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B F Luisi

Publications and source records attributed to B F Luisi.

At least 19 recordsLinked to original sources
PubMed2001

Crystal structure of the Escherichia coli RNA degradosome component enolase.

The crystal structure of Escherichia coli enolase (EC 4.2.1.11, phosphopyruvate hydratase), which is a component of the RNA degradosome, has been determined at 2.5 A. There are four molecules in the asymmetric unit of the C2 cell, and in one of the molecules, flexible loops close onto the active site. This closure mimics the conformation of the substrate-bound intermediate. A comparison of the structure of the E. coli enolase with the eukaryotic enolase structures available (lobster and yeast) indicates a high degree of conservation of the hydrophobic core and the subunit interface of this homodimeric enzyme. The dimer interface is enriched in charged residues compared with other protein homodimers, which may explain our observations from analytical ultracentrifugation that dimerisation is affected by ionic strength. The putative role of enolase in the RNA degradosome is discussed; although it was not possible to ascribe a specific role to it, a structural role is possible.

Animals↗
PubMed2000

A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation.

BACKGROUND: Polynucleotide phosphorylase (PNPase) is a polyribonucleotide nucleotidyl transferase (E.C.2.7.7.8) that degrades mRNA in prokaryotes. Streptomyces antibioticus PNPase also assays as a guanosine 3'-diphosphate 5'-triphosphate (pppGpp) synthetase (E.C.2.7.6.5). It may function to coordinate changes in mRNA lifetimes with pppGpp levels during the Streptomyces lifecycle. RESULTS: The structure of S. antibioticus PNPase without bound RNA but with the phosphate analog tungstate bound at the PNPase catalytic sites was determined by X-ray crystallography and shows a trimeric multidomain protein with a central channel. The structural core has a novel duplicated architecture formed by association of two homologous domains. The tungstate derivative structure reveals the PNPase active site in the second of these core domains. Structure-based sequence analysis suggests that the pppGpp synthetase active site is located in the first core domain. CONCLUSIONS: This is the first structure of a PNPase and shows the structural basis for the trimer assembly, the arrangement of accessory RNA binding domains, and the likely catalytic residues of the PNPase active site. A possible function of the trimer channel is as a contribution to both the processivity of degradation and the regulation of PNPase action by RNA structural elements.

Amino Acid Sequence↗
PubMed1997

X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature.

DNA containing short periodic stretches of adenine residues (known as A-tracts), which are aligned with the helical repeat, exhibit a pronounced macroscopic curvature. This property is thought to arise from the cumulative effects of a distinctive structure of the A-tract. It has also been observed by gel electrophoresis that macroscopic curvature is largely retained when inosine bases are introduced singly into A-tracts but decreases abruptly for pure I-tracts. The structural basis of this effect is unknown. Here we describe X-ray and gel electrophoretic analyses of several oligomers incorporating adenine or inosine bases or both. We find that macroscopic curvature is correlated with a distinctive base-stacking geometry characterized by propeller twisting of the base-pairs. Regions of alternating adenine and inosine bases display large propeller twisting comparable to that of pure A-tracts, whereas the values observed for pure I-tracts are significantly smaller. We also observe in the crystal structures that propeller twist leads to close cross-strand contacts between amino groups from adenine and cytosine bases, indicating an attractive NH-N interaction, which is analogous to the NH-O interaction proposed for A-tracts. This interaction also occurs between adenine bases across an A-T step and may explain in part the different behavior of A-T versus T-A steps in the context of A-tract-induced curvature. We also note that hydration patterns may contribute to propeller-twisted conformation. Based on the present data and other structural and biophysical studies, we propose that DNA macroscopic curvature is related to the structural invariance of A-tract and A-tract-like regions conferred by high propeller twist, cross-strand interactions and characteristic hydration. The implications of these findings to the mechanism of DNA bending are discussed.

Adenine↗
PubMed1993

Specific transcriptional activation in vitro by the herpes simplex virus protein VP16.

The herpes simplex virus protein VP16 interacts with cellular factors, including the protein Oct-1, to activate viral immediate early (IE) gene transcription. We have reproduced this effect by addition of purified, full-length VP16 and the DNA-binding 'POU' domain of Oct-1 (Oct-1/POU) to a HeLa cell in vitro transcription system. Stimulation of transcription was dependent on the IE-specific element, TAATGARAT. In agreement with earlier observations from electrophoretic mobility shift assays, activation was not observed when Oct-2/POU, the DNA-binding domain from the Oct-2 protein, was substituted for Oct-1/POU. Single round transcription assays revealed that, together, VP16 and Oct-1/POU facilitate the assembly of pre-initiation complexes at target gene promoters.

Base Sequence↗
PubMed1993

DNA target selectivity by the vitamin D3 receptor: mechanism of dimer binding to an asymmetric repeat element.

The 1,25-dihydroxyvitamin D3 receptor, like other members of the nuclear receptor superfamily, forms dimers in solution that are probably stabilized by a dyad symmetrical interface formed by the ligand-binding domain. This receptor, however, recognizes DNA targets that are not dyad symmetric but rather are organized as direct repeats of a hexameric sequence with a characteristic 3-bp spacing. Using molecular modeling and site-directed mutagenesis, we have identified regions within the vitamin D3 receptor zinc finger region that confer selectivity for direct repeats with appropriate spacing. Reflecting the organization of the DNA target, these regions, mapping to the tip of the first zinc finger module and the N and C termini of the second finger module, direct asymmetrical protein-protein contacts. A stereochemical model is proposed for these interactions.

Amino Acid Sequence↗
PubMed1993

A mutagenic study of the allosteric linkage of His(HC3)146 beta in haemoglobin.

We have examined the contribution of His(HC3)146 beta to the alkaline Bohr effect of human haemoglobin (HbA) by replacing it with Gln, using site-directed mutagenesis, and studying the structural and functional consequences. Oxygen equilibrium curves of the mutant show that the effect of pH on the oxygen affinity, the alkaline Bohr effect, is half that of HbA in the presence of chloride ion and less than 10% in its absence. Crystallographic analysis shows that the mutation introduced only small structural changes localized to the site of substitution, proving that the replacement of the hydrogen bond between the ionizable side-chain of His146 beta and Asp94 beta by a hydrogen bond between the unionizable side-chain of Gln146 beta and the same aspartate is solely responsible for the reduction of the alkaline Bohr effect. Our data confirm that His(HC3)146 beta is predominantly responsible for the chloride-independent component of the alkaline Bohr effect which results from the breaking of the hydrogen bond between His(HC3)146 beta and Asp(FG1)94 beta accompanying the transition from the quaternary deoxy to oxy-structure.

Allosteric Regulation↗
PubMed1993

On the mechanism of DNA binding by nuclear hormone receptors: a structural and functional perspective.

The nuclear hormone receptor DNA-binding domain consists of two zinc finger-like modules whose amino acids are highly conserved among the members of the receptor superfamily. In this review, we describe the various genetic, biochemical, and structural experiments that have been carried out primarily for the DNA-binding domains of the glucocorticoid and estrogen receptors. We describe how the structural and functional information have permitted us to predict properties of the DNA-binding domains of other nuclear receptors. We postulate how receptors discriminate closely related response elements through sequence-specific contacts and distinguish symmetry of target sites through protein-protein interactions. This mechanism explains in part how the receptors regulate diverse sets of genes from a limited repertoire of core response elements. Lastly, we describe the stereochemical basis of nuclear receptor dysfunction in certain clinical disorders.

Amino Acid Sequence↗
PubMed1991

Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA.

Two crystal structures of the glucocorticoid receptor DNA-binding domain complexed with DNA are reported. The domain has a globular fold which contains two Zn-nucleated substructures of distinct conformation and function. When it binds DNA, the domain dimerizes, placing the subunits in adjacent major grooves. In one complex, the DNA has the symmetrical consensus target sequence; in the second, the central spacing between the target's half-sites is larger by one base pair. This results in one subunit interacting specifically with the consensus target half-site and the other nonspecifically with a noncognate element. The DNA-induced dimer fixes the separation of the subunits' recognition surfaces so that the spacing between the half-sites becomes a critical feature of the target sequence's identity.

Amino Acid Sequence↗
PubMed1988

Crystal structure of trp repressor/operator complex at atomic resolution.

The crystal structure of the trp repressor/operator complex shows an extensive contact surface, including 24 direct and 6 solvent-mediated hydrogen bonds to the phosphate groups of the DNA. There are no direct hydrogen bonds or non-polar contacts to the bases that can explain the repressor's specificity for the operator sequence. Rather, the sequence seems to be recognized indirectly through its effects on the geometry of the phosphate backbone, which in turn permits the formation of a stable interface. Water-mediated polar contacts to the bases also appear to contribute part of the specificity.

Crystallography↗
PubMed1988

The function and structure of the metal coordination sites within the glucocorticoid receptor DNA binding domain.

The glucocorticoid receptor enhances or represses transcription by binding to specific DNA sequences termed glucocorticoid response elements, or GREs. Studies of cloned glucocorticoid receptors reveal that the protein is organized as functional domains, in an arrangement that appears to be common among members of the steroid receptor family. A segment near the centre of the gene specifies DNA binding activity in vitro and contains two sequence motifs similar to 'zinc fingers' found in Xenopus transcription factor IIIA (TFIIIA). Such sequence motifs have been identified in nucleic acid binding proteins from a wide range of organisms. Steroid receptor protein fingers are proposed to bind zinc through two pairs of conserved cysteine residues. We report here that a protein of relative molecular mass 19,000 (Mr = 19 K) encompassing the DNA-binding domain of the glucocorticoid receptor that has been overexpressed in Escherichia coli and purified to homogeneity reversibly ligates two Zn(II) or Cd(II) ions. We show that metal ions are required for specific DNA binding and proper folding. Using EXAFS (extended X-ray absorption fine structure) and visible light spectroscopies, we find that each Zn atom is coordinated in a tetrahedral arrangement by four cysteines.

Amino Acid Sequence↗
PubMed1987

X-ray crystallographic and functional studies of human haemoglobin mutants produced in Escherichia coli.

Human beta-globin was produced in Escherichia coli as a cleavable fusion protein using the expression vector pLcII [Nagai and Thøgersen, Nature 301, p. 810, 1984]. The fusion protein CIIFX beta-globin was purified under denaturing conditions to homogeneity and the authentic beta-globin was liberated by blood coagulation factor Xa. beta-Globin was then folded and reconstituted with haem and alpha-subunits to form fully functional alpha 2 beta 2-tetramers [Nagai et al., Proc. natn. Acad. Sci. USA 82, p. 7252, 1985]. This has enabled us to produce mutants with amino acid substitutions in the beta-subunit at will and in sufficient quantities to study their oxygen-binding properties and three-dimensional structures. We have crystallised three mutants, Hb Nympheas [Cys-93 beta----Ser], Hb Daphne [Cys-93 beta----Ser, His-143 beta----Arg] and Hb Sandra [Cys-93 beta----Ser, Asp-94 beta----Glu], and have solved their structures to high resolution by x-ray crystallography.

Amino Acid Sequence↗
PubMed1980

Na+ transport via Na+/H+ antiport in Halobacterium halobium envelope vesicles.

Using H. halobium cell envelope vesicles containing either bacteriorhodopsin plus Na+ pump, bacteriorhodopsin alone, Na+ pump alone, or no light-responsive pigment altogether, it could be shown that the large majority of light energized Na+ extrusion in these mutants is linked to bacteriorhodopsin and to protonmotive force, and therefore must be facilitated by a Na+/H+ antiporter. Thus, the recently discovered primary Na+ pump makes only a minor contribution to light-mediated Na+ flux. The activity of the Na+/H+ antiporter appears to be independent of the presence of any photoreactive pigments, since an artifical electron donor will drive rapid Na+ extrusion in all of the vesicle preparations tested.

Bacteriorhodopsins↗
PubMedDate not supplied

Crystallographic analysis of mutant human haemoglobins made in Escherichia coli.

The expression of beta-globin in Escherichia coli has enabled us to study the functional role of individual amino-acid residues in haemoglobin (Hb) by site-directed mutagenesis. In contrast to mammalian Hbs, some teleost fish haemoglobins show a drastic lowering of oxygen affinity and cooperativity at low pH, a phenomenon known as the Root effect. We have produced the two mutant haemoglobins Hb Nymphéas [Cys(F9)93 beta----Ser] and Hb Daphne [His(H21)143 beta----Arg, Cys(F9)93 beta----Ser] to investigate this allosteric property. Although these substitutions were thought to be responsible for the Root effect, Hb Nymphéas and Hb Daphne show an increased oxygen affinity and a reduced effect of pH on oxygen affinity. Our X-ray crystallographic studies show that the hydroxyl group of Ser 93 beta forms a hydrogen bond with Asp 94 beta which is in equilibrium with the salt bridge between Asp 94 beta and His 146 beta. The oxygen-binding properties of Hbs Nymphéas and Daphne are accounted for by the partial disruption of the salt bridge.

Amino Acids↗