Linked Life Data

8075070

Source:http://linkedlifedata.com/resource/pubmed/id/8075070

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
35
pubmed:dateCreated
1994-10-4
pubmed:abstractText
Ner repressors of the transposable phages Mu and D108 play a central role in regulating the expression of the early (transposase) operon and in ensuring that phage growth proceeds along a lytic pathway. The latter function is analogous to that performed by the Cro protein of phage lambda. Unlike lambda Cro, however, the structural basis of operator recognition is not known for the Ner repressors. In order to elucidate the structural features underlying operator recognition by Ner repressors, we have employed Raman spectroscopy as a probe of the solution secondary structures of both D108 Ner and Mu Ner. Additionally, we have obtained Raman spectra of the D108 Ner repressor when bound to a 61-base-pair oligodeoxynucleotide containing the 55-base-pair D108 ner binding site. Conformation-sensitive Raman bands show that both D108 and Mu Ner contain similar, highly alpha-helical (approximately 45%) secondary structures. The Raman markers also show that the substantial nonhelical secondary structure of both D108 Ner and Mu Ner is largely beta-stranded. The protein-free 61-bp D108 ner operator exhibits Raman marker bands diagnostic of an uninterrupted B DNA duplex. In the D108 Ner:DNA complex, we find the following: (i) B DNA stereochemistry is fully conserved, although with significant perturbations to the B form backbone geometry, particularly in AT-rich regions of the bound operator. (ii) The specific interactions that occur between Ner repressor and operator involve B DNA major groove sites. (iii) A small (8 +/- 3%) increase in alpha-helix content of the Ner repressor is detected upon operator binding. (iv) Finally, the local environments of many aromatic amino acids are substantially altered in the D108 Ner:DNA complex. We propose a molecular model for binding of D108 Ner to its operator that is consistent with both the present spectroscopic findings and the results of recent biochemical studies. Essential features of this model are bending of the DNA double helix and contact of operator sites with repressor domains bearing sequence homologies with the helix-turn-helix (HTH) motifs of other DNA-binding proteins. The Raman fingerprint of the Ner:DNA complex is shown to be clearly distinguishable from that of the lambda cI:DNA complex, even though both gene regulatory complexes are presumed to employ HTH recognition motifs. The unique Raman signatures observed for these repressor complexes suggest that the Raman methodology may be useful in discriminating different modes of operator recognition by the HTH motifs of regulatory proteins.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Sep
pubmed:issn
0006-2960
pubmed:author
pubmed:issnType
Print
pubmed:day
6
pubmed:volume
33
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
10701-10
pubmed:dateRevised
2008-11-21
pubmed:meshHeading
pubmed-meshheading:8075070-Amides, pubmed-meshheading:8075070-Amino Acid Sequence, pubmed-meshheading:8075070-Base Sequence, pubmed-meshheading:8075070-Binding Sites, pubmed-meshheading:8075070-Coliphages, pubmed-meshheading:8075070-DNA-Binding Proteins, pubmed-meshheading:8075070-Helix-Loop-Helix Motifs, pubmed-meshheading:8075070-Molecular Sequence Data, pubmed-meshheading:8075070-Nucleic Acid Conformation, pubmed-meshheading:8075070-Operator Regions, Genetic, pubmed-meshheading:8075070-Protein Conformation, pubmed-meshheading:8075070-Repressor Proteins, pubmed-meshheading:8075070-Sequence Alignment, pubmed-meshheading:8075070-Sequence Homology, Amino Acid, pubmed-meshheading:8075070-Spectrum Analysis, Raman, pubmed-meshheading:8075070-Tryptophan, pubmed-meshheading:8075070-Tyrosine, pubmed-meshheading:8075070-Viral Proteins, pubmed-meshheading:8075070-Viral Regulatory and Accessory Proteins
pubmed:year
1994
pubmed:articleTitle
Secondary structure and interaction of phage D108 Ner repressor with a 61-base-pair operator: evidence for altered protein and DNA structures in the complex.
pubmed:affiliation
Division of Cell Biology and Biophysics, School of Biological Science, University of Missouri-Kansas City 64110.
pubmed:publicationType
Journal Article, Comparative Study, Research Support, U.S. Gov't, P.H.S., Research Support, Non-U.S. Gov't