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1.
J Biol Chem ; 300(1): 105539, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-38072054

RESUMEN

L-ergothioneine is widely distributed among various microbes to regulate their physiology and pathogenicity within complex environments. One of the key steps in the ergothioneine-biosynthesis pathway, the C-S bond cleavage reaction, uses the pyridoxal 5'-phosphate dependent C-S lyase to produce the final product L-ergothioneine. Here, we present the crystallographic structure of the ergothioneine-biosynthesis C-S lyase EgtE from Mycobacterium smegmatis (MsEgtE) represents the first published structure of ergothioneine-biosynthesis C-S lyases in bacteria and shows the effects of active site residues on the enzymatic reaction. The MsEgtE and the previously reported ergothioneine-biosynthesis C-S lyase Egt2 from Neurospora crassa (NcEgt2) fold similarly. However, discrepancies arise in terms of substrate recognition, as observed through sequence and structure comparison of MsEgtE and NcEgt2. The structural-based sequence alignment of the ergothioneine-biosynthesis C-S lyase from fungi and bacteria shows clear distinctions among the recognized substrate residues, but Arg348 is critical and an extremely conserved residue for substrate recognition. The α14 helix is exclusively found in the bacteria EgtE, which represent the most significant difference between bacteria EgtE and fungi Egt2, possibly resulting from the convergent evolution of bacteria and fungi.


Asunto(s)
Ergotioneína , Liasas , Mycobacterium , Ergotioneína/química , Ergotioneína/metabolismo , Hongos/metabolismo , Liasas/química , Liasas/metabolismo , Mycobacterium/metabolismo , Mycobacterium smegmatis/química , Mycobacterium smegmatis/enzimología , Modelos Moleculares , Estructura Cuaternaria de Proteína , Estructura Terciaria de Proteína
2.
Nature ; 625(7993): 74-78, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-38110574

RESUMEN

Enzymes are recognized as exceptional catalysts for achieving high stereoselectivities1-3, but their ability to control the reactivity and stereoinduction of free radicals lags behind that of chemical catalysts4. Thiamine diphosphate (ThDP)-dependent enzymes5 are well-characterized systems that inspired the development of N-heterocyclic carbenes (NHCs)6-8 but have not yet been proved viable in asymmetric radical transformations. There is a lack of a biocompatible and general radical-generation mechanism, as nature prefers to avoid radicals that may be harmful to biological systems9. Here we repurpose a ThDP-dependent lyase as a stereoselective radical acyl transferase (RAT) through protein engineering and combination with organophotoredox catalysis10. Enzyme-bound ThDP-derived ketyl radicals are selectively generated through single-electron oxidation by a photoexcited organic dye and then cross-coupled with prochiral alkyl radicals with high enantioselectivity. Diverse chiral ketones are prepared from aldehydes and redox-active esters (35 examples, up to 97% enantiomeric excess (e.e.)) by this method. Mechanistic studies reveal that this previously elusive dual-enzyme catalysis/photocatalysis directs radicals with the unique ThDP cofactor and evolvable active site. This work not only expands the repertoire of biocatalysis but also provides a unique strategy for controlling radicals with enzymes, complementing existing chemical tools.


Asunto(s)
Aciltransferasas , Biocatálisis , Luz , Liasas , Acilación , Aciltransferasas/química , Aciltransferasas/metabolismo , Aldehídos/metabolismo , Biocatálisis/efectos de la radiación , Dominio Catalítico , Radicales Libres/metabolismo , Cetonas/metabolismo , Liasas/química , Liasas/metabolismo , Oxidación-Reducción , Ingeniería de Proteínas , Estereoisomerismo , Tiamina Pirofosfato/metabolismo
3.
Structure ; 30(4): 534-536, 2022 04 07.
Artículo en Inglés | MEDLINE | ID: mdl-35395194

RESUMEN

Attachment of bilins to phycobiliproteins is performed by dedicated lyases. In this issue of Structure, Kumarapperuma et al., 2022 present the structure of an E/F type lyase-isomerase that identifies the correct biological interface between active domains, suggesting that a previous E/F lyase misidentified the heterodimer structure from the crystal lattice.


Asunto(s)
Liasas , Pigmentos Biliares , Liasas/química , Ficobiliproteínas/química
4.
Structure ; 30(4): 564-574.e3, 2022 04 07.
Artículo en Inglés | MEDLINE | ID: mdl-35148828

RESUMEN

Chromophore attachment of the light-harvesting apparatus represents one of the most important post-translational modifications in photosynthetic cyanobacteria. Extensive pigment diversity of cyanobacteria critically depends on bilin lyases that covalently attach chemically distinct chromophores to phycobiliproteins. However, how bilin lyases catalyze bilin ligation reactions and how some lyases acquire additional isomerase abilities remain elusive at the molecular level. Here, we report the crystal structure of a representative bilin lyase-isomerase MpeQ. This structure has revealed a "question-mark" protein architecture that unambiguously establishes the active site conserved among the E/F-type bilin lyases. Based on structural, mutational, and modeling data, we demonstrate that stereoselectivity of the active site plays a critical role in conferring the isomerase activity of MpeQ. We further advance a tyrosine-mediated reaction scheme unifying different types of bilin lyases. These results suggest that lyases and isomerase actions of bilin lyases arise from two coupled molecular events of distinct origin.


Asunto(s)
Cianobacterias , Liasas , Pigmentos Biliares/metabolismo , Cianobacterias/metabolismo , Isomerasas/genética , Isomerasas/metabolismo , Liasas/química , Liasas/genética , Liasas/metabolismo , Ficobiliproteínas/metabolismo
5.
Mar Drugs ; 20(1)2022 Jan 12.
Artículo en Inglés | MEDLINE | ID: mdl-35049921

RESUMEN

As a low molecular weight alginate, alginate oligosaccharides (AOS) exhibit improved water solubility, better bioavailability, and comprehensive health benefits. In addition, their biocompatibility, biodegradability, non-toxicity, non-immunogenicity, and gelling capability make them an excellent biomaterial with a dual curative effect when applied in a drug delivery system. In this paper, a novel alginate lyase, Algpt, was cloned and characterized from a marine bacterium, Paenibacillus sp. LJ-23. The purified enzyme was composed of 387 amino acid residues, and had a molecular weight of 42.8 kDa. The optimal pH of Algpt was 7.0 and the optimal temperature was 45 °C. The analysis of the conserved domain and the prediction of the three-dimensional structure indicated that Algpt was a novel alginate lyase. The dominant degradation products of Algpt on alginate were AOS dimer to octamer, depending on the incubation time, which demonstrated that Algpt degraded alginate in an endolytic manner. In addition, Algpt was a salt-independent and thermo-tolerant alginate lyase. Its high stability and wide adaptability endow Algpt with great application potential for the efficient preparation of AOS with different sizes and AOS-based products.


Asunto(s)
Alginatos/química , Liasas/química , Paenibacillus/genética , Animales , Organismos Acuáticos , China , Clonación Molecular , Sistemas de Liberación de Medicamentos
6.
Insect Biochem Mol Biol ; 142: 103722, 2022 03.
Artículo en Inglés | MEDLINE | ID: mdl-35063675

RESUMEN

Tetranychus urticae is a polyphagous spider mite that can feed on more than 1100 plant species including cyanogenic plants. The herbivore genome contains a horizontally acquired gene tetur10g01570 (TuCAS) that was previously shown to participate in cyanide detoxification. To understand the structure and determine the function of TuCAS in T. urticae, crystal structures of the protein with lysine conjugated pyridoxal phosphate (PLP) were determined. These structures reveal extensive TuCAS homology with the ß-substituted alanine synthase family, and they show that this enzyme utilizes a similar chemical mechanism involving a stable α-aminoacrylate intermediate in ß-cyanoalanine and cysteine synthesis. We demonstrate that TuCAS is more efficient in the synthesis of ß-cyanoalanine, which is a product of the detoxification reaction between cysteine and cyanide, than in the biosynthesis of cysteine. Also, the enzyme carries additional enzymatic activities that were not previously described. We show that TuCAS can detoxify cyanide using O-acetyl-L-serine as a substrate, leading to the direct formation of ß-cyanoalanine. Moreover, it catalyzes the reaction between the TuCAS-bound α-aminoacrylate intermediate and aromatic compounds with a thiol group. In addition, we have tested several compounds as TuCAS inhibitors. Overall, this study identifies additional functions for TuCAS and provides new molecular insight into the xenobiotic metabolism of T. urticae.


Asunto(s)
Liasas , Tetranychidae , Animales , Cianuros/metabolismo , Cisteína , Liasas/química , Liasas/genética , Liasas/metabolismo , Plantas/metabolismo , Tetranychidae/metabolismo
7.
J Biol Chem ; 298(1): 101522, 2022 01.
Artículo en Inglés | MEDLINE | ID: mdl-34952003

RESUMEN

Actinobacterial 2-hydroxyacyl-CoA lyase reversibly catalyzes the thiamine diphosphate-dependent cleavage of 2-hydroxyisobutyryl-CoA to formyl-CoA and acetone. This enzyme has great potential for use in synthetic one-carbon assimilation pathways for sustainable production of chemicals, but lacks details of substrate binding and reaction mechanism for biochemical reengineering. We determined crystal structures of the tetrameric enzyme in the closed conformation with bound substrate, covalent postcleavage intermediate, and products, shedding light on active site architecture and substrate interactions. Together with molecular dynamics simulations of the covalent precleavage complex, the complete catalytic cycle is structurally portrayed, revealing a proton transfer from the substrate acyl Cß hydroxyl to residue E493 that returns it subsequently to the postcleavage Cα-carbanion intermediate. Kinetic parameters obtained for mutants E493A, E493Q, and E493K confirm the catalytic role of E493 in the WT enzyme. However, the 10- and 50-fold reduction in lyase activity in the E493A and E493Q mutants, respectively, compared with WT suggests that water molecules may contribute to proton transfer. The putative catalytic glutamate is located on a short α-helix close to the active site. This structural feature appears to be conserved in related lyases, such as human 2-hydroxyacyl-CoA lyase 2. Interestingly, a unique feature of the actinobacterial 2-hydroxyacyl-CoA lyase is a large C-terminal lid domain that, together with active site residues L127 and I492, restricts substrate size to ≤C5 2-hydroxyacyl residues. These details about the catalytic mechanism and determinants of substrate specificity pave the ground for designing tailored catalysts for acyloin condensations for one-carbon and short-chain substrates in biotechnological applications.


Asunto(s)
Acilcoenzima A , Liasas , Acilcoenzima A/química , Acilcoenzima A/metabolismo , Carbono , Catálisis , Dominio Catalítico , Cristalografía por Rayos X , Humanos , Liasas/química , Liasas/metabolismo , Protones , Relación Estructura-Actividad , Especificidad por Sustrato
8.
J Microbiol ; 59(11): 1002-1009, 2021 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-34613607

RESUMEN

The increasing prevalence of foodborne diseases caused by Escherichia coli O157:H7 as well as its ability to form biofilms poses major threats to public health worldwide. With increasing concerns about the limitations of current disinfectant treatments, phage-derived depolymerases may be used as promising biocontrol agents. Therefore, in this study, the characterization, purification, and application of a novel phage depolymerase, Dpo10, specifically targeting the lipopolysaccharides of E. coli O157, was performed. Dpo10, with a molecular mass of 98 kDa, was predicted to possess pectate lyase activity via genome analysis and considered to act as a receptor-binding protein of the phage. We confirmed that the purified Dpo10 showed O-polysaccharide degrading activity only for the E. coli O157 strains by observing its opaque halo. Dpo10 maintained stable enzymatic activities across a wide range of temperature conditions under 55°C and mild basic pH. Notably, Dpo10 did not inhibit bacterial growth but significantly increased the complement-mediated serum lysis of E. coli O157 by degrading its O-polysaccharides. Moreover, Dpo10 inhibited the biofilm formation against E. coli O157 on abiotic polystyrene by 8-fold and stainless steel by 2.56 log CFU/coupon. This inhibition was visually confirmed via fieldemission scanning electron microscopy. Therefore, the novel depolymerase from E. coli siphophage exhibits specific binding and lytic activities on the lipopolysaccharide of E. coli O157 and may be used as a promising anti-biofilm agent against the E. coli O157:H7 strain.


Asunto(s)
Biopelículas , Colifagos/enzimología , Escherichia coli O157/virología , Liasas/metabolismo , Colifagos/química , Colifagos/genética , Escherichia coli O157/fisiología , Liasas/química , Liasas/genética , Acero Inoxidable/análisis , Proteínas Virales/química , Proteínas Virales/genética , Proteínas Virales/metabolismo
9.
Bioorg Chem ; 116: 105322, 2021 11.
Artículo en Inglés | MEDLINE | ID: mdl-34488127

RESUMEN

Bacillary dysentery is a common foodborne disease with an exaggerated mortality rate because of Shigella infection. With the increasing severity of Shigella infection, lyase has been considered as the most promising alternative to antimicrobial agents, owing to the emergence of resistant bacteria and the difficulty in disrupting and eliminating bacterial biofilms. In this study, we cloned and characterised HolSSE1 and LysSSE1, holin, and lysozyme from the S. dysenteriae phage SSE1 with extended bacterial host range against common gram-negative and gram-positive bacteria. In addition, the efficacy of HolSSE1 and LysSSE1 in removing bacterial biofilms was observed on polystyrene surfaces. Moreover, synergistic bacteriostasis was observed when they were used together. Alignment and structural model analysis showed that both HolSSE1 and LysSSE1 are T4 phage proteins that have not yet been identified. Therefore, HolSSE1 and LysSSE1 can be promising biocontrol agents for the prevention and treatment of various pathogenic infections.


Asunto(s)
Antibacterianos/farmacología , Liasas/metabolismo , Shigella dysenteriae/efectos de los fármacos , Antibacterianos/síntesis química , Antibacterianos/química , Biopelículas/efectos de los fármacos , Relación Dosis-Respuesta a Droga , Liasas/química , Pruebas de Sensibilidad Microbiana , Estructura Molecular , Relación Estructura-Actividad
10.
Nat Commun ; 12(1): 3487, 2021 06 09.
Artículo en Inglés | MEDLINE | ID: mdl-34108468

RESUMEN

Fusicoccadiene synthase from Phomopsis amygdali (PaFS) is a unique bifunctional terpenoid synthase that catalyzes the first two steps in the biosynthesis of the diterpene glycoside Fusicoccin A, a mediator of 14-3-3 protein interactions. The prenyltransferase domain of PaFS generates geranylgeranyl diphosphate, which the cyclase domain then utilizes to generate fusicoccadiene, the tricyclic hydrocarbon skeleton of Fusicoccin A. Here, we use cryo-electron microscopy to show that the structure of full-length PaFS consists of a central octameric core of prenyltransferase domains, with the eight cyclase domains radiating outward via flexible linker segments in variable splayed-out positions. Cryo-electron microscopy and chemical crosslinking experiments additionally show that compact conformations can be achieved in which cyclase domains are more closely associated with the prenyltransferase core. This structural analysis provides a framework for understanding substrate channeling, since most of the geranylgeranyl diphosphate generated by the prenyltransferase domains remains on the enzyme for cyclization to form fusicoccadiene.


Asunto(s)
Transferasas Alquil y Aril/química , Diterpenos/metabolismo , Proteínas Fúngicas/química , Transferasas Alquil y Aril/metabolismo , Ascomicetos/química , Ascomicetos/enzimología , Catálisis , Dominio Catalítico , Microscopía por Crioelectrón , Ciclización , Dimetilaliltranstransferasa/química , Dimetilaliltranstransferasa/metabolismo , Proteínas Fúngicas/metabolismo , Glicósidos/biosíntesis , Liasas/química , Liasas/metabolismo , Enzimas Multifuncionales , Fosfatos de Poliisoprenilo/metabolismo , Conformación Proteica
11.
Nat Chem Biol ; 17(7): 800-805, 2021 07.
Artículo en Inglés | MEDLINE | ID: mdl-33958791

RESUMEN

The covalent attachment of one or multiple heme cofactors to cytochrome c protein chains enables cytochrome c proteins to be used in electron transfer and redox catalysis in extracytoplasmic environments. A dedicated heme maturation machinery, whose core component is a heme lyase, scans nascent peptides after Sec-dependent translocation for CXnCH-binding motifs. Here we report the three-dimensional (3D) structure of the heme lyase CcmF, a 643-amino acid integral membrane protein, from Thermus thermophilus. CcmF contains a heme b cofactor at the bottom of a large cavity that opens toward the extracellular side to receive heme groups from the heme chaperone CcmE for cytochrome maturation. A surface groove on CcmF may guide the extended apoprotein to heme attachment at or near a loop containing the functionally essential WXWD motif, which is situated above the putative cofactor binding pocket. The structure suggests heme delivery from within the membrane, redefining the role of the chaperone CcmE.


Asunto(s)
Membrana Celular/metabolismo , Liasas/metabolismo , Membrana Celular/química , Liasas/química , Thermus thermophilus/enzimología
12.
mBio ; 12(3)2021 05 04.
Artículo en Inglés | MEDLINE | ID: mdl-33947751

RESUMEN

In eukaryotes, heme attachment through two thioether bonds to mitochondrial cytochromes c and c1 is catalyzed by either multisubunit cytochrome c maturation system I or holocytochrome c synthetase (HCCS). The former was inherited from the alphaproteobacterial progenitor of mitochondria; the latter is a eukaryotic innovation for which prokaryotic ancestry is not evident. HCCS provides one of a few exemplars of de novo protein innovation in eukaryotes, but structure-function insight of HCCS is limited. Uniquely, euglenozoan protists, which include medically relevant kinetoplastids Trypanosoma and Leishmania parasites, attach heme to mitochondrial c-type cytochromes by a single thioether linkage. Yet the mechanism is unknown, as genes encoding proteins with detectable similarity to any proteins involved in cytochrome c maturation in other taxa are absent. Here, a bioinformatics search for proteins conserved in all hemoprotein-containing kinetoplastids identified kinetoplastid cytochrome c synthetase (KCCS), which we reveal as essential and mitochondrial and catalyzes heme attachment to trypanosome cytochrome c KCCS has no sequence identity to other proteins, apart from a slight resemblance within four short motifs suggesting relatedness to HCCS. Thus, KCCS provides a novel resource for studying eukaryotic cytochrome c maturation, possibly with wider relevance, since mutations in human HCCS leads to disease. Moreover, many examples of mitochondrial biochemistry are different in euglenozoans compared to many other eukaryotes; identification of KCCS thus provides another exemplar of extreme, unusual mitochondrial biochemistry in an evolutionarily divergent group of protists.IMPORTANCE Cytochromes c are essential proteins for respiratory and photosynthetic electron transfer. They are posttranslationally modified by covalent attachment of a heme cofactor. Kinetoplastids include important tropical disease-causing parasites; many aspects of their biology differ from other organisms, including their mammalian or plant hosts. Uniquely, kinetoplastids produce cytochromes c with a type of heme attachment not seen elsewhere in nature and were the only cytochrome c-bearing taxa without evidence of protein machinery to attach heme to the apocytochrome. Using bioinformatics, biochemistry, and molecular genetics, we report how kinetoplastids make their cytochromes c Unexpectedly, they use a highly diverged version of an enzyme used for heme-protein attachment in many eukaryotes. Mutations in the human enzyme lead to genetic disease. Identification of kinetoplastid cytochrome c synthetase, thus, solves an evolutionary unknown, provides a possible target for antiparasite drug development, and an unanticipated resource for studying the mechanistic basis of a human genetic disease.


Asunto(s)
Citocromos c/genética , Citocromos c/fisiología , Eucariontes/fisiología , Biología Computacional , Leishmania mexicana/genética , Leishmania mexicana/fisiología , Liasas/química , Liasas/genética , Liasas/metabolismo , Trypanosoma brucei brucei/genética , Trypanosoma brucei brucei/fisiología
13.
Elife ; 102021 05 11.
Artículo en Inglés | MEDLINE | ID: mdl-33973521

RESUMEN

Cytochromes c are ubiquitous heme proteins in mitochondria and bacteria, all possessing a CXXCH (CysXxxXxxCysHis) motif with covalently attached heme. We describe the first in vitro reconstitution of cytochrome c biogenesis using purified mitochondrial (HCCS) and bacterial (CcsBA) cytochrome c synthases. We employ apocytochrome c and peptide analogs containing CXXCH as substrates, examining recognition determinants, thioether attachment, and subsequent release and folding of cytochrome c. Peptide analogs reveal very different recognition requirements between HCCS and CcsBA. For HCCS, a minimal 16-mer peptide is required, comprised of CXXCH and adjacent alpha helix 1, yet neither thiol is critical for recognition. For bacterial CcsBA, both thiols and histidine are required, but not alpha helix 1. Heme attached peptide analogs are not released from the HCCS active site; thus, folding is important in the release mechanism. Peptide analogs behave as inhibitors of cytochrome c biogenesis, paving the way for targeted control.


From tiny bacteria to the tallest trees, most life on Earth carries a protein called cytochrome c, which helps to create the energy that powers up cells. Cytochrome c does so thanks to its heme, a molecule that enables the chemical reactions required for the energy-creating process. Despite both relying on cytochrome c, animals and bacteria differ in the enzyme they use to attach the heme to the cytochrome. Spotting variations in how this 'cytochrome c synthase' works would help to find compounds that deactivate the enzyme in bacteria, but not in humans. However, studying cytochrome c synthase in living cells is challenging. To bypass this issue, Sutherland, Mendez, Babbitt et al. successfully reconstituted cytochrome c synthases from humans and bacteria in test tubes. This allowed them to examine in detail which structures the enzymes recognize to spot where to attach the heme onto their target. The experiments revealed that human and bacterial synthases actually rely on different parts of the cytochrome c to orient themselves. Different short compounds could also block either the human or bacterial enzyme. Variations between human and bacterial cytochrome c synthase could lead to new antibiotics which deactivate the cytochrome and kill bacteria while sparing patients. The next step is to identify molecules that specifically interfere with cytochrome c synthase in bacteria, and could be tested in clinical trials.


Asunto(s)
Bacterias/enzimología , Citocromos c/metabolismo , Liasas/metabolismo , Mitocondrias/metabolismo , Dominio Catalítico , Escherichia coli/metabolismo , Hemo/metabolismo , Humanos , Técnicas In Vitro , Liasas/química , Péptidos/química , Especificidad por Sustrato
14.
Plant Cell ; 33(2): 306-321, 2021 04 17.
Artículo en Inglés | MEDLINE | ID: mdl-33793793

RESUMEN

Unisexual flowers provide a useful system for studying plant sex determination. In cucumber (Cucumis sativus L.), three major Mendelian loci control unisexual flower development, Female (F), androecious [a; 1-aminocyclopropane-1-carboxylate {ACC} synthase 11, acs11], and Monoecious (M; ACS2), referred to here as the Female, Androecious, Monoecious (FAM) model, in combination with two genes, gynoecious (g, the WIP family C2H2 zinc finger transcription factor gene WIP1) and the ethylene biosynthetic gene ACC oxidase 2 (ACO2). The F locus, conferring gynoecy and the potential for increasing fruit yield, is defined by a 30.2-kb tandem duplication containing three genes. However, the gene that determines the Female phenotype, and its mechanism, remains unknown. Here, we created a set of mutants and revealed that ACS1G is responsible for gynoecy conferred by the F locus. The duplication resulted in ACS1G acquiring a new promoter and expression pattern; in plants carrying the F locus duplication, ACS1G is expressed early in floral bud development, where it functions with ACO2 to generate an ethylene burst. The resulting ethylene represses WIP1 and activates ACS2 to initiate gynoecy. This early ACS1G expression bypasses the need for ACS11 to produce ethylene, thereby establishing a dominant pathway for female floral development. Based on these findings, we propose a model for how these ethylene biosynthesis genes cooperate to control unisexual flower development in cucumber.


Asunto(s)
Cucumis sativus/enzimología , Cucumis sativus/genética , Flores/enzimología , Flores/genética , Liasas/genética , Secuencia de Aminoácidos , Regulación de la Expresión Génica de las Plantas , Sitios Genéticos , Genoma de Planta , Genotipo , Glucuronidasa/metabolismo , Liasas/química , Fenotipo , Plantas Modificadas Genéticamente , ARN Mensajero/genética , ARN Mensajero/metabolismo
15.
Cell Chem Biol ; 28(9): 1333-1346.e7, 2021 09 16.
Artículo en Inglés | MEDLINE | ID: mdl-33773110

RESUMEN

Desulfonation of isethionate by the bacterial glycyl radical enzyme (GRE) isethionate sulfite-lyase (IslA) generates sulfite, a substrate for respiration that in turn produces the disease-associated metabolite hydrogen sulfide. Here, we present a 2.7 Å resolution X-ray structure of wild-type IslA from Bilophila wadsworthia with isethionate bound. In comparison with other GREs, alternate positioning of the active site ß strands allows for distinct residue positions to contribute to substrate binding. These structural differences, combined with sequence variations, create a highly tailored active site for the binding of the negatively charged isethionate substrate. Through the kinetic analysis of 14 IslA variants and computational analyses, we probe the mechanism by which radical chemistry is used for C-S bond cleavage. This work further elucidates the structural basis of chemistry within the GRE superfamily and will inform structure-based inhibitor design of IsIA and thus of microbial hydrogen sulfide production.


Asunto(s)
Carbono/metabolismo , Liasas/metabolismo , Azufre/metabolismo , Bilophila/enzimología , Carbono/química , Cristalografía por Rayos X , Liasas/química , Modelos Moleculares , Azufre/química
16.
Biochimie ; 182: 166-176, 2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33444662

RESUMEN

Selenium is a vital micronutrient in many organisms. While traces are required for microbial utilization, excess amounts are toxic; thus, selenium can be regarded as a biological double-edged sword. Selenium is chemically similar to the essential element sulfur, but curiously, evolution has selected the former over the latter for a subset of oxidoreductases. Enzymes involved in sulfur metabolism are less discriminate in terms of preventing selenium incorporation; however, its specific incorporation into selenoproteins reveals a highly discriminate process that is not completely understood. We have identified SclA, a NifS-like protein in the nosocomial pathogen, Enterococcus faecalis, and characterized its enzymatic activity and specificity for l-selenocysteine over l-cysteine. It is known that Asp-146 is required for selenocysteine specificity in the human selenocysteine lyase. Thus, using computational biology, we compared the bacterial and mammalian enzymes and identified His-100, an Asp-146 ortholog in SclA, and generated site-directed mutants in order to study the residue's potential role in the l-selenocysteine discrimination mechanism. The proteins were overexpressed, purified, and characterized for their biochemical properties. All mutants exhibited varying Michaelis-Menten behavior towards l-selenocysteine, but His-100 was not found to be essential for this activity. Additionally, l-cysteine acted as a competitive inhibitor of all enzymes with higher affinity than l-selenocysteine. Finally, we discovered that SclA exhibited low activity with l-cysteine as a poor substrate regardless of mutations. We conclude that His-100 is not required for l-selenocysteine specificity, underscoring the inherent differences in discriminatory mechanisms between bacterial NifS-like proteins and mammalian selenocysteine lyases.


Asunto(s)
Proteínas Bacterianas/química , Enterococcus faecalis/enzimología , Liasas/química , Selenio/química , Azufre/química , Proteínas Bacterianas/metabolismo , Liasas/metabolismo , Selenio/metabolismo , Especificidad por Sustrato , Azufre/metabolismo
17.
J Am Chem Soc ; 143(2): 785-797, 2021 01 20.
Artículo en Inglés | MEDLINE | ID: mdl-33395523

RESUMEN

We report here on the salient role of protein mobility in accessing conformational landscapes that enable efficient enzyme catalysis. We are focused on yeast enolase, a highly conserved lyase with a TIM barrel domain and catalytic loop, as part of a larger study of the relationship of site selective protein motions to chemical reactivity within superfamilies. Enthalpically hindered variants were developed by replacement of a conserved hydrophobic side chain (Leu 343) with smaller side chains. Leu343 is proximal to the active site base in enolase, and comparative pH rate profiles for the valine and alanine variants indicate a role for side chain hydrophobicity in tuning the pKa of the catalytic base. However, the magnitude of a substrate deuterium isotope effect is almost identical for wild-type (WT) and Leu343Ala, supporting an unchanged rate-determining proton abstraction step. The introduced hydrophobic side chains at position 343 lead to a discontinuous break in both activity and activation energy as a function of side chain volume. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments were performed as a function of time and temperature for WT and Leu343Ala, and provide a spatially resolved map of changes in protein flexibility following mutation. Impacts on protein flexibility are localized to specific networks that arise at the protein-solvent interface and terminate in a loop that has been shown by X-ray crystallography to close over the active site. These interrelated effects are discussed in the context of long-range, solvent-accessible and thermally activated networks that play key roles in tuning the precise distances and interactions among reactants.


Asunto(s)
Liasas/metabolismo , Temperatura , Agua/metabolismo , Sitios de Unión , Biocatálisis , Cinética , Liasas/química , Liasas/genética , Modelos Moleculares , Mutación , Saccharomyces cerevisiae/enzimología , Agua/química
18.
Proteins ; 89(4): 462-467, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33210347

RESUMEN

Cobaltochelatase in aerobic cobalamin biosynthesis is a complex composed of three subunits. The large subunit CobN is a 140-kDa protein and is homologous to the ChlH subunit of magnesium chelatase. Previously we have reported the 2.5-Å structure of a cyanobacterial ChlH. Here we present the 1.8-Å structure of CobN from Mycobacterium tuberculosis. The overall structure of CobN and ChlH is similar, but significant difference occurs in the head domain. Structural comparison of domains between the two proteins unravels candidate regions for substrate binding and helps to locate a triad of residues that may be essential for metal ion binding.


Asunto(s)
Proteínas Bacterianas , Liasas , Mycobacterium tuberculosis/enzimología , Proteínas Bacterianas/química , Proteínas Bacterianas/ultraestructura , Cristalografía , Liasas/química , Liasas/ultraestructura , Modelos Moleculares , Dominios Proteicos
19.
Nat Commun ; 11(1): 4808, 2020 09 23.
Artículo en Inglés | MEDLINE | ID: mdl-32968058

RESUMEN

The creation of artificial enzymes is a key objective of computational protein design. Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve activity. Here, we use room-temperature X-ray crystallography to study changes in the conformational ensemble during evolution of the designed Kemp eliminase HG3 (kcat/KM 146 M-1s-1). We observe that catalytic residues are increasingly rigidified, the active site becomes better pre-organized, and its entrance is widened. Based on these observations, we engineer HG4, an efficient biocatalyst (kcat/KM 103,000 M-1s-1) containing key first and second-shell mutations found during evolution. HG4 structures reveal that its active site is pre-organized and rigidified for efficient catalysis. Our results show how directed evolution circumvents challenges inherent to enzyme design by shifting conformational ensembles to favor catalytically-productive sub-states, and suggest improvements to the design methodology that incorporate ensemble modeling of crystallographic data.


Asunto(s)
Simulación por Computador , Evolución Molecular Dirigida/métodos , Enzimas/química , Evolución Química , Liasas/química , Catálisis , Dominio Catalítico , Cristalografía por Rayos X , Estabilidad de Enzimas , Enzimas/genética , Enzimas/metabolismo , Cinética , Liasas/genética , Liasas/metabolismo , Simulación de Dinámica Molecular , Mutación , Conformación Proteica , Ingeniería de Proteínas
20.
Protein J ; 39(5): 554-562, 2020 10.
Artículo en Inglés | MEDLINE | ID: mdl-32737834

RESUMEN

Biosynthesis of chlorophyll involves several enzymatic reactions of which many are shared with the heme biosynthesis pathway. Magnesium chelatase is the first specific enzyme in the chlorophyll pathway. It catalyzes the formation of Mg-protoporphyrin IX from the insertion of Mg2+ into protoporphyrin IX. The enzyme consists of three subunits encoded by three genes. The three genes are named Xantha-h, Xantha-g and Xantha-f in barley (Hordeum vulgare L.). The products of the genes have a molecular weight of 38, 78 and 148 kDa, respectively, as mature proteins in the chloroplast. Most studies on magnesium chelatase enzymes have been performed using recombinant proteins of Rhodobacter capsulatus, Synechocystis sp. PCC6803 and Thermosynechococcus elongatus, which are photosynthetic bacteria. In the present study we established a recombinant expression system for barley magnesium chelatase with the long-term goal to obtain structural information of this enigmatic enzyme complex from a higher plant. The genes Xantha-h, -g and -f were cloned in plasmid pET15b, which allowed the production of the three subunits as His-tagged proteins in Escherichia coli BL21(DE3)pLysS. The purified subunits stimulated magnesium chelatase activity of barley plastid extracts and produced activity in assays with only recombinant proteins. In preparation for future structural analyses of the barley magnesium chelatase, stability tests were performed on the subunits and activity assays were screened to find an optimal buffer system and pH.


Asunto(s)
Hordeum , Liasas , Proteínas de Plantas , Hordeum/enzimología , Hordeum/genética , Liasas/biosíntesis , Liasas/química , Liasas/genética , Liasas/aislamiento & purificación , Proteínas de Plantas/biosíntesis , Proteínas de Plantas/química , Proteínas de Plantas/genética , Proteínas de Plantas/aislamiento & purificación , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/aislamiento & purificación
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