Document Detail


A proposed architecture for the central domain of the bacterial enhancer-binding proteins based on secondary structure prediction and fold recognition.
MedLine Citation:
PMID:  9070437     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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 (@ontiers 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 substitution that alter the function of the E sigma 54 activators, leaving intact the Central domain ATPase activity, are mapped on region proposed to play an equivalent role as the effector region of the GTPase superfamily.
Authors:
J Osuna; X Soberón; E Morett
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Protein science : a publication of the Protein Society     Volume:  6     ISSN:  0961-8368     ISO Abbreviation:  Protein Sci.     Publication Date:  1997 Mar 
Date Detail:
Created Date:  1997-05-27     Completed Date:  1997-05-27     Revised Date:  2009-11-18    
Medline Journal Info:
Nlm Unique ID:  9211750     Medline TA:  Protein Sci     Country:  UNITED STATES    
Other Details:
Languages:  eng     Pagination:  543-55     Citation Subset:  IM    
Affiliation:
Departamento de Reconocimiento Molecular Bioestructura, Universidad Nacional Autónoma de México, México. joel@ibt.unam.mx
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MeSH Terms
Descriptor/Qualifier:
Amino Acid Sequence
Bacterial Proteins / chemistry*,  metabolism
Enhancer Elements, Genetic*
GTP Phosphohydrolases / metabolism
Models, Molecular
Molecular Sequence Data
Protein Folding*
Protein Structure, Secondary
Sequence Homology, Amino Acid
Chemical
Reg. No./Substance:
0/Bacterial Proteins; EC 3.6.1.-/GTP Phosphohydrolases
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