1YSF

The solution structure of the N-domain of the transcription factor abrB

Summary for 1YSF

• Entry DOI: 10.2210/pdb1ysf/pdb
• Related: 1EKT 1YFB
• Descriptor: Transition state regulatory protein abrB (1 entity in total)
• Functional Keywords: nmr; homodimer; bioinformatics; swapped-hairpin barrel, transcription
• Biological source: Bacillus subtilis
• Total number of polymer chains: 2
• Total formula weight: 13972.47

Authors

Truffault, V.,Djuranovic, S.,Coles, M. (deposition date: 2005-02-08, release date: 2005-04-12, Last modification date: 2024-05-22)

Primary citation

Coles, M.,Djuranovic, S.,Soding, J.,Frickey, T.,Koretke, K.,Truffault, V.,Martin, J.,Lupas, A.N.
AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels.
Structure, 13:919-928, 2005

PubMed Abstract: AbrB is a key transition-state regulator of Bacillus subtilis. Based on the conservation of a betaalphabeta structural unit, we proposed a beta barrel fold for its DNA binding domain, similar to, but topologically distinct from, double-psi beta barrels. However, the NMR structure revealed a novel fold, the "looped-hinge helix." To understand this discrepancy, we undertook a bioinformatics study of AbrB and its homologs; these form a large superfamily, which includes SpoVT, PrlF, MraZ, addiction module antidotes (PemI, MazE), plasmid maintenance proteins (VagC, VapB), and archaeal PhoU homologs. MazE and MraZ form swapped-hairpin beta barrels. We therefore reexamined the fold of AbrB by NMR spectroscopy and found that it also forms a swapped-hairpin barrel. The conservation of the core betaalphabeta element supports a common evolutionary origin for swapped-hairpin and double-psi barrels, which we group into a higher-order class, the cradle-loop barrels, based on the peculiar shape of their ligand binding site.

PubMed: 15939023
DOI: 10.1016/j.str.2005.03.017

Experimental method

SOLUTION NMR