Plant ecology: Coexistence of tropical tree species.
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Aging↗
Biomedical subjects
Patrick J Baker
Publications and source records attributed to Patrick J Baker.
Alanine dehydrogenase from the psychrophilic bacterium strain PA-43: overexpression, molecular characterization, and sequence analysis.
The gene encoding alanine dehydrogenase (AlaDH; EC 1.4.1.1) from the marine psychrophilic bacterium strain PA-43 was cloned, sequenced, and overexpressed in Escherichia coli. The primary structure was deduced on the basis of the nucleotide sequence. The enzyme subunit contains 371 amino acid residues, and the sequence is 90% and 77% identical, respectively, to AlaDHs from Shewanella Ac10 and Vibrio proteolyticus. The half-life of PA-43 AlaDH at 52 degrees C is 9 min, and it is thus more thermolabile than the AlaDH from Shewanella Ac10 or V. proteolyticus. The enzyme showed strong specificity for NAD(+) and l-alanine as substrates. The apparent K(m) for NAD(+) was temperature dependent (0.04 mM-0.23 mM from 15 degrees C to 55 degrees C). A comparison of the PA-43 deduced amino acid sequence to the solved three-dimensional structure of Phormidium lapideum AlaDH showed that there were likely to be fewer salt bridges in the PA-43 enzyme, which would increase enzyme flexibility and decrease thermostability. The hydrophobic surface character of the PA-43 enzyme was greater than that of P. lapideum AlaDH, by six residues. However, no particular modification or suite of modifications emerged as being clearly responsible for the psychrophilic character of PA-43 AlaDH.
Acclimatization↗
The structure of Escherichia coli RusA endonuclease reveals a new Holliday junction DNA binding fold.
Holliday junction resolution performed by a variety of structure-specific endonucleases is a key step in DNA recombination and repair. It is believed that all resolvases carry out their reaction chemistries in a similar fashion, utilizing a divalent cation to facilitate the hydrolysis of the phosphodiester backbone of the DNA, but their architecture varies. To date, with the exception of bacteriophage T4 endonuclease VII, each of the known resolvase enzyme structures has been categorized into one of two families: the integrases and the nucleases. We have now determined the structure of the Escherichia coli RusA Holliday junction resolvase, which reveals a fourth structural class for these enzymes. The structure suggests that dimer formation is essential for Mg(2+) cation binding and hence catalysis and that like the other resolvases, RusA distorts its Holliday junction target upon binding. Key residues identified by mutagenesis experiments are well positioned to interact with the DNA.
Amino Acid Sequence↗
Endogenous and exogenous ice-nucleating agents constrain supercooling in the hatchling painted turtle.
Hatchlings of the painted turtle (Chrysemys picta) commonly hibernate in their shallow, natal nests. Survival at temperatures below the limit of freeze tolerance (approximately -4 degrees C) apparently depends on their ability to remain supercooled, and, whereas previous studies have reported that supercooling capacity improves markedly with cold acclimation, the mechanistic basis for this change is incompletely understood. We report that the crystallization temperature (T(c)) of recently hatched (summer) turtles acclimated to 22 degrees C and reared on a substratum of vermiculite or nesting soil was approximately 5 degrees C higher than the T(c) determined for turtles acclimated to 4 degrees C and tested in winter. This increase in supercooling capacity coincided with elimination of substratum (and, in fewer cases, eggshell) that the hatchlings had ingested; however, this association was not necessarily causal because turtles reared on a paper-covered substratum did not ingest exogenous matter but nevertheless showed a similar increase in supercooling capacity. Our results for turtles reared on paper revealed that seasonal development of supercooling capacity fundamentally requires elimination of ice-nucleating agents (INA) of endogenous origin: summer turtles, but not winter turtles, produced feces (perhaps derived from residual yolk) that expressed ice-nucleating activity. Ingestion of vermiculite or eggshell, which had modest ice-nucleating activity, had no effect on the T(c), whereas ingestion of nesting soil, which contained two classes of potent INA, markedly reduced the supercooling capacity of summer turtles. This effect persisted long after the turtles had purged their guts of soil particles, because the T(c) of winter turtles reared on nesting soil (mean +/- S.E.M.=-11.6+/-1.4 degrees C) was approximately 6 degrees C higher than the T(c) of winter turtles reared on vermiculite or paper. Experiments in which winter turtles were fed INA commonly found in nesting soil showed that water-soluble, organic agents can remain fully active for at least one month. Such INA may account for the limited supercooling capacity (T(c) approximately -7.5 degrees C) we found in turtles overwintering in natural nests and may therefore pose a formidable challenge to the winter survival of hatchling C. picta.
Acclimatization↗
Crystallization and preliminary X-ray crystallographic studies on the class II cholesterol oxidase from Burkholderia cepacia containing bound flavin.
Burkholderia cepacia cholesterol oxidase (ChoS) is a 58.7 kDa molecular-weight flavoenzyme which has been categorized as a 3beta-hydroxysteroid oxidase converting the 3beta-hydroxyl group of a range of hydroxysteroids to the corresponding ketone. Analysis of enzymes with this activity has shown that two classes of cholesterol oxidase can be defined. Enzymes belonging to class I contain non-covalently bound FAD, whereas the class II enzymes contain FAD covalently bound to an active-site histidine. Despite catalysing the same chemical reaction, the class I and class II enzymes show no sequence similarity and have a different molecular architecture. Crystals of a recombinant class II enzyme from B. cepacia have been grown by the hanging-drop vapour-diffusion method using polyethylene glycol as a precipitating agent. The crystals belong to space group P3(1)21, with unit-cell parameters a = b = 119.6, c = 101.1 A, and have one subunit in the asymmetric unit. These crystals diffract to at least 2.0 A resolution at the Daresbury SRS and are suitable for a full structure determination. Ultimately, analysis of the structure of B. cepacia ChoS may allow the characteristics and structural features which contribute to its suitability as a diagnostic reagent for the detection of cholesterol and unresolved mechanistic features of the class II enzymes to be understood.
Burkholderia cepacia↗
Crystallization and preliminary X-ray analysis of substrate complexes of leucine dehydrogenase from Thermoactinomyces intermedius.
Leucine dehydrogenase is an octameric enzyme which belongs to the superfamily of amino-acid dehydrogenases and catalyses the reversible oxidative deamination of leucine to 2-ketoisocaproate, with the corresponding reduction of the cofactor NAD(+). Catalysis by this enzyme is thought to involve a large-scale motion of the enzyme's two domains between an 'open' and 'closed' form, with the latter representing a conformation of the enzyme in which the partners involved in the hydride-transfer reaction are appropriately positioned for catalysis. Whilst a structure for the open form of the enzyme has been determined, the nature of the closed form has yet to be observed. In order to trap a closed form, crystals of the complexes of leucine dehydrogenase from Thermoactinomyces intermedius with 2-ketoisocaproate and with 2-ketoisocaproate and NAD(+) have been obtained by the hanging-drop vapour-diffusion method using PEG 4000 as a precipitant. The crystals of the binary complex with 2-ketoisocaproate belong to space group P2(1)2(1)2(1), with approximate unit-cell parameters a = 106, b = 118, c = 320 A and an octamer in the asymmetric unit, corresponding to a V(M) of 3.1 A(3) Da(-1). The crystals of the non-productive ternary complex belong to space group P6(1) or P6(5), with approximate unit-cell parameters a = b = 117, c = 502 A and an octamer in the asymmetric unit, corresponding to a V(M) of 3.0 A(3) Da(-1). These crystals diffract X-rays on a synchrotron-radiation source to at least 2.8 and 3.3 A resolution, respectively, and are suitable for a full structure determination.
Amino Acid Oxidoreductases↗
Crystallization and preliminary X-ray crystallographic studies on acyl-(acyl carrier protein) from Escherichia coli.
Acyl carrier proteins carry the lipid substrate to the enzymes of the fatty acid synthase system. Crystals of Escherichia coli acyl carrier protein to which a butyryl group has been attached via a thioester link to the phosphopantetheine prosthetic arm have been obtained by the hanging-drop vapour-diffusion method. These crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 27.6, b = 41.6, c = 63.7 A. The asymmetric unit appears to contain one subunit, corresponding to a packing density of 2.1 A(3) Da(-1). Crystals of the selenomethionine-substituted (SeMet) protein were obtained using different conditions and belong to space group P6(3), with unit-cell parameters a = b = 63.4, c = 37.0 A, alpha = beta = 90, gamma = 120 degrees and with a monomer in the asymmetric unit (V(M) = 2.5 A(3) Da(-1)). Crystals of a SeMet butyryl-ACP I62M variant were obtained using the conditions for the native protein. Like the native crystals, these belong to space group P2(1)2(1)2(1) and have unit-cell parameters a = 27.3, b = 41.9, c = 64.5 A. A data set suitable for MAD phasing was collected from the crystals of the I62M variant to 1.8 A resolution on the ESRF beamline ID14-4.
Acyl Carrier Protein↗
The crystal structure of diadenosine tetraphosphate hydrolase from Caenorhabditis elegans in free and binary complex forms.
The crystal structure of C. elegans Ap(4)A hydrolase has been determined for the free enzyme and a binary complex at 2.0 A and 1.8 A, respectively. Ap(4)A hydrolase has a key role in regulating the intracellular Ap(4)A levels and hence potentially the cellular response to metabolic stress and/or differentiation and apoptosis via the Ap(3)A/Ap(4)A ratio. The structures reveal that the enzyme has the mixed alpha/beta fold of the Nudix family and also show how the enzyme binds and locates its substrate with respect to the catalytic machinery of the Nudix motif. These results suggest how the enzyme can catalyze the hydrolysis of a range of related dinucleoside tetraphosphate, but not triphosphate, compounds through precise orientation of key elements of the substrate.
Acid Anhydride Hydrolases↗
X-ray crystallographic studies on butyryl-ACP reveal flexibility of the structure around a putative acyl chain binding site.
Acyl carrier protein (ACP) is an essential cofactor in biosynthesis of fatty acids and many other reactions that require acyl transfer steps. We have determined the first crystal structures of an acylated form of ACP from E. coli, that of butyryl-ACP. Our analysis of the molecular surface of ACP reveals a plastic hydrophobic cavity in the vicinity of the phosphopantethylated Ser36 residue that is expanded and occupied by the butyryl and beta-mercaptoethylamine moieties of the acylated 4'-phosphopantetheine group in one of our crystal forms. In the other form, the cavity is contracted, and we propose that the protein has adopted the conformation after delivery of substrate into the active site of a partner enzyme.
Acyl Carrier Protein↗