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1.
Nat Commun ; 15(1): 2740, 2024 Mar 28.
Artículo en Inglés | MEDLINE | ID: mdl-38548733

RESUMEN

Photoreceptor proteins utilise chromophores to sense light and trigger a biological response. The discovery that adenosylcobalamin (or coenzyme B12) can act as a light-sensing chromophore heralded a new field of B12-photobiology. Although microbial genome analysis indicates that photoactive B12-binding domains form part of more complex protein architectures, regulating a range of molecular-cellular functions in response to light, experimental evidence is lacking. Here we identify and characterise a sub-family of multi-centre photoreceptors, termed photocobilins, that use B12 and biliverdin (BV) to sense light across the visible spectrum. Crystal structures reveal close juxtaposition of the B12 and BV chromophores, an arrangement that facilitates optical coupling. Light-triggered conversion of the B12 affects quaternary structure, in turn leading to light-activation of associated enzyme domains. The apparent widespread nature of photocobilins implies involvement in light regulation of a wider array of biochemical processes, and thus expands the scope for B12 photobiology. Their characterisation provides inspiration for the design of broad-spectrum optogenetic tools and next generation bio-photocatalysts.


Asunto(s)
Pigmentos Biliares , Fotorreceptores Microbianos , Fotoquímica , Biliverdina , Proteínas Bacterianas/metabolismo , Fotorreceptores Microbianos/química , Luz
2.
Biomol NMR Assign ; 18(1): 33-44, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38472728

RESUMEN

The backbone 1H, 13C and 15N resonance assignment of Ubiquitin Specific Protease 7 catalytic domain (residues 208-554) was performed in its complex with a small molecule ligand and in its apo form as a reference. The amide 1H-15N signal intensities were boosted by an amide hydrogen exchange protocol, where expressed 2H, 13C, 15N-labeled protein was unfolded and re-folded to ensure exchange of amide deuterons to protons. The resonance assignments were used to determine chemical shift perturbations on ligand binding, which are consistent with the binding site observed by crystallography.


Asunto(s)
Dominio Catalítico , Resonancia Magnética Nuclear Biomolecular , Ligandos , Humanos , Isótopos de Nitrógeno
3.
J Am Chem Soc ; 144(47): 21648-21657, 2022 11 30.
Artículo en Inglés | MEDLINE | ID: mdl-36379007

RESUMEN

Understanding and controlling peptide foldamer conformation in phospholipid bilayers is a key step toward their use as molecular information relays in membranes. To this end, a new 19F "reporter" tag has been developed and attached to dynamic peptide foldamers. The (R)-1-(trifluoromethyl)ethylamido ((R)-TFEA) reporter was attached to the C-terminus of α-amino-iso-butyric acid (Aib) foldamers. Crystallography confirmed that the foldamers adopted 310 helical conformations. Variable temperature (VT) NMR spectroscopy in organic solvents showed that the (R)-TFEA reporter had an intrinsic preference for P helicity, but the overall screw-sense was dominated by a chiral "controller" at the N-terminus. The 19F NMR chemical shift of the CF3 resonance was correlated with the ability of different N-terminal groups to induce either an M or a P helix in solution. In bilayers, a similar correlation was found. Solution 19F NMR spectroscopy on small unilamellar vesicle (SUV) suspensions containing the same family of (R)-TFEA-labeled foldamers showed broadened but resolvable 19F resonances, with each chemical shift mirroring their relative positions in organic solvents. These studies showed that foldamer conformational preferences are the same in phospholipid bilayers as in organic solvents and also revealed that phospholipid chirality has little influence on conformation.


Asunto(s)
Aminoácidos , Péptidos , Modelos Moleculares , Espectroscopía de Resonancia Magnética , Péptidos/química , Aminoácidos/química , Fosfolípidos/química , Solventes
4.
ACS Catal ; 12(5): 3149-3164, 2022 Mar 04.
Artículo en Inglés | MEDLINE | ID: mdl-35692864

RESUMEN

Understanding the factors that underpin the enormous catalytic proficiencies of enzymes is fundamental to catalysis and enzyme design. Enzymes are, in part, able to achieve high catalytic proficiencies by utilizing the binding energy derived from nonreacting portions of the substrate. In particular, enzymes with substrates containing a nonreacting phosphodianion group coordinated in a distal site have been suggested to exploit this binding energy primarily to facilitate a conformational change from an open inactive form to a closed active form, rather than to either induce ground state destabilization or stabilize the transition state. However, detailed structural evidence for the model is limited. Here, we use ß-phosphoglucomutase (ßPGM) to investigate the relationship between binding a phosphodianion group in a distal site, the adoption of a closed enzyme form, and catalytic proficiency. ßPGM catalyzes the isomerization of ß-glucose 1-phosphate to glucose 6-phosphate via phosphoryl transfer reactions in the proximal site, while coordinating a phosphodianion group of the substrate(s) in a distal site. ßPGM has one of the largest catalytic proficiencies measured and undergoes significant domain closure during its catalytic cycle. We find that side chain substitution at the distal site results in decreased substrate binding that destabilizes the closed active form but is not sufficient to preclude the adoption of a fully closed, near-transition state conformation. Furthermore, we reveal that binding of a phosphodianion group in the distal site stimulates domain closure even in the absence of a transferring phosphoryl group in the proximal site, explaining the previously reported ß-glucose 1-phosphate inhibition. Finally, our results support a trend whereby enzymes with high catalytic proficiencies involving phosphorylated substrates exhibit a greater requirement to stabilize the closed active form.

5.
Nucleic Acids Res ; 50(8): 4732-4754, 2022 05 06.
Artículo en Inglés | MEDLINE | ID: mdl-35420136

RESUMEN

SUMOylation is critical for numerous cellular signalling pathways, including the maintenance of genome integrity via the repair of DNA double-strand breaks (DSBs). If misrepaired, DSBs can lead to cancer, neurodegeneration, immunodeficiency and premature ageing. Using systematic human proteome microarray screening combined with widely applicable carbene footprinting, genetic code expansion and high-resolution structural profiling, we define two non-conventional and topology-selective SUMO2-binding regions on XRCC4, a DNA repair protein important for DSB repair by non-homologous end-joining (NHEJ). Mechanistically, the interaction of SUMO2 and XRCC4 is incompatible with XRCC4 binding to three other proteins important for NHEJ-mediated DSB repair. These findings are consistent with SUMO2 forming a redundant NHEJ layer with the potential to regulate different NHEJ complexes at distinct levels including, but not limited to, XRCC4 interactions with XLF, LIG4 and IFFO1. Regulation of NHEJ is not only relevant for carcinogenesis, but also for the design of precision anti-cancer medicines and the optimisation of CRISPR/Cas9-based gene editing. In addition to providing molecular insights into NHEJ, this work uncovers a conserved SUMO-binding module and provides a rich resource on direct SUMO binders exploitable towards uncovering SUMOylation pathways in a wide array of cellular processes.


Asunto(s)
Reparación del ADN por Unión de Extremidades , Reparación del ADN , Roturas del ADN de Doble Cadena , Enzimas Reparadoras del ADN/metabolismo , Humanos , Análisis por Micromatrices , Unión Proteica , Proteínas Modificadoras Pequeñas Relacionadas con Ubiquitina , Sumoilación
6.
Biomol NMR Assign ; 15(2): 389-395, 2021 10.
Artículo en Inglés | MEDLINE | ID: mdl-34173222

RESUMEN

DNA double-strand breaks (DSBs) represent the most cytotoxic DNA lesions, as-if mis- or unrepaired-they can cause cell death or lead to genome instability, which in turn can cause cancer. DSBs are repaired by two major pathways termed homologous recombination and non-homologous end-joining (NHEJ). NHEJ is responsible for repairing the vast majority of DSBs arising in human cells. Defects in NHEJ factors are also associated with microcephaly, primordial dwarfism and immune deficiencies. One of the key proteins important for mediating NHEJ is XRCC4. XRCC4 is a dimer, with the dimer interface mediated by an extended coiled-coil. The N-terminal head domain forms a mixed alpha-beta globular structure. Numerous factors interact with the C-terminus of the coiled-coil domain, which is also associated with significant self-association between XRCC4 dimers. A range of construct lengths of human XRCC4 were expressed and purified, and the 1-164 variant had the best NMR properties, as judged by consistent linewidths, and chemical shift dispersion. In this work we report the 1H, 15 N and 13C backbone resonance assignments of human XRCC4 in the solution form of the 1-164 construct. Assignments were obtained by heteronuclear multidimensional NMR spectroscopy. In total, 156 of 161 assignable residues of XRCC4 were assigned to resonances in the TROSY spectrum, with an additional 11 resonances assigned to His-Tag residues. Prediction of solution secondary structure from a chemical shift analysis using the TALOS + webserver is in good agreement with the published X-ray crystal structures of this protein.


Asunto(s)
Reparación del ADN por Unión de Extremidades
7.
ACS Catal ; 11(5): 2865-2878, 2021 Mar 05.
Artículo en Inglés | MEDLINE | ID: mdl-33763291

RESUMEN

The UbiD family of reversible (de)carboxylases depends on the recently discovered prenylated-FMN (prFMN) cofactor for activity. The model enzyme ferulic acid decarboxylase (Fdc1) decarboxylates unsaturated aliphatic acids via a reversible 1,3-cycloaddition process. Protein engineering has extended the Fdc1 substrate range to include (hetero)aromatic acids, although catalytic rates remain poor. This raises the question how efficient decarboxylation of (hetero)aromatic acids is achieved by other UbiD family members. Here, we show that the Pseudomonas aeruginosa virulence attenuation factor PA0254/HudA is a pyrrole-2-carboxylic acid decarboxylase. The crystal structure of the enzyme in the presence of the reversible inhibitor imidazole reveals a covalent prFMN-imidazole adduct is formed. Substrate screening reveals HudA and selected active site variants can accept a modest range of heteroaromatic compounds, including thiophene-2-carboxylic acid. Together with computational studies, our data suggests prFMN covalent catalysis occurs via electrophilic aromatic substitution and links HudA activity with the inhibitory effects of pyrrole-2-carboxylic acid on P. aeruginosa quorum sensing.

8.
Nat Commun ; 11(1): 5538, 2020 11 02.
Artículo en Inglés | MEDLINE | ID: mdl-33139716

RESUMEN

Enzyme regulation is vital for metabolic adaptability in living systems. Fine control of enzyme activity is often delivered through post-translational mechanisms, such as allostery or allokairy. ß-phosphoglucomutase (ßPGM) from Lactococcus lactis is a phosphoryl transfer enzyme required for complete catabolism of trehalose and maltose, through the isomerisation of ß-glucose 1-phosphate to glucose 6-phosphate via ß-glucose 1,6-bisphosphate. Surprisingly for a gatekeeper of glycolysis, no fine control mechanism of ßPGM has yet been reported. Herein, we describe allomorphy, a post-translational control mechanism of enzyme activity. In ßPGM, isomerisation of the K145-P146 peptide bond results in the population of two conformers that have different activities owing to repositioning of the K145 sidechain. In vivo phosphorylating agents, such as fructose 1,6-bisphosphate, generate phosphorylated forms of both conformers, leading to a lag phase in activity until the more active phosphorylated conformer dominates. In contrast, the reaction intermediate ß-glucose 1,6-bisphosphate, whose concentration depends on the ß-glucose 1-phosphate concentration, couples the conformational switch and the phosphorylation step, resulting in the rapid generation of the more active phosphorylated conformer. In enabling different behaviours for different allomorphic activators, allomorphy allows an organism to maximise its responsiveness to environmental changes while minimising the diversion of valuable metabolites.


Asunto(s)
Fosfotransferasas (Fosfomutasas)/metabolismo , Procesamiento Proteico-Postraduccional , Regulación Alostérica , Sitio Alostérico , Cristalografía por Rayos X , Pruebas de Enzimas , Glucosa-6-Fosfato/análogos & derivados , Glucosa-6-Fosfato/metabolismo , Glucofosfatos/metabolismo , Glucólisis , Isomerismo , Cinética , Conformación Molecular , Fosforilación , Fosfotransferasas (Fosfomutasas)/genética , Fosfotransferasas (Fosfomutasas)/aislamiento & purificación , Fosfotransferasas (Fosfomutasas)/ultraestructura , Prolina/química , Dominios Proteicos , Espectroscopía de Protones por Resonancia Magnética , Proteínas Recombinantes/genética , Proteínas Recombinantes/aislamiento & purificación , Proteínas Recombinantes/metabolismo , Proteínas Recombinantes/ultraestructura
9.
Commun Biol ; 3(1): 402, 2020 07 29.
Artículo en Inglés | MEDLINE | ID: mdl-32728168

RESUMEN

Prion diseases, a group of incurable, lethal neurodegenerative disorders of mammals including humans, are caused by prions, assemblies of misfolded host prion protein (PrP). A single point mutation (G127V) in human PrP prevents prion disease, however the structural basis for its protective effect remains unknown. Here we show that the mutation alters and constrains the PrP backbone conformation preceding the PrP ß-sheet, stabilising PrP dimer interactions by increasing intermolecular hydrogen bonding. It also markedly changes the solution dynamics of the ß2-α2 loop, a region of PrP structure implicated in prion transmission and cross-species susceptibility. Both of these structural changes may affect access to protein conformers susceptible to prion formation and explain its profound effect on prion disease.


Asunto(s)
Enfermedades por Prión/genética , Proteínas Priónicas/genética , Priones/genética , Conformación Proteica , Animales , Humanos , Mutación Puntual/genética , Enfermedades por Prión/patología , Proteínas Priónicas/ultraestructura , Priones/ultraestructura , Conformación Proteica en Lámina beta/genética
10.
Structure ; 27(10): 1537-1546.e4, 2019 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-31402220

RESUMEN

Intrinsically disordered proteins (IDPs) underpin biological regulation and hence are highly desirable drug-development targets. NMR is normally the tool of choice for studying the conformational preferences of IDPs, but the association of regions with residual structure into partially collapsed states can lead to poor spectral quality. The bHLH-LZ domain of the oncoprotein Myc is an archetypal example of such behavior. To circumvent spectral limitations, we apply chemical denaturant titration (CDT)-NMR, which exploits the predictable manner in which chemical denaturants disrupt residual structure and the rapid exchange between conformers in IDP ensembles. The secondary structure propensities and tertiary interactions of Myc are determined for all bHLH-LZ residues, including those with poor NMR properties under native conditions. This reveals conformations that are not predictable using existing crystal structures. The CDT-NMR method also maps sites perturbed by the prototype Myc inhibitor, 10058-F4, to areas of residual structure.


Asunto(s)
Proteínas Proto-Oncogénicas c-myc/química , Proteínas Proto-Oncogénicas c-myc/metabolismo , Sitios de Unión , Secuencias Hélice-Asa-Hélice , Humanos , Modelos Moleculares , Resonancia Magnética Nuclear Biomolecular , Desnaturalización Proteica , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Tiazoles/farmacología
11.
ACS Catal ; 9(4): 2854-2865, 2019 Apr 05.
Artículo en Inglés | MEDLINE | ID: mdl-31057985

RESUMEN

The biological production of FDCA is of considerable value as a potential replacement for petrochemical-derived monomers such as terephthalate, used in polyethylene terephthalate (PET) plastics. HmfF belongs to an uncharacterized branch of the prenylated flavin (prFMN) dependent UbiD family of reversible (de)carboxylases and is proposed to convert 2,5-furandicarboxylic acid (FDCA) to furoic acid in vivo. We present a detailed characterization of HmfF and demonstrate that HmfF can catalyze furoic acid carboxylation at elevated CO2 levels in vitro. We report the crystal structure of a thermophilic HmfF from Pelotomaculum thermopropionicum, revealing that the active site located above the prFMN cofactor contains a furoic acid/FDCA binding site composed of residues H296-R304-R331 specific to the HmfF branch of UbiD enzymes. Variants of the latter are compromised in activity, while H296N alters the substrate preference to pyrrole compounds. Solution studies and crystal structure determination of an engineered dimeric form of the enzyme revealed an unexpected key role for a UbiD family wide conserved Leu residue in activity. The structural insights into substrate and cofactor binding provide a template for further exploitation of HmfF in the production of FDCA plastic precursors and improve our understanding of catalysis by members of the UbiD enzyme family.

12.
Methods Enzymol ; 620: 145-166, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31072485

RESUMEN

The incorporation of stable isotopes into proteins is beneficial or essential for a range of experiments, including NMR, neutron scattering and reflectometry, proteomic mass spectrometry, vibrational spectroscopy and "heavy" enzyme kinetic isotope effect (KIE) measurements. Here, we present detailed protocols for the stable isotopic labeling of pentaerythritol tetranitrate reductase (PETNR) via recombinant expression in E. coli. PETNR is an ene-reductase belonging to the Old Yellow Enzyme (OYE) family of flavoenzymes, and is regarded as a model system for studying hydride transfer reactions. Included is a discussion of how efficient back-exchange of amide protons in the protein core can be achieved and how the intrinsic flavin mononucleotide (FMN) cofactor can be exchanged, allowing the production of isotopologues with differentially labeled protein and cofactor. In addition to a thorough description of labeling strategies, we briefly exemplify how data analysis and interpretation of "heavy" enzyme KIEs can be performed.


Asunto(s)
Pruebas de Enzimas/métodos , Marcaje Isotópico/métodos , Oxidorreductasas/química , Dicroismo Circular , Escherichia coli/metabolismo , Mononucleótido de Flavina/metabolismo , Cinética , Isótopos de Nitrógeno/química , Oxidorreductasas/genética , Oxidorreductasas/metabolismo , Espectroscopía de Protones por Resonancia Magnética , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo
13.
ACS Catal ; 9(5): 4394-4401, 2019 May 03.
Artículo en Inglés | MEDLINE | ID: mdl-31080692

RESUMEN

Catechol-O-methyltransferase (COMT) is a model S-adenosyl-l-methionine (SAM) dependent methyl transferase, which catalyzes the methylation of catecholamine neurotransmitters such as dopamine in the primary pathway of neurotransmitter deactivation in animals. Despite extensive study, there is no consensus view of the physical basis of catalysis in COMT. Further progress requires experimental data that directly probes active site geometry, protein dynamics and electrostatics, ideally in a range of positions along the reaction coordinate. Here we establish that sinefungin, a fungal-derived inhibitor of SAM-dependent enzymes that possess transition state-like charge on the transferring group, can be used as a transition state analog of COMT when combined with a catechol. X-ray crystal structures and NMR backbone assignments of the ternary complexes of the soluble form of human COMT containing dinitrocatechol, Mg2+ and SAM or sinefungin were determined. Comparison and further analysis with the aid of density functional theory calculations and molecular dynamics simulations provides evidence for active site "compaction", which is driven by electrostatic stabilization between the transferring methyl group and "equatorial" active site residues that are orthogonal to the donor-acceptor (pseudo reaction) coordinate. We propose that upon catecholamine binding and subsequent proton transfer to Lys 144, the enzyme becomes geometrically preorganized, with little further movement along the donor-acceptor coordinate required for methyl transfer. Catalysis is then largely facilitated through stabilization of the developing charge on the transferring methyl group via "equatorial" H-bonding and electrostatic interactions orthogonal to the donor-acceptor coordinate.

14.
J Biol Chem ; 293(24): 9301-9310, 2018 06 15.
Artículo en Inglés | MEDLINE | ID: mdl-29695509

RESUMEN

Myelocytomatosis proto-oncogene transcription factor (Myc) is an intrinsically disordered protein with critical roles in cellular homeostasis and neoplastic transformation. It is tightly regulated in the cell, with Myc phosphorylation playing a major role. In addition to the well-described tandem phosphorylation of Thr-52 and Ser-62 in the Myc transactivation domain linked to its degradation, P21 (RAC1)-activated kinase 2 (PAK2)-mediated phosphorylation of serine and threonine residues in the C-terminal basic helix-loop-helix leucine zipper (bHLH-LZ) region regulates Myc transcriptional activity. Here we report that PAK2 preferentially phosphorylates Myc twice, at Thr-358 and Ser-373, with only a minor fraction being modified at the previously identified Thr-400 site. For transcriptional activity, Myc binds E-box DNA elements, requiring its heterodimerization with Myc-associated factor X (Max) via the bHLH-LZ regions. Using isothermal calorimetry (ITC), we found that Myc phosphorylation destabilizes this ternary protein-DNA complex by decreasing Myc's affinity for Max by 2 orders of magnitude, suggesting a major effect of phosphorylation on this complex. Phosphomimetic substitutions revealed that Ser-373 dominates the effect on Myc-Max heterodimerization. Moreover, a T400D substitution disrupted Myc's affinity for Max. ITC, NMR, and CD analyses of several Myc variants suggested that the effect of phosphorylation on the Myc-Max interaction is caused by secondary structure disruption during heterodimerization rather than by a change in the structurally disordered state of Myc or by phosphorylation-induced electrostatic repulsion in the heterodimer. Our findings provide critical insights into the effects of PAK2-catalyzed phosphorylation of Myc on its interactions with Max and DNA.


Asunto(s)
Factores de Transcripción Básicos con Cremalleras de Leucinas y Motivos Hélice-Asa-Hélice/metabolismo , ADN/metabolismo , Proteínas Proto-Oncogénicas c-myc/metabolismo , Secuencia de Aminoácidos , Factores de Transcripción Básicos con Cremalleras de Leucinas y Motivos Hélice-Asa-Hélice/química , Humanos , Modelos Moleculares , Fosforilación , Unión Proteica , Conformación Proteica , Conformación Proteica en Hélice alfa , Mapas de Interacción de Proteínas , Estabilidad Proteica , Proto-Oncogenes Mas , Proteínas Proto-Oncogénicas c-myc/química
15.
ACS Catal ; 8(12): 11589-11599, 2018 Dec 07.
Artículo en Inglés | MEDLINE | ID: mdl-31119061

RESUMEN

Many enzymes that catalyze hydride transfer reactions work via a mechanism dominated by quantum mechanical tunneling. The involvement of fast vibrational modes of the reactive complex is often inferred in these reactions, as in the case of the NAD(P)H-dependent pentaerythritol tetranitrate reductase (PETNR). Herein, we interrogated the H-transfer mechanism in PETNR by designing conservative (L25I and I107L) and side chain shortening (L25A and I107A) PETNR variants and using a combination of experimental approaches (stopped-flow rapid kinetics, X-ray crystallography, isotope/temperature dependence studies of H-transfer and NMR spectroscopy). X-ray data show subtle changes in the local environment of the targeted side chains but no major structural perturbation caused by mutagenesis of these two second sphere active site residues. However, temperature dependence studies of H-transfer revealed a coenzyme-specific and complex thermodynamic equilibrium between different reactive configurations in PETNR-coenzyme complexes. We find that mutagenesis of these second sphere "noncatalytic" residues affects differently the reactivity of PETNR with NADPH and NADH coenzymes. We attribute this to subtle, dynamic structural changes in the PETNR active site, the effects of which impact differently in the nonequivalent reactive geometries of PETNR-NADH and PETNR-NADPH complexes. This inference is confirmed through changes observed in the NMR chemical shift data for PETNR complexes with unreactive 1,4,5,6-tetrahydro-NAD(P) analogues. We show that H-transfer rates can (to some extent) be buffered through entropy-enthalpy compensation, but that use of integrated experimental tools reveals hidden complexities that implicate a role for dynamics in this relatively simple H-transfer reaction. Similar approaches are likely to be informative in other enzymes to understand the relative importance of (distal) hydrophobic side chains and dynamics in controlling the rates of enzymatic H-transfer.

16.
J Biol Chem ; 293(7): 2272-2287, 2018 02 16.
Artículo en Inglés | MEDLINE | ID: mdl-29259125

RESUMEN

The UbiD family of reversible decarboxylases act on aromatic, heteroaromatic, and unsaturated aliphatic acids and utilize a prenylated flavin mononucleotide (prFMN) as cofactor, bound adjacent to a conserved Glu-Arg-Glu/Asp ionic network in the enzyme's active site. It is proposed that UbiD activation requires oxidative maturation of the cofactor, for which two distinct isomers, prFMNketimine and prFMNiminium, have been observed. It also has been suggested that only the prFMNiminium form is relevant to catalysis, which requires transient cycloaddition between substrate and cofactor. Using Aspergillus niger Fdc1 as a model system, we reveal that isomerization of prFMNiminium to prFMNketimine is a light-dependent process that is largely independent of the Glu277-Arg173-Glu282 network and accompanied by irreversible loss of activity. On the other hand, efficient catalysis was highly dependent on an intact Glu-Arg-Glu network, as only Glu → Asp substitutions retain activity. Surprisingly, oxidative maturation to form the prFMNiminium species is severely affected only for the R173A variant. In summary, the unusual irreversible isomerization of prFMN is light-dependent and probably proceeds via high-energy intermediates but is independent of the Glu-Arg-Glu network. Our results from mutagenesis, crystallographic, spectroscopic, and kinetic experiments indicate a clear role for the Glu-Arg-Glu network in both catalysis and oxidative maturation.


Asunto(s)
Aspergillus niger/enzimología , Carboxiliasas/química , Carboxiliasas/metabolismo , Mononucleótido de Flavina/metabolismo , Proteínas Fúngicas/química , Proteínas Fúngicas/metabolismo , Aspergillus niger/química , Aspergillus niger/genética , Sitios de Unión , Carboxiliasas/genética , Catálisis , Dominio Catalítico , Secuencia Conservada , Mononucleótido de Flavina/química , Proteínas Fúngicas/genética , Isomerismo , Cinética , Oxidación-Reducción
17.
Biomol NMR Assign ; 12(1): 79-83, 2018 04.
Artículo en Inglés | MEDLINE | ID: mdl-29168057

RESUMEN

Pentaerythritol tetranitrate reductase (PETNR) is a flavoenzyme possessing a broad substrate specificity and is a member of the Old Yellow Enzyme family of oxidoreductases. As well as having high potential as an industrial biocatalyst, PETNR is an excellent model system for studying hydrogen transfer reactions. Mechanistic studies performed with PETNR using stopped-flow methods have shown that tunneling contributes towards hydride transfer from the NAD(P)H coenzyme to the flavin mononucleotide (FMN) cofactor and fast protein dynamics have been inferred to facilitate this catalytic step. Herein, we report the near-complete 1H, 15N and 13C backbone resonance assignments of PETNR in a stoichiometric complex with the FMN cofactor in its native oxidized form, which were obtained using heteronuclear multidimensional NMR spectroscopy. A total of 97% of all backbone resonances were assigned, with 333 out of a possible 344 residues assigned in the 1H-15N TROSY spectrum. This is the first report of an NMR structural study of a flavoenzyme from the Old Yellow Enzyme family and it lays the foundation for future investigations of functional dynamics in hydride transfer catalytic mechanism.


Asunto(s)
Enterobacter cloacae/enzimología , Resonancia Magnética Nuclear Biomolecular , Oxidorreductasas/química , Modelos Moleculares , Conformación Proteica en Hélice alfa
18.
Biomol NMR Assign ; 11(2): 251-256, 2017 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-28866776

RESUMEN

Human phosphoglycerate kinase (PGK) is an energy generating glycolytic enzyme that catalyses the transfer of a phosphoryl group from 1,3-bisphosphoglycerate (BPG) to ADP producing 3-phosphoglycerate (3PG) and ATP. PGK is composed of two α/ß Rossmann-fold domains linked by a central α-helix and the active site is located in the cleft formed between the N-domain which binds BPG or 3PG, and the C-domain which binds the nucleotides ADP or ATP. Domain closure is required to bring the two substrates into close proximity for phosphoryl transfer to occur, however previous structural studies involving a range of native substrates and substrate analogues only yielded open or partly closed PGK complexes. X-ray crystallography using magnesium trifluoride (MgF3-) as a isoelectronic and near-isosteric mimic of the transferring phosphoryl group (PO3-), together with 3PG and ADP has been successful in trapping human PGK in a fully closed transition state analogue (TSA) complex. In this work we report the 1H, 15N and 13C backbone resonance assignments of human PGK in the solution conformation of the fully closed PGK:3PG:MgF3:ADP TSA complex. Assignments were obtained by heteronuclear multidimensional NMR spectroscopy. In total, 97% of all backbone resonances were assigned in the complex, with 385 out of a possible 399 residues assigned in the 1H-15N TROSY spectrum. Prediction of solution secondary structure from a chemical shift analysis using the TALOS-N webserver is in good agreement with the published X-ray crystal structure of this complex.


Asunto(s)
Adenosina Difosfato/metabolismo , Fluoruros/metabolismo , Gliceraldehído 3-Fosfato/metabolismo , Compuestos de Magnesio/metabolismo , Resonancia Magnética Nuclear Biomolecular , Fosfoglicerato Quinasa/química , Fosfoglicerato Quinasa/metabolismo , Humanos , Modelos Moleculares , Unión Proteica , Conformación Proteica en Hélice alfa
19.
Angew Chem Int Ed Engl ; 56(33): 9732-9735, 2017 08 07.
Artículo en Inglés | MEDLINE | ID: mdl-28498638

RESUMEN

We report X-ray crystallographic and 19 F NMR studies of the G-protein RhoA complexed with MgF3- , GDP, and RhoGAP, which has the mutation Arg85'Ala. When combined with DFT calculations, these data permit the identification of changes in transition state (TS) properties. The X-ray data show how Tyr34 maintains solvent exclusion and the core H-bond network in the active site by relocating to replace the missing Arg85' sidechain. The 19 F NMR data show deshielding effects that indicate the main function of Arg85' is electronic polarization of the transferring phosphoryl group, primarily mediated by H-bonding to O3G and thence to PG . DFT calculations identify electron-density redistribution and pinpoint why the TS for guanosine 5'-triphosphate (GTP) hydrolysis is higher in energy when RhoA is complexed with RhoGAPArg85'Ala relative to wild-type (WT) RhoGAP. This study demonstrates that 19 F NMR measurements, in combination with X-ray crystallography and DFT calculations, can reliably dissect the response of small GTPases to site-specific modifications.


Asunto(s)
Teoría Funcional de la Densidad , GTP Fosfohidrolasas/genética , Cristalografía por Rayos X , Flúor/química , GTP Fosfohidrolasas/química , GTP Fosfohidrolasas/metabolismo , Espectroscopía de Resonancia Magnética , Modelos Moleculares , Mutación
20.
Biomol NMR Assign ; 11(1): 57-61, 2017 04.
Artículo en Inglés | MEDLINE | ID: mdl-27981425

RESUMEN

Catechol O-methyltransferase (COMT) is an enzyme that plays a major role in catechol neurotransmitter deactivation. Inhibition of COMT can increase neurotransmitter levels, which provides a means of treatment for Parkinson's disease, schizophrenia and depression. COMT exists as two isozymes: a soluble cytoplasmic form (S-COMT), expressed in the liver and kidneys and a membrane-bound form (MB-COMT), found mostly in the brain. Here we report the backbone 1H, 15N and 13C chemical shift assignments of S-COMT in complex with S-adenosyl-L-methionine, 3,5-dinitrocatechol and Mg2+. Assignments were obtained by heteronuclear multidimensional NMR spectroscopy. In total, 97 % of all backbone resonances were assigned in the complex, with 205 out of a possible 215 residues assigned in the 1H-15N TROSY spectrum. Prediction of solution secondary structure from a chemical shift analysis using the TALOS+ webserver is in good agreement with published X-ray crystal structures.


Asunto(s)
Catecol O-Metiltransferasa/química , Catecol O-Metiltransferasa/metabolismo , Catecoles/metabolismo , Resonancia Magnética Nuclear Biomolecular , S-Adenosilmetionina/metabolismo , Sitios de Unión , Humanos , Modelos Moleculares , Conformación Proteica , Solubilidad
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