Protein Science, Vol 6, Issue 3 543-555, Copyright © 1997 by Cold Spring Harbor Laboratory Press

ARTICLE

A proposed architecture for the Central domain of the bacterial enhancer-binding proteins based on secondary structure prediction and fold recognition

J. OSUNA, X. SOBERON and E. MORETT
Departamento de Reconocimiento Molecular y Bioestructura, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico. P.O. Box 510-3, Cuernavaca, Mor., 62250 Mexico

The expression of genes transcribed by the RNA polymerase with the alternative sigma factor {sigma}(54) (E{sigma}(54)) is absolutely dependent on activator proteins that bind to enhancer-like sites, located far upstream from the promoter. These unique prokaryotic proteins, known as enhancer-binding proteins (EBP), mediate open promoter complex formation in a reaction dependent on NTP hydrolysis. The best characterized proteins of this family of regulators are NtrC and NifA, which activate genes required for ammonia assimilation and nitrogen fixation, respectively. In a recent IRBM course (``Frontiers of protein structure prediction,'' IRBM, Pomezia, Italy, 1995; see web site http://www.mrc-cpe.cam.uk/irbm-course95/), one of us (J.O.) participated in the elaboration of the proposal that the Central domain of the EBPs might adopt the classical mononucleotide-binding fold. This suggestion was based on the results of a new protein fold recognition algorithm (Map) and in the mapping of correlated mutations calculated for the sequence family on the same mononucleotide-binding fold topology. In this work, we present new data that support the previous conclusion. The results from a number of different secondary structure prediction programs suggest that the Central domain could adopt an {alpha}/{beta} topology. The fold recognition programs ProFIT 0.9, 3D PROFILE combined with secondary structure prediction, and 123D suggest a mononucleotide-binding fold topology for the Central domain amino acid sequence. Finally, and most importantly, three of five reported residue alterations that impair the Central domain ATPase activity of the E{sigma}(54) activators are mapped to polypeptide regions that might be playing equivalent roles as those involved in nucleotide-binding in the mononucleotide-binding proteins. Furthermore, the known residue substitutions that alter the function of the E{sigma}(54) activators, leaving intact the Central domain ATPase activity, are mapped on a region proposed to play an equivalent role as the effector region of the GTPase superfamily.
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