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S E Phillips

Publications and source records attributed to S E Phillips.

At least 55 records · Page 3Linked to original sources

Crystallization and initial X-ray analysis of beta-crustacyanin, the dimer of apoproteins A2 and C1, each with a bound astaxanthin molecule.

Crystals of beta-crustacyanin, a carotenoid-binding protein from lobster carapace, have been grown under oil from solutions containing sodium potassium phosphate as precipitant. They grow slowly over a period of months to reach maximal dimensions of 0.5 x 0.1 x 0.1 mm, and belong to space group P622 with cell dimensions: a = b = 124.39, c = 188.86 A and gamma = 120 degrees. The crystals diffract to beyond 3 A but are very radiation sensitive, limiting the resolution of usable data. The unit-cell volume suggests that there are two beta-crustacyanin molecules per asymmetric unit.

Journal Article↗

Crystallization and preliminary crystallographic analysis of RepA1, a replication control protein of the RepFIC replicon of enterotoxin plasmid EntP307.

RepA1 protein is essential for replication of the RepFIC replicon of enterotoxin plasmid EntP307 and is thought to interact directly with the origin of replication. We have purified RepA1 from an over-producing expression system and have prepared single crystals using a macroseeding technique. The crystals belong to space group P2(1)2(1)2(1) or P2(1)2(1)2, with cell dimensions a = 61 A, b = 67 A, and c = 243 A. They diffract X-rays to 3.3 A resolution and probably contain two 40,000 molecular weight RepA1 molecules per asymmetric unit.

Bacterial Proteins↗

Effects of systematic variation of the minimal Escherichia coli met consensus operator site: in vivo and in vitro met repressor binding.

We have produced a set of sequence variants based upon the idealized, minimal Escherichia coli met operator in which each position within the basic recognition unit, the 8 bp met box (dAGACGTCT), has been changed to all other possible sequences containing single symmetrical base substitutions. The effects of these sequence variations have been assayed in vivo by monitoring the production of beta-galactosidase from a standard promoter regulated by the operator variants, and in vitro by gel-retardation assay. The two sets of data are consistent and correlate well with expectations based on the three-dimensional structure of the holorepressor bound to a minimal idealized operator and the results of in vitro evolution experiments. Comparison with two natural operators, metA and metC, suggests that in vivo, with non-consensus operators, the repressor binds to at least four consecutive met boxes.

Bacterial Proteins↗

Crystal structure of a quinoenzyme: copper amine oxidase of Escherichia coli at 2 A resolution.

BACKGROUND: Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). RESULTS: The crystal structure of amine oxidase from Escherichia coli has been determined in both an active and an inactive form. The only structural differences are in the active site, where differences in copper coordination geometry and in the position and interactions of the redox cofactor, TPQ, are observed. Each subunit of the mushroom-shaped dimer comprises four domains: a 440 amino acid C-terminal beta sandwich domain, which contains the active site and provides the dimer interface, and three smaller peripheral alpha/beta domains (D1-D3), each of about 100 amino acids. D2 and D3 show remarkable structural and sequence similarity to each other and are conserved throughout the quinoenzyme family. In contrast, D1 is absent from some amine oxidases. The active sites are well buried from solvent and lie some 35 A apart, connected by a pair of beta hairpin arms. CONCLUSIONS: The crystal structure of E. coli copper amine oxidase reveals a number of unexpected features and provides a basis for investigating the intriguing similarities and differences in catalytic mechanism of members of this enzyme family. In addition to the three conserved histidines that bind the copper, our studies identify a number of other conserved residues close to the active site, including a candidate for the catalytic base and a fourth conserved histidine which is involved in an interesting intersubunit interaction.

Amine Oxidase (Copper-Containing)↗

Structure and mechanism of galactose oxidase. The free radical site.

Crystallographic and spectroscopic studies on galactose oxidase have shown that the active site involves a free radical on tyrosine 272, one of the ligands coordinated to the Cu2+ cofactor. A novel thioether bond between tyrosine 272 and cysteine 228, and a stacking tryptophan 290, over this bond, are features of the crystal structure. The present study describes the development of a high level heterologous expression system for galactose oxidase and the construction of mutational variants at these key active site residues. The expressed wild-type enzyme and mutational variants (W290H and C228G) have been characterized by x-ray crystallography, visible spectroscopy, and catalytic activity measurements. A further variant protein, Y272F, could not be purified. The data establish that the thioether bond and stacking tryptophan are essential for activity and further support a role for tryptophan 290 as a component of the free radical site.

Base Sequence↗

Crystal structure of a free radical enzyme, galactose oxidase.

The crystal structure of the copper-containing enzyme, galactose oxidase, has been solved by multiple isomorphous replacement and refined to a resolution of 1.7 A. The X-ray structure reveals a unique polypeptide fold. The protein can be divided into three domains, all of which consist almost entirely of beta-strands. The structure of the second domain is particularly striking, 28 beta-strands arranged in a pseudo 7-fold symmetry. The copper site is on the surface of the protein and extremely rich in aromatic side-chains. The copper ion has two histidines, two tyrosines, and one external ligand in distorted square pyramidal coordination. The presence of pyrroloquinoline quinone as a covalently bound cofactor in GOase has been excluded. Instead, an unexpected covalent linkage between Tyr272 and Cys228 has been observed, whose functional role may relate to the presence of a tyrosine free radical at Tyr272. The tyrosine free radical could be stabilized by delocalization to Cys228 and stacking interactions with Trp290. A structural model for substrate binding is proposed that offers an explanation for the substrate specificity of the enzyme and many of the spectroscopic and enzymological data. Although the model lacks direct confirmation at present, it should provide a stimulus for further spectroscopic and crystallographic studies.

Amino Acid Sequence↗

Electrostatic activation of Escherichia coli methionine repressor.

BACKGROUND: The three-dimensional structure of the Escherichia coli methionine repressor (met repressor) is relatively unperturbed by the binding of its corepressor, S-adenosylmethionine (SAM), and of operator DNA. The positively charged corepressor binds to sites on the repressor remote from the DNA-binding site, and despite the lack of induced structural change is able to raise the affinity for operator DNA by a factor of up to 1000. Neutral corepressor analogues also bind to the repressor, but do not increase operator affinity. These observations suggest that the corepressor effect may be electrostatic. RESULTS: Using the program DELPHI, we have calculated electrostatic potentials for the repressor and its complexes, and have obtained results consistent with an electrostatic model for repressor activation. The positive potential originating from the corepressor is propagated through the repressor-operator complex, and is significant at DNA phosphate groups buried in the protein-DNA interface. The rank order of calculated electrostatic interaction energies for complexes with SAM, and two closely-related analogues, is in agreement with experimental measurements of the corresponding repressor-operator affinities. CONCLUSION: Long-range (> 10 A) electrostatic interactions between bound corepressor and operator phosphate groups in the repressor-operator complex may be sufficient to explain repressor activation Met repressor could, therefore, be an electrostatically triggered genetic switch.

Apoproteins↗

Induced flip.

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Binding Sites↗

Prenatal detection of an inverted X chromosome in a male.

An unusual case of an X chromosome with a pericentric inversion (p11.3q21.3) was detected prenatally in a male fetus. This inversion has not been previously characterized. Although the inverted chromosome was transmitted through the mother, no living males on the maternal side were detected with the aberrant chromosome. Replication studies were performed on cultures of maternal peripheral blood lymphocytes, and it was determined that the inverted X chromosome was early replicating in approximately half of the cells. Following genetic counseling, the pregnancy was continued and a healthy male infant was delivered at term. Cytogenetic analysis of peripheral blood performed in the newborn period confirmed the prenatal findings. The child is developing normally at 3 years of age.

Adult↗