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1.
Mol Cell ; 66(2): 206-220.e9, 2017 Apr 20.
Artículo en Inglés | MEDLINE | ID: mdl-28416140

RESUMEN

Cells exposed to hypoxia experience replication stress but do not accumulate DNA damage, suggesting sustained DNA replication. Ribonucleotide reductase (RNR) is the only enzyme capable of de novo synthesis of deoxyribonucleotide triphosphates (dNTPs). However, oxygen is an essential cofactor for mammalian RNR (RRM1/RRM2 and RRM1/RRM2B), leading us to question the source of dNTPs in hypoxia. Here, we show that the RRM1/RRM2B enzyme is capable of retaining activity in hypoxia and therefore is favored over RRM1/RRM2 in order to preserve ongoing replication and avoid the accumulation of DNA damage. We found two distinct mechanisms by which RRM2B maintains hypoxic activity and identified responsible residues in RRM2B. The importance of RRM2B in the response to tumor hypoxia is further illustrated by correlation of its expression with a hypoxic signature in patient samples and its roles in tumor growth and radioresistance. Our data provide mechanistic insight into RNR biology, highlighting RRM2B as a hypoxic-specific, anti-cancer therapeutic target.


Asunto(s)
Proteínas de Ciclo Celular/metabolismo , Neoplasias del Colon/enzimología , Replicación del ADN , ADN de Neoplasias/biosíntesis , Oxígeno/metabolismo , Ribonucleótido Reductasas/metabolismo , Proteínas Supresoras de Tumor/metabolismo , Animales , Apoptosis , Proteínas de Ciclo Celular/química , Proteínas de Ciclo Celular/genética , Neoplasias del Colon/genética , Neoplasias del Colon/patología , Neoplasias del Colon/radioterapia , Daño del ADN , ADN de Neoplasias/genética , Femenino , Células HCT116 , Humanos , Ratones Endogámicos BALB C , Ratones Desnudos , Interferencia de ARN , Tolerancia a Radiación , Ribonucleósido Difosfato Reductasa/metabolismo , Ribonucleótido Reductasas/química , Ribonucleótido Reductasas/genética , Factores de Tiempo , Transfección , Carga Tumoral , Hipoxia Tumoral , Proteínas Supresoras de Tumor/química , Proteínas Supresoras de Tumor/genética , Ensayos Antitumor por Modelo de Xenoinjerto
2.
Extremophiles ; 22(3): 553-562, 2018 May.
Artículo en Inglés | MEDLINE | ID: mdl-29523972

RESUMEN

YcfD from Escherichia coli is a homologue of the human ribosomal oxygenases NO66 and MINA53, which catalyse histidyl-hydroxylation of the 60S subunit and affect cellular proliferation (Ge et al., Nat Chem Biol 12:960-962, 2012). Bioinformatic analysis identified a potential homologue of ycfD in the thermophilic bacterium Rhodothermus marinus (ycfDRM). We describe studies on the characterization of ycfDRM, which is a functional 2OG oxygenase catalysing (2S,3R)-hydroxylation of the ribosomal protein uL16 at R82, and which is active at significantly higher temperatures than previously reported for any other 2OG oxygenase. Recombinant ycfDRM manifests high thermostability (Tm 84 °C) and activity at higher temperatures (Topt 55 °C) than ycfDEC (Tm 50.6 °C, Topt 40 °C). Mass spectrometric studies on purified R. marinus ribosomal proteins demonstrate a temperature-dependent variation in uL16 hydroxylation. Kinetic studies of oxygen dependence suggest that dioxygen availability can be a limiting factor for ycfDRM catalysis at high temperatures, consistent with incomplete uL16 hydroxylation observed in R. marinus cells. Overall, the results that extend the known range of ribosomal hydroxylation, reveal the potential for ycfD-catalysed hydroxylation to be regulated by temperature/dioxygen availability, and that thermophilic 2OG oxygenases are of interest from a biocatalytic perspective.


Asunto(s)
Proteínas de Escherichia coli/metabolismo , Oxigenasas de Función Mixta/metabolismo , Rhodothermus/enzimología , Proteínas Ribosómicas/metabolismo , Estabilidad de Enzimas , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Hidroxilación , Oxigenasas de Función Mixta/química , Oxigenasas de Función Mixta/genética , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Rhodothermus/genética , Proteínas Ribosómicas/química , Proteínas Ribosómicas/genética , Homología de Secuencia
3.
J Biol Chem ; 290(32): 19726-42, 2015 Aug 07.
Artículo en Inglés | MEDLINE | ID: mdl-26112411

RESUMEN

The hypoxia-inducible factor (HIF) hydroxylases regulate hypoxia sensing in animals. In humans, they comprise three prolyl hydroxylases (PHD1-3 or EGLN1-3) and factor inhibiting HIF (FIH). FIH is an asparaginyl hydroxylase catalyzing post-translational modification of HIF-α, resulting in reduction of HIF-mediated transcription. Like the PHDs, FIH is proposed to have a hypoxia-sensing role in cells, enabling responses to changes in cellular O2 availability. PHD2, the most important human PHD isoform, is proposed to be biochemically/kinetically suited as a hypoxia sensor due to its relatively high sensitivity to changes in O2 concentration and slow reaction with O2. To ascertain whether these parameters are conserved among the HIF hydroxylases, we compared the reactions of FIH and PHD2 with O2. Consistent with previous reports, we found lower Km(app)(O2) values for FIH than for PHD2 with all HIF-derived substrates. Under pre-steady-state conditions, the O2-initiated FIH reaction is significantly faster than that of PHD2. We then investigated the kinetics with respect to O2 of the FIH reaction with ankyrin repeat domain (ARD) substrates. FIH has lower Km(app)(O2) values for the tested ARDs than HIF-α substrates, and pre-steady-state O2-initiated reactions were faster with ARDs than with HIF-α substrates. The results correlate with cellular studies showing that FIH is active at lower O2 concentrations than the PHDs and suggest that competition between HIF-α and ARDs for FIH is likely to be biologically relevant, particularly in hypoxic conditions. The overall results are consistent with the proposal that the kinetic properties of individual oxygenases reflect their biological capacity to act as hypoxia sensors.


Asunto(s)
Ancirinas/metabolismo , Subunidad alfa del Factor 1 Inducible por Hipoxia/metabolismo , Prolina Dioxigenasas del Factor Inducible por Hipoxia/metabolismo , Hipoxia/metabolismo , Oxigenasas de Función Mixta/metabolismo , Oxígeno/metabolismo , Proteínas Represoras/metabolismo , Secuencia de Aminoácidos , Animales , Ancirinas/genética , Biocatálisis , Escherichia coli/genética , Escherichia coli/metabolismo , Expresión Génica , Regulación de la Expresión Génica , Humanos , Hipoxia/genética , Subunidad alfa del Factor 1 Inducible por Hipoxia/genética , Prolina Dioxigenasas del Factor Inducible por Hipoxia/genética , Cinética , Oxigenasas de Función Mixta/genética , Datos de Secuencia Molecular , Estructura Terciaria de Proteína , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Proteínas Represoras/genética , Transducción de Señal , Transcripción Genética
4.
Biochemistry ; 54(39): 6093-105, 2015 Oct 06.
Artículo en Inglés | MEDLINE | ID: mdl-26368022

RESUMEN

The Fe(II)- and 2-oxoglutarate (2-OG)-dependent dioxygenases comprise a large and diverse enzyme superfamily the members of which have multiple physiological roles. Despite this diversity, these enzymes share a common chemical mechanism and a core structural fold, a double-stranded ß-helix (DSBH), as well as conserved active site residues. The prolyl hydroxylases are members of this large superfamily. Prolyl hydroxylases are involved in collagen biosynthesis and oxygen sensing in mammalian cells. Structural-mechanistic studies with prolyl hydroxylases have broader implications for understanding mechanisms in the Fe(II)- and 2-OG-dependent dioxygenase superfamily. Here, we describe crystal structures of an N-terminally truncated viral collagen prolyl hydroxylase (vCPH). The crystal structure shows that vCPH contains the conserved DSBH motif and iron binding active site residues of 2-OG oxygenases. Molecular dynamics simulations are used to delineate structural changes in vCPH upon binding its substrate. Kinetic investigations are used to report on reaction cycle intermediates and compare them to the closest homologues of vCPH. The study highlights the utility of vCPH as a model enzyme for broader mechanistic analysis of Fe(II)- and 2-OG-dependent dioxygenases, including those of biomedical interest.


Asunto(s)
Hierro/química , Phycodnaviridae/enzimología , Prolil Hidroxilasas/química , Proteínas Virales/química , Secuencias de Aminoácidos , Dominio Catalítico , Cristalografía por Rayos X
5.
J Antimicrob Chemother ; 70(2): 463-9, 2015 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-25324420

RESUMEN

OBJECTIVES: Metallo-ß-lactamase (MBL)-based resistance is a threat to the use of most ß-lactam antibiotics. Multiple variants of the New Delhi MBL (NDM) have recently been reported. Previous reports indicate that the substitutions affect NDM activity despite being located outside the active site. This study compares the biochemical properties of seven clinically reported NDM variants. METHODS: NDM variants were generated by site-directed mutagenesis; recombinant proteins were purified to near homogeneity. Thermal stability and secondary structures of the variants were investigated using differential scanning fluorimetry and circular dichroism; kinetic parameters and MIC values were investigated for representative carbapenem, cephalosporin and penicillin substrates. RESULTS: The substitutions did not affect the overall folds of the NDM variants, within limits of detection; however, differences in thermal stabilities were observed. NDM-8 was the most stable variant with a melting temperature of 72°C compared with 60°C for NDM-1. In contrast to some previous studies, kcat/KM values were similar for carbapenem and penicillin substrates for NDM variants, but differences in kinetics were observed for cephalosporin substrates. Apparent substrate inhibition was observed with nitrocefin for variants containing the M154L substitution. In all cases, cefoxitin and ceftazidime were poorly hydrolysed with kcat/KM values <1 s(-1) µM(-1). CONCLUSIONS: These results do not define major differences in the catalytic efficiencies of the studied NDM variants and carbapenem or penicillin substrates. Differences in the kinetics of cephalosporin hydrolysis were observed. The results do reveal that the clinically observed substitutions can make substantial differences in thermodynamic stability, suggesting that this may be a factor in MBL evolution.


Asunto(s)
Bacterias/genética , Bacterias/metabolismo , Variación Genética , beta-Lactamasas/genética , beta-Lactamasas/metabolismo , Antibacterianos/farmacología , Bacterias/efectos de los fármacos , Clonación Molecular , Escherichia coli/efectos de los fármacos , Escherichia coli/genética , Escherichia coli/metabolismo , Humanos , Hidrólisis , Cinética , Espectrometría de Masas , Pruebas de Sensibilidad Microbiana , Modelos Moleculares , Mutagénesis Sitio-Dirigida , Plásmidos/genética , Conformación Proteica , Estabilidad Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Termodinámica , beta-Lactamasas/química
6.
Biochem J ; 463(3): 363-72, 2014 Nov 01.
Artículo en Inglés | MEDLINE | ID: mdl-25120187

RESUMEN

The prolyl hydroxylase domain proteins (PHDs) catalyse the post-translational hydroxylation of the hypoxia-inducible factor (HIF), a modification that regulates the hypoxic response in humans. The PHDs are Fe(II)/2-oxoglutarate (2OG) oxygenases; their catalysis is proposed to provide a link between cellular HIF levels and changes in O2 availability. Transient kinetic studies have shown that purified PHD2 reacts slowly with O2 compared with some other studied 2OG oxygenases, a property which may be related to its hypoxia-sensing role. PHD2 forms a stable complex with Fe(II) and 2OG; crystallographic and kinetic analyses indicate that an Fe(II)-co-ordinated water molecule, which must be displaced before O2 binding, is relatively stable in the active site of PHD2. We used active site substitutions to investigate whether these properties are related to the slow reaction of PHD2 with O2. While disruption of 2OG binding in a R383K variant did not accelerate O2 activation, we found that substitution of the Fe(II)-binding aspartate for a glutamate residue (D315E) manifested significantly reduced Fe(II) binding, yet maintained catalytic activity with a 5-fold faster reaction with O2. The results inform on how the precise active site environment of oxygenases can affect rates of O2 activation and provide insights into limiting steps in PHD catalysis.


Asunto(s)
Prolina Dioxigenasas del Factor Inducible por Hipoxia/química , Hierro/química , Ácidos Cetoglutáricos/química , Oxígeno/química , Dominio Catalítico , Cationes Bivalentes , Hidroxilación , Prolina Dioxigenasas del Factor Inducible por Hipoxia/antagonistas & inhibidores , Prolina Dioxigenasas del Factor Inducible por Hipoxia/genética , Isoquinolinas/química , Cinética , Manganeso/química , Mutagénesis Sitio-Dirigida , Oligopéptidos/química , Unión Proteica , Agua/química , Zinc/química
7.
Biochemistry ; 53(15): 2483-93, 2014 Apr 22.
Artículo en Inglés | MEDLINE | ID: mdl-24684493

RESUMEN

Deacetoxycephalosporin C synthase (DAOCS) catalyzes the oxidative ring expansion of penicillin N (penN) to give deacetoxycephalosporin C (DAOC), which is the committed step in the biosynthesis of the clinically important cephalosporin antibiotics. DAOCS belongs to the family of non-heme iron(II) and 2-oxoglutarate (2OG) dependent oxygenases, which have substantially conserved active sites and are proposed to employ a consensus mechanism proceeding via formation of an enzyme·Fe(II)·2OG·substrate ternary complex. Previously reported kinetic and crystallographic studies led to the proposal of an unusual "ping-pong" mechanism for DAOCS, which was significantly different from other members of the 2OG oxygenase superfamily. Here we report pre-steady-state kinetics and binding studies employing mass spectrometry and NMR on the DAOCS-catalyzed penN ring expansion that demonstrate the viability of ternary complex formation in DAOCS catalysis, arguing for the generality of the proposed consensus mechanism for 2OG oxygenases.


Asunto(s)
Transferasas Intramoleculares/química , Ácidos Cetoglutáricos/química , Oxigenasas/química , Proteínas de Unión a las Penicilinas/química , Catálisis , Cristalografía por Rayos X , Cinética , Espectrometría de Masas , Resonancia Magnética Nuclear Biomolecular
8.
Biochem J ; 449(2): 491-6, 2013 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-23092293

RESUMEN

Histone N(ϵ)-methyl lysine demethylases are important in epigenetic regulation. KDM4E (histone lysine demethylase 4E) is a representative member of the large Fe(II)/2-oxoglutarate- dependent family of human histone demethylases. In the present study we report kinetic studies on the reaction of KDM4E with O2. Steady-state assays showed that KDM4E has a graded response to O2 over a physiologically relevant range of O2 concentrations. Pre-steady state assays implied that KDM4E reacts slowly with O2 and that there are variations in the reaction kinetics which are dependent on the methylation status of the substrate. The results demonstrate the potential for histone demethylase activity to be regulated by oxygen availability.


Asunto(s)
Histonas/metabolismo , Histona Demetilasas con Dominio de Jumonji/metabolismo , Ácidos Cetoglutáricos/metabolismo , Oxígeno/metabolismo , Biocatálisis/efectos de los fármacos , Relación Dosis-Respuesta a Droga , Histonas/química , Humanos , Hierro/metabolismo , Ácidos Cetoglutáricos/química , Cinética , Lisina/metabolismo , Estructura Molecular , Oxígeno/farmacología , Péptidos/metabolismo , Espectrofotometría , Especificidad por Sustrato , Succinatos/química , Succinatos/metabolismo
9.
ACS Chem Biol ; 14(8): 1737-1750, 2019 08 16.
Artículo en Inglés | MEDLINE | ID: mdl-31287655

RESUMEN

Fe(II)- and 2-oxoglutarate (2OG)-dependent JumonjiC domain-containing histone demethylases (JmjC KDMs) are "epigenetic eraser" enzymes involved in the regulation of gene expression and are emerging drug targets in oncology. We screened a set of clinically used iron chelators and report that they potently inhibit JMJD2A (KDM4A) in vitro. Mode of action investigations revealed that one compound, deferasirox, is a bona fide active site-binding inhibitor as shown by kinetic and spectroscopic studies. Synthesis of derivatives with improved cell permeability resulted in significant upregulation of histone trimethylation and potent cancer cell growth inhibition. Deferasirox was also found to inhibit human 2OG-dependent hypoxia inducible factor prolyl hydroxylase activity. Therapeutic effects of clinically used deferasirox may thus involve transcriptional regulation through 2OG oxygenase inhibition. Deferasirox might provide a useful starting point for the development of novel anticancer drugs targeting 2OG oxygenases and a valuable tool compound for investigations of KDM function.


Asunto(s)
Deferasirox/farmacología , Inhibidores Enzimáticos/farmacología , Quelantes del Hierro/farmacología , Histona Demetilasas con Dominio de Jumonji/antagonistas & inhibidores , Dominio Catalítico/efectos de los fármacos , Línea Celular Tumoral , Desmetilación/efectos de los fármacos , Epigénesis Genética/efectos de los fármacos , Histonas/metabolismo , Humanos , Histona Demetilasas con Dominio de Jumonji/química
10.
Curr Protoc Pharmacol ; 80(1): 3.15.1-3.15.12, 2018 03.
Artículo en Inglés | MEDLINE | ID: mdl-30040204

RESUMEN

Histone modifications, including lysine methylation marks on histone tails, modulate the accessibility of genes for transcription. Changes in histone tail methylation patterns can cause transcriptional activation or repression. The dynamic regulation of lysine methylation patterns is enabled by two distinct groups of enzymes: histone methyltransferases (KMTs) and demethylases (KDMs). The Jumonji C (JmjC) domain-containing lysine histone demethylases (JmjC-KDMs) alter the methylation levels of histone tails by removing tri-, di-, or mono-methylation marks. Because JmjC-KDMs activities are dysfunctional in cancer and other clinical conditions, they are targets for drug discovery. Efforts are underway to develop high-throughput assays capable of identifying selective, small-molecule inhibitors of KDMs. Detailed in this unit are protocols for mass spectrometry-based and formaldehyde dehydrogenase-coupled enzyme-based assays that can be used to identify inhibitors of JmjC-KDMs. © 2018 by John Wiley & Sons, Inc.


Asunto(s)
Pruebas de Enzimas , Histona Demetilasas con Dominio de Jumonji/metabolismo , Aldehído Oxidorreductasas/metabolismo , Formaldehído/metabolismo , Espectrometría de Masas
11.
Hypoxia (Auckl) ; 6: 57-71, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-30519597

RESUMEN

BACKGROUND: In humans and other animals, the chronic hypoxic response is mediated by hypoxia inducible transcription factors (HIFs) which regulate the expression of genes that counteract the effects of limiting oxygen. Prolyl hydroxylases (PHDs) act as hypoxia sensors for the HIF system in organisms ranging from humans to the simplest animal Trichoplax adhaerens. METHODS: We report structural and biochemical studies on the T. adhaerens HIF prolyl hydroxylase (TaPHD) that inform about the evolution of hypoxia sensing in animals. RESULTS: High resolution crystal structures (≤1.3 Å) of TaPHD, with and without its HIFα substrate, reveal remarkable conservation of key active site elements between T. adhaerens and human PHDs, which also manifest in kinetic comparisons. CONCLUSION: Conserved structural features of TaPHD and human PHDs include those apparently enabling the slow binding/reaction of oxygen with the active site Fe(II), the formation of a stable 2-oxoglutarate complex, and a stereoelectronically promoted change in conformation of the hydroxylated proline-residue. Comparison of substrate selectivity between the human PHDs and TaPHD provides insights into the selectivity determinants of HIF binding by the PHDs, and into the evolution of the multiple HIFs and PHDs present in higher animals.

12.
ChemMedChem ; 13(18): 1949-1956, 2018 09 19.
Artículo en Inglés | MEDLINE | ID: mdl-30047603

RESUMEN

The natural product tripartin has been reported to inhibit the N-methyl-lysine histone demethylase KDM4A. A synthesis of tripartin starting from 3,5-dimethoxyphenylacrylic acid was developed, and the enantiomers were separated by chiral HPLC. We observed that both tripartin enantiomers manifested an apparent increase in H3K9me3 levels when dosed in cells, as measured by western blot analysis. Thus, there is no enantiomeric discrimination toward this natural product in terms of its effects on cellular histone methylation status. Interestingly, tripartin did not inhibit isolated KDM4A-E under our assay conditions (IC50 >100 µm). Tripartin analogues with a dichloromethylcarbinol group derived from the indanone scaffold were synthesized and found to be inactive against isolated recombinant KDM4 enzymes and in cell-based assays. Although the precise cellular mode of action of tripartin is unclear, our evidence suggests that it may affect histone methylation status via a mechanism other than direct inhibition of the KDM4 histone demethylases.


Asunto(s)
Productos Biológicos/farmacología , Inhibidores Enzimáticos/farmacología , Hidrocarburos Clorados/farmacología , Indanos/farmacología , Productos Biológicos/síntesis química , Productos Biológicos/química , Relación Dosis-Respuesta a Droga , Inhibidores Enzimáticos/síntesis química , Inhibidores Enzimáticos/química , Células HCT116 , Humanos , Hidrocarburos Clorados/síntesis química , Hidrocarburos Clorados/química , Indanos/síntesis química , Indanos/química , Histona Demetilasas con Dominio de Jumonji , Estructura Molecular , Relación Estructura-Actividad , Células Tumorales Cultivadas
13.
J Mol Biol ; 429(19): 2895-2906, 2017 09 15.
Artículo en Inglés | MEDLINE | ID: mdl-28827149

RESUMEN

Methylation of lysine-4 of histone H3 (H3K4men) is an important regulatory factor in eukaryotic transcription. Removal of the transcriptionally activating H3K4 methylation is catalyzed by histone demethylases, including the Jumonji C (JmjC) KDM5 subfamily. The JmjC KDMs are Fe(II) and 2-oxoglutarate (2OG)-dependent oxygenases, some of which are associated with cancer. Altered levels of tricarboxylic acid (TCA) cycle intermediates and the associated metabolites D- and L-2-hydroxyglutarate (2HG) can cause changes in chromatin methylation status. We report comprehensive biochemical, structural and cellular studies on the interaction of TCA cycle intermediates with KDM5B, which is a current medicinal chemistry target for cancer. The tested TCA intermediates were poor or moderate KDM5B inhibitors, except for oxaloacetate and succinate, which were shown to compete for binding with 2OG. D- and L-2HG were moderate inhibitors at levels that might be relevant in cancer cells bearing isocitrate dehydrogenase mutations. Crystallographic analyses with succinate, fumarate, L-malate, oxaloacetate, pyruvate and D- and L-2HG support the kinetic studies showing competition with 2OG. An unexpected binding mode for oxaloacetate was observed in which it coordinates the active site metal via its C-4 carboxylate rather than the C-1 carboxylate/C-2 keto groups. Studies employing immunofluorescence antibody-based assays reveal no changes in H3K4me3 levels in cells ectopically overexpressing KDM5B in response to dosing with TCA cycle metabolite pro-drug esters, suggesting that the high levels of cellular 2OG may preclude inhibition. The combined results reveal the potential for KDM5B inhibition by TCA cycle intermediates, but suggest that in cells, such inhibition will normally be effectively competed by 2OG.


Asunto(s)
Inhibidores Enzimáticos/metabolismo , Glutaratos/metabolismo , Histona Demetilasas con Dominio de Jumonji/química , Histona Demetilasas con Dominio de Jumonji/metabolismo , Proteínas Nucleares/química , Proteínas Nucleares/metabolismo , Proteínas Represoras/química , Proteínas Represoras/metabolismo , Ácidos Tricarboxílicos/metabolismo , Cristalografía por Rayos X , Cinética , Modelos Moleculares , Unión Proteica , Conformación Proteica
14.
J Inorg Biochem ; 163: 185-193, 2016 10.
Artículo en Inglés | MEDLINE | ID: mdl-27498591

RESUMEN

Metallo-ß-lactamases (MBLs) catalyse the hydrolysis of almost all ß-lactam antibacterials including the latest generation carbapenems and are a growing worldwide clinical problem. It is proposed that MBLs employ one or two zinc ion cofactors in vivo. Isolated MBLs are reported to use transition metal ions other than zinc, including copper, cadmium and manganese, with iron ions being a notable exception. We report kinetic and biophysical studies with the di-iron(II)-substituted metallo-ß-lactamase II from Bacillus cereus (di-Fe(II) BcII) and the clinically relevant B1 subclass Verona integron-encoded metallo-ß-lactamase 2 (di-Fe(II) VIM-2). The results reveal that MBLs can employ ferrous iron in catalysis, but with altered kinetic and inhibition profiles compared to the zinc enzymes. A crystal structure of di-Fe(II) BcII reveals only small overall changes in the active site compared to the di-Zn(II) enzyme including retention of the di-metal bridging water; however, the positions of the metal ions are altered in the di-Fe(II) compared to the di-Zn(II) structure. Stopped-flow analyses reveal that the mechanism of nitrocefin hydrolysis by both di-Fe(II) BcII and di-Fe(II) VIM-2 is altered compared to the di-Zn(II) enzymes. Notably, given that the MBLs are the subject of current medicinal chemistry efforts, the results raise the possibility the Fe(II)-substituted MBLs may be of clinical relevance under conditions of low zinc availability, and reveal potential variation in inhibitor activity against the differently metallated MBLs.


Asunto(s)
Bacillus cereus/enzimología , Proteínas Bacterianas/química , Hierro/química , Metaloproteínas/química , beta-Lactamasas/química
15.
Chem Sci ; 6(2): 956-963, 2015 Feb 19.
Artículo en Inglés | MEDLINE | ID: mdl-25717359

RESUMEN

Metallo-ß-lactamases (MBLs) catalyse the hydrolysis of almost all ß-lactam antibiotics. We report biophysical and kinetic studies on the São Paulo MBL (SPM-1), which reveal its Zn(ii) ion usage and mechanism as characteristic of the clinically important di-Zn(ii) dependent B1 MBL subfamily. Biophysical analyses employing crystallography, dynamic 19F NMR and ion mobility mass spectrometry, however, reveal that SPM-1 possesses loop and mobile element regions characteristic of the B2 MBLs. These include a mobile α3 region which is important in catalysis and determining inhibitor selectivity. SPM-1 thus appears to be a hybrid B1/B2 MBL. The results have implications for MBL evolution and inhibitor design.

16.
Nat Commun ; 5: 3423, 2014 Mar 05.
Artículo en Inglés | MEDLINE | ID: mdl-24594748

RESUMEN

Accumulation of (R)-2-hydroxyglutarate in cells results from mutations to isocitrate dehydrogenase that correlate with cancer. A recent study reports that (R)-, but not (S)-2-hydroxyglutarate, acts as a co-substrate for the hypoxia-inducible factor prolyl hydroxylases via enzyme-catalysed oxidation to 2-oxoglutarate. Here we investigate the mechanism of 2-hydroxyglutarate-enabled activation of 2-oxoglutarate oxygenases, including prolyl hydroxylase domain 2, the most important human prolyl hydroxylase isoform. We observe that 2-hydroxyglutarate-enabled catalysis by prolyl hydroxylase domain 2 is not enantiomer-specific and is stimulated by ferrous/ferric ion and reducing agents including L-ascorbate. The results reveal that 2-hydroxyglutarate is oxidized to 2-oxoglutarate non-enzymatically, likely via iron-mediated Fenton-chemistry, at levels supporting in vitro catalysis by 2-oxoglutarate oxygenases. Succinic semialdehyde and succinate are also identified as products of 2-hydroxyglutarate oxidation. Overall, the results rationalize the reported effects of 2-hydroxyglutarate on catalysis by prolyl hydroxylases in vitro and suggest that non-enzymatic 2-hydroxyglutarate oxidation may be of biological interest.


Asunto(s)
Oxidorreductasas de Alcohol/metabolismo , Glutaratos/química , Glutaratos/metabolismo , Oxigenasas/metabolismo , Ácido Ascórbico/metabolismo , Ácido Succínico/metabolismo , Ácido gamma-Aminobutírico/análogos & derivados , Ácido gamma-Aminobutírico/metabolismo
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