1NWQ

CRYSTAL STRUCTURE OF C/EBPALPHA-DNA COMPLEX

Summary for 1NWQ

• Entry DOI: 10.2210/pdb1nwq/pdb
• Related: 1DH3
• Descriptor: 5'-D(*TP*TP*CP*CP*TP*AP*TP*TP*GP*CP*GP*CP*AP*AP*TP*CP*CP*AP*GP*TP*T)-3', 5'-D(*AP*AP*AP*CP*TP*GP*GP*AP*TP*TP*GP*CP*GP*CP*AP*AP*TP*AP*GP*GP*A)-3', CCAAT/enhancer binding protein alpha, ... (4 entities in total)
• Functional Keywords: basic leucine zipper, protein-dna complex, transcription-dna complex, transcription/dna
• Biological source: Rattus norvegicus (Norway rat)
• Cellular location: Nucleus: P05554
• Total number of polymer chains: 4
• Total formula weight: 27740.96

Authors

Miller, M.,Shuman, J.D.,Sebastian, T.,Dauter, Z.,Johnson, P.F. (deposition date: 2003-02-06, release date: 2003-05-13, Last modification date: 2023-08-16)

Primary citation

Miller, M.,Shuman, J.D.,Sebastian, T.,Dauter, Z.,Johnson, P.F.
Structural Basis for DNA Recognition by the Basic Region Leucine Zipper Transcription Factor CCAAT/enhancer Binding Protein Alpha
J.Biol.Chem., 278:15178-15184, 2003

PubMed Abstract: CCAAT/enhancer-binding proteins (C/EBPs) are basic region leucine zipper (bZIP) transcription factors that regulate cell differentiation, growth, survival, and inflammation. To understand the molecular basis of DNA recognition by the C/EBP family we determined the x-ray structure of a C/EBPalpha bZIP polypeptide bound to its cognate DNA site (A(-5)T(-4)T(-3)G(-2)C(-1)G(1)C(2)A(3)A(4)T(5)) and characterized several basic region mutants. Binding specificity is provided by interactions of basic region residues Arg(289), Asn(292), Ala(295), Val(296), Ser(299), and Arg(300) with DNA bases. A striking feature of the C/EBPalpha protein-DNA interface that distinguishes it from known bZIP-DNA complexes is the central role of Arg(289), which is hydrogen-bonded to base A(3), phosphate, Asn(292) (invariant in bZIPs), and Asn(293). The conformation of Arg(289) is also restricted by Tyr(285). In accordance with the structural model, mutation of Arg(289) or a pair of its interacting partners (Tyr(285) and Asn(293)) abolished C/EBPalpha binding activity. Val(296) (Ala in most other bZIPs) contributes to C/EBPalpha specificity by discriminating against purines at position -3 and imposing steric restraints on the invariant Arg(300). Mutating Val(296) to Ala strongly enhanced C/EBPalpha binding to cAMP response element (CRE) sites while retaining affinity for C/EBP sites. Thus, Arg(289) is essential for formation of the complementary protein-DNA interface, whereas Val(296) functions primarily to restrict interactions with related sequences such as CRE sites rather than specifying binding to C/EBP sites. Our studies also help to explain the phenotypes of mice carrying targeted mutations in the C/EBPalpha bZIP region.

PubMed: 12578822
DOI: 10.1074/jbc.M300417200

Experimental method

X-RAY DIFFRACTION (2.8 Å)