5OS9

Structure of the B3 DNA-Binding Domain of NGA1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

DNA recognition by Arabidopsis transcription factors ABI3 and NGA1.

Sasnauskas, G.Manakova, E.Lapenas, K.Kauneckaite, K.Siksnys, V.

(2018) FEBS J. 285: 4041-4059

  • DOI: 10.1111/febs.14649

  • PubMed Abstract: 
  • B3 transcription factors constitute a large plant-specific protein superfamily, which plays a central role in plant life. Family members are characterized by the presence of B3 DNA-binding domains (DBDs). To date, only a few B3 DBDs were structurally ...

    B3 transcription factors constitute a large plant-specific protein superfamily, which plays a central role in plant life. Family members are characterized by the presence of B3 DNA-binding domains (DBDs). To date, only a few B3 DBDs were structurally characterized; therefore, the DNA recognition mechanism of other family members remains to be elucidated. Here, we analyze DNA recognition mechanism of two structurally uncharacterized B3 transcription factors, ABI3 and NGA1. Guided by the structure of the DNA-bound B3 domain of Arabidopsis transcriptional repressor VAL1, we have performed mutational analysis of the ABI3 B3 domain. We demonstrate that both VAL1-B3 and ABI3-B3 recognize the Sph/RY DNA sequence 5'-TGCATG-3' via a conserved set of base-specific contacts. We have also solved a 1.8 Å apo-structure of NGA1-B3, DBD of Arabidopsis transcription factor NGA1. We show that NGA1-B3, like the structurally related RAV1-B3 domain, is specific for the 5'-CACCTG-3' DNA sequence, albeit tolerates single base pair substitutions at the 5'-terminal half of the recognition site. Employing distance-dependent fluorophore quenching, we show that NGA1-B3 binds the asymmetric recognition site in a defined orientation, with the 'N-arm' and 'C-arm' structural elements interacting with the 5'- and 3'-terminal nucleotides of the 5'-CACCTG-3' sequence, respectively. Mutational analysis guided by the model of DNA-bound NGA1-B3 helped us identify NGA1-B3 residues involved in base-specific and DNA backbone contacts, providing new insights into the mechanism of DNA recognition by plant B3 domains of RAV and REM families.


    Organizational Affiliation

    Institute of Biotechnology, Vilnius University, Lithuania.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
B3 domain-containing transcription factor NGA1
A, B
124Arabidopsis thalianaMutation(s): 0 
Gene Names: NGA1
Find proteins for O82799 (Arabidopsis thaliana)
Go to UniProtKB:  O82799
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A, B
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 30.758α = 90.00
b = 151.179β = 90.00
c = 47.513γ = 90.00
Software Package:
Software NamePurpose
MoRDaphasing
XDSdata reduction
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Council of LithuaniaLithuaniaMIP-106/2015

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2018-09-19
    Type: Data collection, Database references
  • Version 1.2: 2018-11-14
    Type: Data collection, Database references