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1.
FEBS J ; 290(12): 3243-3257, 2023 06.
Article in English | MEDLINE | ID: mdl-36708234

ABSTRACT

Synthetic cannabinoid receptor agonists (SCRAs) are one of the fastest growing classes of recreational drugs. Despite their growth in use, their vast chemical diversity and rapidly changing landscape of structures make understanding their effects challenging. In particular, the side effects for SCRA use are extremely diverse, but notably include severe outcomes such as cardiac arrest. These side effects appear at odds with the main putative mode of action, as full agonists of cannabinoid receptors. We have hypothesized that SCRAs may act as MAO inhibitors, owing to their structural similarity to known monoamine oxidase inhibitors (MAOI's) as well as matching clinical outcomes (hypertensive crisis) of 'monoaminergic toxicity' for users of MAOIs and some SCRA use. We have studied the potential for SCRA-mediated inhibition of MAO-A and MAO-B via a range of SCRAs used commonly in the UK, as well as structural analogues to prove the atomistic determinants of inhibition. By combining in silico and experimental kinetic studies we demonstrate that SCRAs are MAO-A-specific inhibitors and their affinity can vary significantly between SCRAs, most notably affected by the nature of the SCRA 'head' group. Our data allow us to posit a putative mechanism of inhibition. Crucially our data demonstrate that SCRA activity is not limited to just cannabinoid receptor agonism and that alternative interactions might account for some of the diversity of the observed side effects and that these effects can be SCRA-specific.


Subject(s)
Cannabinoid Receptor Agonists , Illicit Drugs , Cannabinoid Receptor Agonists/pharmacology , Cannabinoid Receptor Agonists/chemistry , Kinetics , Monoamine Oxidase Inhibitors/pharmacology , Monoamine Oxidase
2.
Curr Res Struct Biol ; 4: 256-270, 2022.
Article in English | MEDLINE | ID: mdl-36106339

ABSTRACT

Nitrile hydratases (NHases) are important biocatalysts for the enzymatic conversion of nitriles to industrially-important amides such as acrylamide and nicotinamide. Although thermostability in this enzyme class is generally low, there is not sufficient understanding of its basis for rational enzyme design. The gene expressing the Co-type NHase from the moderate thermophile, Geobacillus pallidus RAPc8 (NRRL B-59396), was subjected to random mutagenesis. Four mutants were selected that were 3 to 15-fold more thermostable than the wild-type NHase, resulting in a 3.4-7.6 â€‹kJ/mol increase in the activation energy of thermal inactivation at 63 â€‹°C. High resolution X-ray crystal structures (1.15-1.80 â€‹Å) were obtained of the wild-type and four mutant enzymes. Mutant 9E, with a resolution of 1.15 â€‹Å, is the highest resolution crystal structure obtained for a nitrile hydratase to date. Structural comparisons between the wild-type and mutant enzymes illustrated the importance of salt bridges and hydrogen bonds in enhancing NHase thermostability. These additional interactions variously improved thermostability by increased intra- and inter-subunit interactions, preventing cooperative unfolding of α-helices and stabilising loop regions. Some hydrogen bonds were mediated via a water molecule, specifically highlighting the significance of structured water molecules in protein thermostability. Although knowledge of the mutant structures makes it possible to rationalize their behaviour, it would have been challenging to predict in advance that these mutants would be stabilising.

3.
ACS Catal ; 12(18): 11444-11455, 2022 Sep 16.
Article in English | MEDLINE | ID: mdl-36158901

ABSTRACT

A 2-keto-3-deoxygluconate aldolase from the hyperthermophile Sulfolobus solfataricus catalyzes the nonstereoselective aldol reaction of pyruvate and d-glyceraldehyde to produce 2-keto-3-deoxygluconate (d-KDGlc) and 2-keto-3-deoxy-d-galactonate (d-KDGal). Previous investigations into curing the stereochemical promiscuity of this hyperstable aldolase used high-resolution structures of the aldolase bound to d-KDGlc or d-KDGal to identify critical amino acids involved in substrate binding for mutation. This structure-guided approach enabled mutant variants to be created that could stereoselectively catalyze the aldol reaction of pyruvate and natural d-glyceraldehyde to selectively afford d-KDGlc or d-KDGal. Here we describe the creation of two further mutants of this Sulfolobus aldolase that can be used to catalyze aldol reactions between pyruvate and non-natural l-glyceraldehyde to enable the diastereoselective synthesis of l-KDGlc and l-KDGal. High-resolution crystal structures of all four variant aldolases have been determined (both unliganded and liganded), including Variant 1 with d-KDGlc, Variant 2 with pyruvate, Variant 3 with l-KDGlc, and Variant 4 with l-KDGal. These structures have enabled us to rationalize the observed changes in diastereoselectivities in these variant-catalyzed aldol reactions at a molecular level. Interestingly, the active site of Variant 4 was found to be sufficiently flexible to enable catalytically important amino acids to be replaced while still retaining sufficient enzymic activity to enable production of l-KDGal.

4.
Work Employ Soc ; 36(4): 591-609, 2022 Aug.
Article in English | MEDLINE | ID: mdl-35935451

ABSTRACT

The importance of remaining in, or re-entering, the labour market is emphasised by governments internationally. While this may bring benefits, progressive disabilities such as dementia affect an individual's employability. Although employers have legal obligations to support employees with disabilities, research suggests that employers are not providing this support to employees living with dementia and are undermining their capabilities. Drawing on interview data from 38 key informants collected over two studies, we explore the potential for supporting and promoting the employability of people living with dementia. A model of sustainable employability based on the Capability Approach is used as a lens to explore this issue. The findings demonstrate the implications of progressive disabilities for employability when the worker and their family are faced with dealing with a disability in a period of uncertainty with a lack of public and workplace understanding.

5.
ACS Catal ; 11(24): 14854-14863, 2021 Dec 17.
Article in English | MEDLINE | ID: mdl-34956689

ABSTRACT

Uncovering the role of global protein dynamics in enzyme turnover is needed to fully understand enzyme catalysis. Recently, we have demonstrated that the heat capacity of catalysis, ΔC P ‡, can reveal links between the protein free energy landscape, global protein dynamics, and enzyme turnover, suggesting that subtle changes in molecular interactions at the active site can affect long-range protein dynamics and link to enzyme temperature activity. Here, we use a model promiscuous enzyme (glucose dehydrogenase from Sulfolobus solfataricus) to chemically map how individual substrate interactions affect the temperature dependence of enzyme activity and the network of motions throughout the protein. Utilizing a combination of kinetics, red edge excitation shift (REES) spectroscopy, and computational simulation, we explore the complex relationship between enzyme-substrate interactions and the global dynamics of the protein. We find that changes in ΔC P ‡ and protein dynamics can be mapped to specific substrate-enzyme interactions. Our study reveals how subtle changes in substrate binding affect global changes in motion and flexibility extending throughout the protein.

6.
Aging Ment Health ; 25(1): 134-141, 2021 01.
Article in English | MEDLINE | ID: mdl-31549517

ABSTRACT

OBJECTIVES: As working lives extend and there is better recognition of early-onset dementias, employers need to consider dementia as a workplace concern. With suitable support, people living with dementia can continue employment - although, this is not appropriate for all. The requirement for employers to support employees living with dementia has human rights and legal foundations. This article considers whether employers consider dementia as a workplace concern; and the policies and/or practices available to support employees living with dementia. Thus, it develops understanding of whether employers are meeting their human rights/legislative obligations. METHOD: A sequential mixed-methods approach was employed, with data collection undertaken in Scotland (United Kingdom). An online survey was sent to employers across Scotland, with 331 participating. Thirty employer interviews were conducted, with the survey results informing the interview approach. RESULTS: The survey and interview data were analyzed separately and then combined and presented thematically. The themes identified were (1) Dementia as a workplace concern, (2) Support for employees living with dementia and (3) Employer policy development and awareness raising. The findings demonstrate dementia awareness, but this knowledge is not applied to employment situations. There was little evidence suggesting that the rights of employees living with dementia are consistently upheld. CONCLUSION: This research sends out strong messages about the rights and legal position of person living with dementia which cannot be ignored. The continuing potential of employees living with dementia and their legal rights are not consistently recognized. This highlights the need for robust training interventions for employers.


Subject(s)
Dementia , Workplace , Humans , Scotland , Surveys and Questionnaires , United Kingdom
7.
BMC Biotechnol ; 19(1): 17, 2019 03 20.
Article in English | MEDLINE | ID: mdl-30894163

ABSTRACT

BACKGROUND: Parageobacillus thermoglucosidasius is a thermophilic and ethanol-producing bacterium capable of utilising both hexose and pentose sugars for fermentation. The organism has been proposed to be a suitable organism for the production of bioethanol from lignocellulosic feedstocks. These feedstocks may be difficult to degrade, and a potential strategy to optimise this process is to engineer strains that secrete hydrolases that liberate increased amounts of sugars from those feedstocks. However, very little is known about protein transport in P. thermoglucosidasius and the limitations of that process, and as a first step we investigated whether there were bottlenecks in the secretion of a model protein. RESULTS: A secretory enzyme, xylanase (XynA1), was produced with and without its signal peptide. Cell cultures were fractionated into cytoplasm, membrane, cell wall, and extracellular milieu protein extracts, which were analysed using immunoblotting and enzyme activity assays. The main bottleneck identified was proteolytic degradation of XynA1 during or after its translocation. A combination of mass spectrometry and bioinformatics indicated the presence of several proteases that might be involved in this process. CONCLUSION: The creation of protease-deficient strains may be beneficial towards the development of P. thermoglucosidasius as a platform organism for industrial processes.


Subject(s)
Geobacillus/metabolism , Peptide Hydrolases/metabolism , Protease Inhibitors/administration & dosage , Xylosidases/metabolism , Cells, Cultured , Extracellular Fluid , Geobacillus/genetics , Peptide Hydrolases/analysis , Protein Sorting Signals , Proteolysis , Proteome/analysis , Xylosidases/analysis
8.
Biochemistry ; 57(26): 3797-3806, 2018 07 03.
Article in English | MEDLINE | ID: mdl-29812914

ABSTRACT

The thermoacidophilic archaea Picrophilus torridus and Sulfolobus solfataricus catabolize glucose via a nonphosphorylative Entner-Doudoroff pathway and a branched Entner-Doudoroff pathway, respectively. Key enzymes for these Entner-Doudoroff pathways are the aldolases, 2-keto-3-deoxygluconate aldolase (KDG-aldolase) and 2-keto-3-deoxy-6-phosphogluconate aldolase [KD(P)G-aldolase]. KDG-aldolase from P. torridus (Pt-KDG-aldolase) is highly specific for the nonphosphorylated substrate, 2-keto-3-deoxygluconate (KDG), whereas KD(P)G-aldolase from S. solfataricus [Ss-KD(P)G-aldolase] is an enzyme that catalyzes the cleavage of both KDG and 2-keto-3-deoxy-6-phosphogluconate (KDPG), with a preference for KDPG. The structural basis for the high specificity of Pt-KDG-aldolase for KDG as compared to the more promiscuous Ss-KD(P)G-aldolase has not been analyzed before. In this work, we report the elucidation of the structure of Ss-KD(P)G-aldolase in complex with KDPG at 2.35 Å and that of KDG-aldolase from P. torridus at 2.50 Å resolution. By superimposition of the active sites of the two enzymes, and subsequent site-directed mutagenesis studies, a network of four amino acids, namely, Arg106, Tyr132, Arg237, and Ser241, was identified in Ss-KD(P)G-aldolase that interact with the negatively charged phosphate group of KDPG, thereby increasing the affinity of the enzyme for KDPG. This KDPG-binding network is absent in Pt-KDG-aldolase, which explains the low catalytic efficiency of KDPG cleavage.


Subject(s)
Aldehyde-Lyases/chemistry , Archaeal Proteins/chemistry , Gluconates/chemistry , Sulfolobus solfataricus/enzymology , Thermoplasmales/enzymology , Models, Molecular , Protein Domains , Structure-Activity Relationship
9.
Acta Crystallogr F Struct Biol Commun ; 74(Pt 3): 179-186, 2018 Mar 01.
Article in English | MEDLINE | ID: mdl-29497023

ABSTRACT

Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a key enzyme in homofermentative metabolism where ethanol is the major product. PDCs are thiamine pyrophosphate- and Mg2+ ion-dependent enzymes that catalyse the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. As this enzyme class is rare in bacteria, current knowledge of bacterial PDCs is extremely limited. One approach to further the understanding of bacterial PDCs is to exploit the diversity provided by evolution. Ancestral sequence reconstruction (ASR) is a method of computational molecular evolution to infer extinct ancestral protein sequences, which can then be synthesized and experimentally characterized. Through ASR a novel PDC was generated, designated ANC27, that shares only 78% amino-acid sequence identity with its closest extant homologue (Komagataeibacter medellinensis PDC, GenBank accession No. WP_014105323.1), yet is fully functional. Crystals of this PDC diffracted to 3.5 Šresolution. The data were merged in space group P3221, with unit-cell parameters a = b = 108.33, c = 322.65 Å, and contained two dimers (two tetramer halves) in the asymmetric unit. The structure was solved by molecular replacement using PDB entry 2wvg as a model, and the final R values were Rwork = 0.246 (0.3671 in the highest resolution bin) and Rfree = 0.319 (0.4482 in the highest resolution bin). Comparison with extant bacterial PDCs supports the previously observed correlation between decreased tetramer interface area (and number of interactions) and decreased thermostability.


Subject(s)
Acetobacteraceae/enzymology , Pyruvate Decarboxylase/chemistry , Acetobacteraceae/classification , Amino Acid Sequence , Catalytic Domain , Crystallization , Crystallography, X-Ray , Models, Molecular , Protein Conformation
10.
Extremophiles ; 21(4): 733-742, 2017 Jul.
Article in English | MEDLINE | ID: mdl-28493148

ABSTRACT

To obtain new insights into community compositions of hyperthermophilic microorganisms, defined as having optimal growth temperatures of 80 °C and above, sediment and water samples were taken from two shallow marine hydrothermal vents (I and II) with temperatures of 100 °C at Vulcano Island, Italy. A combinatorial approach of denaturant gradient gel electrophoresis (DGGE) and metagenomic sequencing was used for microbial community analyses of the samples. In addition, enrichment cultures, growing anaerobically on selected polysaccharides such as starch and cellulose, were also analyzed by the combinatorial approach. Our results showed a high abundance of hyperthermophilic archaea, especially in sample II, and a comparable diverse archaeal community composition in both samples. In particular, the strains of the hyperthermophilic anaerobic genera Staphylothermus and Thermococcus, and strains of the aerobic hyperthermophilic genus Aeropyrum, were abundant. Regarding the bacterial community, ε-Proteobacteria, especially the genera Sulfurimonas and Sulfurovum, were highly abundant. The microbial diversity of the enrichment cultures changed significantly by showing a high dominance of archaea, particularly the genera Thermococcus and Palaeococcus, depending on the carbon source and the selected temperature.


Subject(s)
Archaea/classification , Bacteria/classification , Hydrothermal Vents/microbiology , Marine Biology , Archaea/genetics , Bacteria/genetics , Italy , RNA, Ribosomal, 16S/genetics
11.
Microb Cell Fact ; 16(1): 58, 2017 Apr 05.
Article in English | MEDLINE | ID: mdl-28381218

ABSTRACT

BACKGROUND: Geobacillus thermoglucosidasius is a thermophilic, natural ethanol producer and a potential candidate for commercial bioethanol production. Previously, G. thermoglucosidasius has been genetically modified to create an industrially-relevant ethanol production strain. However, creating chromosomal integrations and deletions in Geobacillus spp. is laborious. Here we describe a new technique to create marker-less mutations in Geobacillus utilising a novel homologous recombination process. RESULTS: Our technique incorporates counter-selection using ß-glucosidase and the synthetic substrate X-Glu, in combination with a two-step homologous recombination process where the first step is a selectable double-crossover event that deletes the target gene. We demonstrate how we have utilised this technique to delete two components of the proteinaceous shell of the Geobacillus propanediol-utilization microcompartment, and simultaneously introduce an oxygen-sensitive promoter in front of the remaining shell-component genes and confirm its functional incorporation. CONCLUSION: The selectable deletion of the target gene in the first step of our process prevents re-creation of wild-type which can occur in most homologous recombination techniques, circumventing the need for PCR screening to identify mutants. Our new technique therefore offers a faster, more efficient method of creating mutants in Geobacillus.


Subject(s)
Alleles , Gene Deletion , Genetic Engineering/methods , Geobacillus/genetics , Homologous Recombination , Mutation , Ethanol/metabolism , Polymerase Chain Reaction , Promoter Regions, Genetic , Sequence Deletion , beta-Glucosidase/metabolism
12.
Acta Crystallogr F Struct Biol Commun ; 72(Pt 9): 700-6, 2016 09.
Article in English | MEDLINE | ID: mdl-27599861

ABSTRACT

Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a thiamine pyrophosphate- and Mg(2+) ion-dependent enzyme that catalyses the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. It is rare in bacteria, but is a key enzyme in homofermentative metabolism, where ethanol is the major product. Here, the previously unreported crystal structure of the bacterial pyruvate decarboxylase from Zymobacter palmae is presented. The crystals were shown to diffract to 2.15 Šresolution. They belonged to space group P21, with unit-cell parameters a = 204.56, b = 177.39, c = 244.55 Šand Rr.i.m. = 0.175 (0.714 in the highest resolution bin). The structure was solved by molecular replacement using PDB entry 2vbi as a model and the final R values were Rwork = 0.186 (0.271 in the highest resolution bin) and Rfree = 0.220 (0.300 in the highest resolution bin). Each of the six tetramers is a dimer of dimers, with each monomer sharing its thiamine pyrophosphate across the dimer interface, and some contain ethylene glycol mimicking the substrate pyruvate in the active site. Comparison with other bacterial PDCs shows a correlation of higher thermostability with greater tetramer interface area and number of interactions.


Subject(s)
Bacterial Proteins/chemistry , Halomonadaceae/chemistry , Magnesium/chemistry , Pyruvate Decarboxylase/chemistry , Pyruvic Acid/chemistry , Thiamine Pyrophosphate/chemistry , Amino Acid Sequence , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Catalytic Domain , Cations, Divalent , Cloning, Molecular , Crystallography, X-Ray , Escherichia coli/genetics , Escherichia coli/metabolism , Ethylene Glycol/chemistry , Gene Expression , Halomonadaceae/enzymology , Kinetics , Magnesium/metabolism , Models, Molecular , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Protein Multimerization , Pyruvate Decarboxylase/genetics , Pyruvate Decarboxylase/metabolism , Pyruvic Acid/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Substrate Specificity , Thiamine Pyrophosphate/metabolism
13.
Protein Sci ; 25(11): 2045-2053, 2016 11.
Article in English | MEDLINE | ID: mdl-27571338

ABSTRACT

Acetylating aldehyde dehydrogenases (AcAldDH) catalyse the acetylation of Coenzyme-A (CoA), or in reverse generate acetaldehyde from Acetyl-CoA using NADH as a co-factor. This article reports the expression, purification, enzyme assay, and X-ray crystal structures of an AcAldDH from Geobacillus thermoglucosidasius (GtAcAldDH) to 2.1Å and in complex with CoA and NAD+ to 4.0Å. In the structure, the AcAldDH forms a close-knit dimer, similar to that seen in other Alcohol Dehydrogenase (ADH) structures. In GtAcAldDH, these dimers associate via their N-termini to form weakly interacting tetramers. This mode of tetrameric association is also seen in an unpublished AcAldDH deposited in the PDB, but is in contrast to all other ADH structures, (including the one other published AcAldDH found in a bacterial microcompartment), in which the dimers bury a large surface area including the C-termini. This novel mode of association sequesters the active sites and potentially reactive acyl-enzyme intermediates in the center of the tetramer. In other respects, the structure is very similar to the other AcAldDH, binding the cofactors in a corresponding fashion. This similarity enabled the identification of a shortened substrate cavity in G. thermoglucosidasius AcAldDH, explaining the limitations on the length of substrate accepted by the enzyme.


Subject(s)
Aldehyde Oxidoreductases/chemistry , Bacterial Proteins/chemistry , Coenzyme A/chemistry , Geobacillus stearothermophilus/enzymology , NAD/chemistry , Crystallography, X-Ray , Protein Domains
14.
Biochem J ; 463(3): 405-12, 2014 Nov 01.
Article in English | MEDLINE | ID: mdl-25088564

ABSTRACT

The four-component polypeptides of the 2-oxoacid dehydrogenase complex from the thermophilic archaeon Thermoplasma acidophilum assemble to give an active multienzyme complex possessing activity with the branched-chain 2-oxoacids derived from leucine, isoleucine and valine, and with pyruvate. The dihydrolipoyl acyl-transferase (E2) core of the complex is composed of identical trimer-forming units that assemble into a novel 42-mer structure comprising octahedral and icosahedral geometric aspects. From our previously determined structure of this catalytic core, the inter-trimer interactions involve a tyrosine residue near the C-terminus secured in a hydrophobic pocket of an adjacent trimer like a ball-and-socket joint. In the present study, we have deleted the five C-terminal amino acids of the E2 polypeptide (IIYEI) and shown by equilibrium centrifugation that it now only assembles into a trimeric enzyme. This was confirmed by SAXS analysis, although this technique showed the presence of approximately 20% hexamers. The crystal structure of the trimeric truncated E2 core has been determined and shown to be virtually identical with the ones observed in the 42-mer, demonstrating that removal of the C-terminal anchor does not significantly affect the individual monomer or trimer structures. The truncated E2 is still able to bind both 2-oxoacid decarboxylase (E1) and dihydrolipoamide dehydrogenase (E3) components to give an active complex with catalytic activity similar to the native multienzyme complex. This is the first report of an active mini-complex for this enzyme, and raises the question of why all 2-oxoacid dehydrogenase complexes assemble into such large structures.


Subject(s)
Archaeal Proteins/chemistry , Multienzyme Complexes/chemistry , Oxidoreductases/chemistry , Thermoplasma/enzymology , Archaeal Proteins/genetics , Crystallography, X-Ray , Dihydrolipoamide Dehydrogenase/chemistry , Enzyme Stability , Hot Temperature , Kinetics , Multienzyme Complexes/genetics , Oxidoreductases/genetics , Protein Conformation , Scattering, Small Angle
15.
Genome Announc ; 2(3)2014 Jun 05.
Article in English | MEDLINE | ID: mdl-24903881

ABSTRACT

Thermophilic Geobacillus spp. can efficiently hydrolyze hemicellulose polymers and are therefore of interest in biotechnological applications. Here we report the genome sequences of two hemicellulolytic strains, Geobacillus sp. CAMR12739 and CAMR5420.

16.
Proteins ; 82(10): 2657-70, 2014 Oct.
Article in English | MEDLINE | ID: mdl-24948467

ABSTRACT

Citrate synthase (CS) catalyses the entry of carbon into the citric acid cycle and is highly-conserved structurally across the tree of life. Crystal structures of dimeric CSs are known in both "open" and "closed" forms, which differ by a substantial domain motion that closes the substrate-binding clefts. We explore both the static rigidity and the dynamic flexibility of CS structures from mesophilic and extremophilic organisms from all three evolutionary domains. The computational expense of this wide-ranging exploration is kept to a minimum by the use of rigidity analysis and rapid all-atom simulations of flexible motion, combining geometric simulation and elastic network modeling. CS structures from thermophiles display increased structural rigidity compared with the mesophilic enzyme. A CS structure from a psychrophile, stabilized by strong ionic interactions, appears to display likewise increased rigidity in conventional rigidity analysis; however, a novel modified analysis, taking into account the weakening of the hydrophobic effect at low temperatures, shows a more appropriate decreased rigidity. These rigidity variations do not, however, affect the character of the flexible dynamics, which are well conserved across all the structures studied. Simulation trajectories not only duplicate the crystallographically observed symmetric open-to-closed transitions, but also identify motions describing a previously unidentified antisymmetric functional motion. This antisymmetric motion would not be directly observed in crystallography but is revealed as an intrinsic property of the CS structure by modeling of flexible motion. This suggests that the functional motion closing the binding clefts in CS may be independent rather than symmetric and cooperative.


Subject(s)
Bacterial Proteins/chemistry , Citrate (si)-Synthase/chemistry , Models, Molecular , Animals , Arthrobacter/enzymology , Arthrobacter/growth & development , Bacillus subtilis/enzymology , Bacterial Proteins/metabolism , Binding Sites , Catalytic Domain , Citrate (si)-Synthase/metabolism , Databases, Protein , Enzyme Stability , Hydrophobic and Hydrophilic Interactions , Ligands , Molecular Dynamics Simulation , Protein Conformation , Pyrobaculum/enzymology , Pyrobaculum/growth & development , Pyrococcus furiosus/enzymology , Pyrococcus furiosus/growth & development , Sulfolobus solfataricus/enzymology , Sulfolobus solfataricus/growth & development , Sus scrofa , Thermoplasma/enzymology , Thermoplasma/growth & development , Thermus thermophilus/enzymology , Thermus thermophilus/growth & development
17.
Acta Crystallogr D Biol Crystallogr ; 70(Pt 5): 1366-74, 2014 May.
Article in English | MEDLINE | ID: mdl-24816105

ABSTRACT

Geobacillus thermoglucosidasius is a thermophilic bacterium that is able to ferment both C6 and C5 sugars to produce ethanol. During growth on hemicellulose biomass, an intracellular ß-xylosidase catalyses the hydrolysis of xylo-oligosaccharides to the monosaccharide xylose, which can then enter the pathways of central metabolism. The gene encoding a G. thermoglucosidasius ß-xylosidase belonging to CAZy glycoside hydrolase family GH52 has been cloned and expressed in Escherichia coli. The recombinant enzyme has been characterized and a high-resolution (1.7 Å) crystal structure has been determined, resulting in the first reported structure of a GH52 family member. A lower resolution (2.6 Å) structure of the enzyme-substrate complex shows the positioning of the xylobiose substrate to be consistent with the proposed retaining mechanism of the family; additionally, the deep cleft of the active-site pocket, plus the proximity of the neighbouring subunit, afford an explanation for the lack of catalytic activity towards the polymer xylan. Whilst the fold of the G. thermoglucosidasius ß-xylosidase is completely different from xylosidases in other CAZy families, the enzyme surprisingly shares structural similarities with other glycoside hydrolases, despite having no more than 13% sequence identity.


Subject(s)
Geobacillus/enzymology , Xylosidases/chemistry , Xylosidases/metabolism , Catalytic Domain , Cloning, Molecular , Crystallography, X-Ray , Disaccharides/chemistry , Disaccharides/metabolism , Escherichia coli/genetics , Models, Molecular , Protein Conformation , Xylosidases/genetics
18.
PLoS One ; 9(1): e87063, 2014.
Article in English | MEDLINE | ID: mdl-24489835

ABSTRACT

Metagenomic analyses have advanced our understanding of ecological microbial diversity, but to what extent can metagenomic data be used to predict the metabolic capacity of difficult-to-study organisms and their abiotic environmental interactions? We tackle this question, using a comparative genomic approach, by considering the molecular basis of aerobiosis within archaea. Lipoylation, the covalent attachment of lipoic acid to 2-oxoacid dehydrogenase multienzyme complexes (OADHCs), is essential for metabolism in aerobic bacteria and eukarya. Lipoylation is catalysed either by lipoate protein ligase (LplA), which in archaea is typically encoded by two genes (LplA-N and LplA-C), or by a lipoyl(octanoyl) transferase (LipB or LipM) plus a lipoic acid synthetase (LipA). Does the genomic presence of lipoylation and OADHC genes across archaea from diverse habitats correlate with aerobiosis? First, analyses of 11,826 biotin protein ligase (BPL)-LplA-LipB transferase family members and 147 archaeal genomes identified 85 species with lipoylation capabilities and provided support for multiple ancestral acquisitions of lipoylation pathways during archaeal evolution. Second, with the exception of the Sulfolobales order, the majority of species possessing lipoylation systems exclusively retain LplA, or either LipB or LipM, consistent with archaeal genome streamlining. Third, obligate anaerobic archaea display widespread loss of lipoylation and OADHC genes. Conversely, a high level of correspondence is observed between aerobiosis and the presence of LplA/LipB/LipM, LipA and OADHC E2, consistent with the role of lipoylation in aerobic metabolism. This correspondence between OADHC lipoylation capacity and aerobiosis indicates that genomic pathway profiling in archaea is informative and that well characterized pathways may be predictive in relation to abiotic conditions in difficult-to-study extremophiles. Given the highly variable retention of gene repertoires across the archaea, the extension of comparative genomic pathway profiling to broader metabolic and homeostasis networks should be useful in revealing characteristics from metagenomic datasets related to adaptations to diverse environments.


Subject(s)
Alcohol Oxidoreductases/genetics , Archaea/enzymology , Archaea/genetics , Genomics/methods , Lipoylation , Multigene Family , Aerobiosis , Alcohol Oxidoreductases/metabolism , Anaerobiosis , Biotin/metabolism , Genes, Archaeal , Ligases/genetics , Phylogeny , Substrate Specificity , Thioctic Acid/metabolism
19.
Acta Crystallogr D Biol Crystallogr ; 69(Pt 10): 2104-15, 2013 Oct.
Article in English | MEDLINE | ID: mdl-24100328

ABSTRACT

Bifunctional alcohol/aldehyde dehydrogenase (ADHE) enzymes are found within many fermentative microorganisms. They catalyse the conversion of an acyl-coenzyme A to an alcohol via an aldehyde intermediate; this is coupled to the oxidation of two NADH molecules to maintain the NAD(+) pool during fermentative metabolism. The structure of the alcohol dehydrogenase (ADH) domain of an ADHE protein from the ethanol-producing thermophile Geobacillus thermoglucosidasius has been determined to 2.5 Šresolution. This is the first structure to be reported for such a domain. In silico modelling has been carried out to generate a homology model of the aldehyde dehydrogenase domain, and this was subsequently docked with the ADH-domain structure to model the structure of the complete ADHE protein. This model suggests, for the first time, a structural mechanism for the formation of the large multimeric assemblies or `spirosomes' that are observed for this ADHE protein and which have previously been reported for ADHEs from other organisms.


Subject(s)
Alcohol Dehydrogenase/chemistry , Biofuels/microbiology , Ethanol , Geobacillus/enzymology , Models, Molecular , Alcohol Dehydrogenase/genetics , Alcohol Dehydrogenase/isolation & purification , Amino Acid Sequence , Crystallography, X-Ray , Fermentation , Geobacillus/genetics , Geobacillus/growth & development , Molecular Sequence Data , Multienzyme Complexes/chemistry , Multienzyme Complexes/genetics
20.
FEBS Lett ; 587(17): 2738-43, 2013 Sep 02.
Article in English | MEDLINE | ID: mdl-23810865

ABSTRACT

The discovery of an additional step in the progression of an enzyme from the active to inactive state under the influence of temperature has led to a better match with experimental data for all enzymes that follow Michaelis-Menten kinetics, and to an increased understanding of the process. The new model of the process, the Equilibrium Model, describes an additional mechanism by which temperature affects the activity of enzymes, with implications for ecological, metabolic, structural, and applied studies of enzymes.


Subject(s)
Enzymes/chemistry , Algorithms , Biocatalysis , Kinetics , Models, Chemical , Temperature
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