SNAP output for PDB entry 1qn9 [SNAP web server]

PDB-id

1qn9; SNAP-derived features in text and JSON formats; DNAproDB

Class

tata box-binding protein (tbp)

Method

X-ray (1.9 Å)

Summary

Crystal structure of the c(-29) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.

Reference

Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999): "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.

Abstract

Cocrystal structures of wild-type TATA box-binding protein (TBP) recognizing 10 naturally occurring TATA elements have been determined at 2.3-1.8 A resolution, and compared with our 1.9 A resolution structure of TBP bound to the Adenovirus major late promoter (AdMLP) TATA box (5'-TATAAAAG-3'). Minor-groove recognition by the saddle-shaped protein induces the same conformational change in each of these oligonucleotides, despite variations in promoter sequence that reduce the efficiency of transcription initiation. Three molecular mechanisms explain assembly of diverse TBP-TATA element complexes. (1) T --> A and A --> T transversions leave the minor-groove face unchanged, permitting formation of TBP-DNA complexes on many A/T-rich core promoter sequences. (2) Cavities in the interface between TBP and the minor-groove face of the AdMLP TATA box accommodate the exocyclic NH(2) groups of G in a TACA box and in a TATAAG box. (3) Formation of a C:G Hoogsteen basepair in a TATAAAC box eliminates steric clashes that would be produced by the Watson-Crick base pair. We conclude that the structure of the TBP-TATA box complex found at the heart of the polymerase II (pol II) transcription machinery has remained constant over the course of evolution, despite variations in TBP and its DNA targets.