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1.
Biochemistry ; 62(16): 2442-2449, 2023 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-37526986

RESUMO

The interplay between active-site chemistry and functionally relevant enzyme motions can provide useful insights into selective enzyme modulation. Modulation of the hypoxia-sensing function of factor-inhibiting-HIF-1 (FIH) enzyme is a potential therapeutic strategy in disease states such as ischemia and cancer. The hypoxia-sensing function of FIH relies in major part on the tight coupling of the first half of the catalytic mechanism which involves O2 activation and eventual succinate production to the second half which involves HIF-1α/CTAD substrate hydroxylation. In this study, we demonstrate the role of a loop hinge domain in FIH (FIH102-118) called the 100s loop in maintaining this particular tight coupling. Molecular dynamics patterns from Gaussian Network Model (iGNM) database analysis of FIH identified the 100s loop as one dynamic domain containing a hinge residue (Tyr102) with a potential substrate positioning role. Enzymological and biophysical studies of the 100s loop point mutants revealed altered enzyme kinetics with the exception of the conservative FIH mutant Y102F, which suggests a sterics-related role for this residue. Removal of the bulk of Tyr102 (Y102A) resulted in succinate production, autohydroxylation, and an O2 binding environment comparable to wild-type FIH. However, the HIF-1α/CTAD substrate hydroxylation of this mutant was significantly reduced which implies that (1) the FIH loop hinge residue Tyr102 does not affect O2 activation, (2) the stacking steric interaction of Tyr102 is important in substrate positioning for productive hydroxylation, and (3) Tyr102 is important for the synchronization of O2 activation and substrate hydroxylation.

2.
Methods Enzymol ; 679: 363-380, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36682871

RESUMO

Primary kinetic isotope effects (KIEs) provide unique insight into enzymatic reactions, as they can reveal rate-limiting steps and detailed chemical mechanisms. HIF hydroxylases, part of a family of 2-oxoglutarate (2OG) oxygenases are central to the regulation of many crucial biological processes through O2-sensing, but present a challenge to monitor due to the large size of the protein substrate and the similarity between native and hydroxylated substrate. MALDI-TOF MS is a convenient tool to measure peptide masses, which can also be used to measure the discontinuous kinetics of peptide hydroxylation for Factor Inhibiting HIF (FIH). Using this technique, rate data can be observed from the mole-fraction of CTAD and CTAD-OH in small volumes, allowing noncompetitive H/D KIEs to be measured. Slow dCTAD substrate leads to extensive uncoupling of O2 consumption from peptide hydroxylation, leading to enzyme autohydroxylation, which is observed using UV-vis spectroscopy. Simultaneously measuring both the normal product, CTAD-OH, and the uncoupled product, autohydroxylated enzyme, the KIE on the microscopic step of hydrogen atom transfer (HAT) can be estimated. MALDI-MS analysis is a strong method for monitoring reactions that hydroxylate peptides, and can be generalized to other similar reactions, and simultaneous kinetic detection of branched products can provide valuable insight on microscopic KIEs at intermediate mechanistic steps.


Assuntos
Peptídeos , Proteínas Repressoras , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Proteínas Repressoras/química , Cinética , Hidroxilação , Peptídeos/metabolismo
3.
Biochemistry ; 60(44): 3315-3322, 2021 11 09.
Artigo em Inglês | MEDLINE | ID: mdl-34714626

RESUMO

Cellular hypoxia plays a crucial role in tissue development and adaptation to pO2. Central to cellular oxygen sensing is factor-inhibiting HIF-1α (FIH), an α-ketoglutarate (αKG)/non-heme iron(II)-dependent dioxygenase that hydroxylates a specific asparagine residue of hypoxia inducible factor-1α (HIF-1α). The high KM(O2) and rate-limiting decarboxylation step upon O2 activation are key features of the enzyme that classify it as an oxygen sensor and set it apart from other αKG/Fe(II)-dependent dioxygenases. Although the chemical intermediates following decarboxylation are presumed to follow the consensus mechanism of other αKG/Fe(II)-dependent dioxygenases, experiments have not previously demonstrated these canonical steps in FIH. In this work, a deuterated peptide substrate was used as a mechanistic probe for the canonical hydrogen atom transfer (HAT). Our data show a large kinetic isotope effect (KIE) in steady-state kinetics (Dkcat = 10 ± 1), revealing that the HAT occurs and is partially rate limiting on kcat. Kinetic studies showed that the deuterated peptide led FIH to uncouple O2 activation and provided the opportunity to spectroscopically observe the ferryl intermediate. This enzyme uncoupling was used as an internal competition with respect to the fate of the ferryl intermediate, demonstrating a large observed KIE on the uncoupling (Dk5 = 1.147 ± 0.005) and an intrinsic KIE on the HAT step (Dk > 15). The close energy barrier between αKG decarboxylation and HAT distinguishes FIH as an O2-sensing enzyme and is crucial for ensuring substrate specificity in the regulation of cellular O2 homeostasis.


Assuntos
Hipóxia Celular/fisiologia , Hidrogênio/metabolismo , Oxigenases de Função Mista/metabolismo , Proteínas Repressoras/metabolismo , Aclimatação , Adaptação Fisiológica , Dioxigenases/metabolismo , Metabolismo Energético/fisiologia , Homeostase , Humanos , Hipóxia , Subunidade alfa do Fator 1 Induzível por Hipóxia/metabolismo , Isótopos , Cinética , Oxigenases de Função Mista/fisiologia , Proteínas Repressoras/fisiologia , Especificidade por Substrato
4.
Biochemistry ; 58(39): 4047-4057, 2019 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-31499004

RESUMO

Protein dynamics are crucial for the mechanistically ordered enzymes to bind to their substrate in the correct sequence and perform catalysis. Factor-inhibiting HIF-1 (FIH) is a nonheme Fe(II) α-ketoglutarate-dependent oxygenase that is a key hypoxia (low pO2) sensor in humans. As these hypoxia-sensing enzymes follow a multistep chemical mechanism consuming α-ketoglutarate, a protein substrate that is hydroxylated, and O2, understanding protein flexibility and the order of substrate binding may aid in the development of strategies for selective targeting. The primary substrate of FIH is the C-terminal transactivation domain (CTAD) of hypoxia-inducible factor 1α (HIF) that is hydroxylated on the side chain of Asn803. We assessed changes in protein flexibility connected to metal and αKG binding, finding that (M+αKG) binding significantly stabilized the cupin barrel core of FIH as evidenced by enhanced thermal stability and decreased protein dynamics as assessed by global amide hydrogen/deuterium exchange mass spectrometry and limited proteolysis. Confirming predictions of the consensus mechanism, (M+αKG) increased the affinity of FIH for CTAD as measured by titrations monitoring intrinsic tryptophan fluorescence. The decreased protein dynamics caused by (M+αKG) enforces a sequentially ordered substrate binding sequence in which αKG binds before CTAD, suggesting that selective inhibition may require inhibitors that target the binding sites of both αKG and the prime substrate. A consequence of the correlation between dynamics and αKG binding is that all relevant ligands must be included in binding-based inhibitor screens, as shown by testing permutations of M, αKG, and inhibitor.


Assuntos
Subunidade alfa do Fator 1 Induzível por Hipóxia/química , Ácidos Cetoglutáricos/química , Oxigenases de Função Mista/química , Proteínas Repressoras/química , Sítios de Ligação , Catálise , Dicroísmo Circular , Escherichia coli/metabolismo , Humanos , Espectrometria de Massa com Troca Hidrogênio-Deutério , Hidroxilação , Subunidade alfa do Fator 1 Induzível por Hipóxia/metabolismo , Ácidos Cetoglutáricos/metabolismo , Cinética , Manganês/química , Oxigenases de Função Mista/metabolismo , Oxigênio/metabolismo , Plasmídeos/química , Ligação Proteica , Domínios Proteicos , Proteólise , Proteínas Repressoras/metabolismo , Especificidade por Substrato
5.
J Exp Biol ; 222(Pt 12)2019 06 24.
Artigo em Inglês | MEDLINE | ID: mdl-31160427

RESUMO

Embryos of Austrofundulus limnaeus can tolerate extreme environmental stresses by entering into a state of metabolic and developmental arrest known as diapause. Oxidative stress is ubiquitous in aerobic organisms and the unique biology and ecology of A. limnaeus likely results in frequent and repeated exposures to oxidative stress during development. The antioxidant capacity of A. limnaeus was explored during development by measuring antioxidant capacity due to small molecules and several enzymatic antioxidant systems. Diapause II embryos can survive for several days in 1% hydrogen peroxide without indications of negative effects. Surprisingly, both small and large molecule antioxidant systems have the highest capacity during early development, which may be due to maternal provisioning. Antioxidant capacity is largely invested in small molecules during early development and in enzymatic systems during late development. The switch in antioxidant mechanisms and decline in small molecule antioxidants during development correlates with the loss of extreme anoxia tolerance.


Assuntos
Antioxidantes/metabolismo , Ciprinodontiformes/metabolismo , Anaerobiose , Animais , Embrião não Mamífero/metabolismo , Desenvolvimento Embrionário/fisiologia
6.
Inorg Chem ; 57(20): 12588-12595, 2018 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-30252455

RESUMO

α-Ketoglutarate (αKG) dependent oxygenases comprise a large superfamily of enzymes that activate O2 for varied reactions. While most of these enzymes contain a nonheme Fe bound by a His2(Asp/Glu) facial triad, a small number of αKG-dependent halogenases require only the two His ligands to bind Fe and activate O2. The enzyme "factor inhibiting HIF" (FIH) contains a His2Asp facial triad and selectively hydroxylates polypeptides; however, removal of the Asp ligand in the Asp201→Gly variant leads to a highly active enzyme, seemingly without a complete facial triad. Herein, we report on the formation of an Fe-Cl cofactor structure for the Asp201→Gly FIH variant using X-ray absorption spectroscopy (XAS), which provides insight into the structure of the His2Cl facial triad found in halogenases. The Asp201→Gly variant supports anion dependent peptide hydroxylation, demonstrating the requirement for a complete His2X facial triad to support O2 reactivity. Our results indicated that exogenous ligand binding to form a complete His2X facial triad was essential for O2 activation and provides a structural model for the His2Cl-bound nonheme Fe found in halogenases.


Assuntos
Cloretos/química , Ferro/metabolismo , Oxigenases de Função Mista/metabolismo , Oxigênio/metabolismo , Proteínas Repressoras/metabolismo , Absorciometria de Fóton , Substituição de Aminoácidos , Cloretos/metabolismo , Ferro/química , Ligantes , Oxigenases de Função Mista/química , Ligação Proteica , Conformação Proteica , Proteínas Repressoras/química
7.
J Am Chem Soc ; 140(37): 11777-11783, 2018 09 19.
Artigo em Inglês | MEDLINE | ID: mdl-30148961

RESUMO

FIH [factor inhibiting HIF (hypoxia inducible factor)] is an α-ketoglutarate (αKG)-dependent nonheme iron enzyme that catalyzes the hydroxylation of the C-terminal transactivation domain (CAD) asparagine residue in HIF-1α to regulate cellular oxygen levels. The role of the facial triad carboxylate ligand in O2 activation and catalysis was evaluated by replacing the Asp201 residue with Gly (D201G), Ala (D201A), and Glu (D201E). Magnetic circular dichroism (MCD) spectroscopy showed that the (FeII)FIH variants were all 6-coordinate (6C) and the αKG plus CAD bound FIH variants were all 5-coordinate (5C), mirroring the behavior of the wild-type ( wt) enzyme. When only αKG is bound, all FIH variants exhibited weaker FeII-OH2 bonds for the sixth ligand compared to wt, and for αKG-bound D201E this is either extremely weak or the site is 5C, demonstrating that the Asp201 residue plays an important role in the wt enzyme in ensuring that the (FeII/αKG)FIH site remains 6C. Variable-temperature, variable-field (VTVH) MCD spectroscopy showed that all of the αKG- and CAD-bound FIH variants, though 5C, have different ground-state geometric and electronic structures, which impair their oxygen activation rates. Comparison of O2 consumption to substrate hydroxylation kinetics revealed uncoupling between the two half reactions in the variants. Thus, the Asp201 residue also ensures fidelity between CAD substrate binding and oxygen activation, enabling tightly coupled turnover.


Assuntos
Ácidos Carboxílicos/metabolismo , Compostos Ferrosos/metabolismo , Ácidos Cetoglutáricos/metabolismo , Oxigenases de Função Mista/metabolismo , Oxigênio/metabolismo , Ácidos Carboxílicos/química , Compostos Ferrosos/química , Humanos , Ácidos Cetoglutáricos/química , Oxigenases de Função Mista/química , Conformação Molecular , Oxigênio/química
8.
J Inorg Biochem ; 178: 63-69, 2018 01.
Artigo em Inglês | MEDLINE | ID: mdl-29078149

RESUMO

Non-heme Fe(II)/α-ketoglutarate (αKG)-dependent oxygenases catalyze a wide array of reactions through coupling oxidative decarboxylation of αKG to substrate oxygenation. This class of enzymes follows a sequential mechanism in which O2 reacts only after binding primary substrate, raising questions over how protein structure tailors molecular access to the Fe(II) cofactor. The enzyme "factor inhibiting hypoxia inducible factor" (FIH) senses pO2 in human cells by hydroxylating the C-terminal transactivation domain (CTAD), suggesting that structural elements limiting molecular access to the active site may limit the pO2 response. In this study, we tested the impact of a solvent-accessible tunnel in FIH on molecular access to the active site in FIH. The size of the tunnel was increased through alanine point mutagenesis (Y93A, E105A, and Q147A), followed by a suite of mechanistic and spectroscopic probes. Steady-state kinetics varying O2 or CTAD indicated that O2 passage through the tunnel was not affected by Ala substitutions, allowing us to conclude that this narrow tunnel did not impact pO2 sensing by FIH. Steady-state kinetics with varied αKG concentrations revealed increased substrate inhibition for the Ala variants, suggesting that a second αKG molecule may bind near the active site of FIH. If this solvent-accessible tunnel is the O2 entry tunnel, it may be narrow in order to permit O2 access while preventing metabolic intermediates, such as αKG, from inhibiting FIH under physiological conditions.


Assuntos
Fator 1 Induzível por Hipóxia/antagonistas & inibidores , Fator 1 Induzível por Hipóxia/química , Ácidos Cetoglutáricos/metabolismo , Oxigenases/metabolismo , Domínio Catalítico , Ácido Cítrico/química , Ácido Cítrico/farmacologia , Relação Dose-Resposta a Droga , Eletroforese em Gel de Poliacrilamida , Variação Genética , Humanos , Fator 1 Induzível por Hipóxia/genética , Ácidos Cetoglutáricos/química , Cinética , Ácido Oxaloacético/química , Ácido Oxaloacético/farmacologia , Oxigenases/química , Solventes/química
9.
J Inorg Biochem ; 166: 26-33, 2017 01.
Artigo em Inglês | MEDLINE | ID: mdl-27815979

RESUMO

The factor inhibiting hypoxia inducible factor-1α (FIH) is a nonheme Fe(II)/αKG oxygenase using a 2-His-1-Asp facial triad. FIH activates O2 via oxidative decarboxylation of α-ketoglutarate (αKG) to generate an enzyme-based oxidant which hydroxylates the Asn803 residue within the C-terminal transactivation domain (CTAD) of HIF-1α. Tight coupling of these two sequential reactions requires a structural linkage between the Fe(II) and the substrate binding site to ensure that O2 activation occurs after substrate binds. We tested the hypothesis that the facial triad carboxylate (Asp201) of FIH linked substrate binding and O2 binding sites. Asp201 variants of FIH were constructed and thoroughly characterized in vitro using steady-state kinetics, crystallography, autohydroxylation, and coupling measurements. Our studies revealed each variant activated O2 with a catalytic efficiency similar to that of wild-type (WT) FIH (kcataKM(O2)=0.17µM-1min-1), but led to defects in the coupling of O2 activation to substrate hydroxylation. Steady-state kinetics showed similar catalytic efficiencies for hydroxylation by WT-FIH (kcat/KM(CTAD)=0.42µM-1min-1) and D201G (kcat/KM(CTAD)=0.34µM-1min-1); hydroxylation by D201E was greatly impaired, while hydroxylation by D201A was undetectable. Analysis of the crystal structure of the D201E variant revealed steric crowding near the diffusible ligand site supporting a role for sterics from the facial triad carboxylate in the O2 binding order. Our data support a model in which the facial triad carboxylate Asp201 provides both steric and polar contacts to favor O2 access to the Fe(II) only after substrate binds, leading to coupled turnover in FIH and other αKG oxygenases.


Assuntos
Oxigenases de Função Mista/química , Oxigênio/química , Proteínas Repressoras/química , Substituição de Aminoácidos , Asparagina/química , Asparagina/genética , Asparagina/metabolismo , Catálise , Domínio Catalítico , Cristalografia por Raios X , Humanos , Hidroxilação , Oxigenases de Função Mista/genética , Oxigenases de Função Mista/metabolismo , Mutação de Sentido Incorreto , Oxigênio/metabolismo , Proteínas Repressoras/genética , Proteínas Repressoras/metabolismo
10.
Biochemistry ; 55(2): 277-86, 2016 Jan 19.
Artigo em Inglês | MEDLINE | ID: mdl-26727884

RESUMO

The Fe(2+)/α-ketoglutarate (αKG)-dependent oxygenases use molecular oxygen to conduct a wide variety of reactions with important biological implications, such as DNA base excision repair, histone demethylation, and the cellular hypoxia response. These enzymes follow a sequential mechanism in which O2 binds and reacts after the primary substrate binds, making those structural factors that promote productive O2 binding central to their chemistry. A large challenge in this field is to identify strategies that engender productive turnover. Factor inhibiting HIF (FIH) is a Fe(2+)/αKG-dependent oxygenase that forms part of the O2 sensing machinery in human cells by hydroxylating the C-terminal transactivation domain (CTAD) found within the HIF-1α protein. The structure of FIH was determined with the O2 analogue NO bound to Fe, offering the first direct insight into the gas binding geometry in this enzyme. Through a combination of density functional theory calculations, {FeNO}(7) electron paramagnetic resonance spectroscopy, and ultraviolet-visible absorption spectroscopy, we demonstrate that CTAD binding stimulates O2 reactivity by altering the orientation of the bound gas molecule. Although unliganded FIH binds NO with moderate affinity, the bound gas can adopt either of two orientations with similar stability; upon CTAD binding, NO adopts a single preferred orientation that is appropriate for supporting oxidative decarboxylation. Combined with other studies of related enzymes, our data suggest that substrate-induced reorientation of bound O2 is the mechanism utilized by the αKG oxygenases to tightly couple O2 activation to substrate hydroxylation.


Assuntos
Ácidos Cetoglutáricos/metabolismo , Oxigenases de Função Mista/metabolismo , Oxigenases/metabolismo , Proteínas Repressoras/metabolismo , Espectroscopia de Ressonância de Spin Eletrônica , Humanos , Ferro/metabolismo , Óxido Nítrico/metabolismo , Oxigênio/metabolismo , Estrutura Secundária de Proteína , Especificidade por Substrato
11.
Biochemistry ; 54(18): 2851-7, 2015 May 12.
Artigo em Inglês | MEDLINE | ID: mdl-25857330

RESUMO

PHD2 is a 2-oxoglutarate, non-heme Fe(2+)-dependent oxygenase that senses O2 levels in human cells by hydroxylating two prolyl residues in the oxygen-dependent degradation domain (ODD) of HIF1α. Identifying the active site contacts that determine the rate of reaction at limiting O2 concentrations is crucial for understanding how this enzyme senses pO2 and may suggest methods for chemically altering hypoxia responses. A hydrogen bonding network extends from the Fe(II) cofactor through ordered waters to the Thr(387) residue in the second coordination sphere. Here we tested the impact of the side chain of Thr(387) on the reactivity of PHD2 toward O2 through a combination of point mutagenesis, steady state kinetic experiments and {FeNO}(7) EPR spectroscopy. The steady state kinetic parameters for Thr(387) → Asn were very similar to those of wild-type (WT) PHD2, but kcat and kcat/KM(O2) for Thr(387) → Ala were increased by roughly 15-fold. X-Band electron paramagnetic resonance spectroscopy of the {FeNO}(7) centers of the (Fe+NO+2OG) enzyme forms showed the presence of a more rhombic line shape in Thr(387) → Ala than in WT PHD2, indicating an altered conformation for bound gas in this variant. Here we show that the side chain of residue Thr(387) plays a significant role in determining the rate of turnover by PHD2 at low O2 concentrations.


Assuntos
Alanina/genética , Prolina Dioxigenases do Fator Induzível por Hipóxia/química , Oxigênio/química , Treonina/genética , Espectroscopia de Ressonância de Spin Eletrônica , Humanos , Prolina Dioxigenases do Fator Induzível por Hipóxia/genética , Cinética , Mutação Puntual , Proteínas Recombinantes de Fusão/química
13.
Biochemistry ; 53(36): 5750-8, 2014 Sep 16.
Artigo em Inglês | MEDLINE | ID: mdl-25119663

RESUMO

Nonheme Fe(II)/αKG-dependent oxygenases catalyze diverse reactions, typically inserting an O atom from O2 into a C-H bond. Although the key to their catalytic cycle is the fact that binding and positioning of primary substrate precede O2 activation, the means by which substrate binding stimulates turnover is not well understood. Factor Inhibiting HIF (FIH) is a Fe(II)/αKG-dependent oxygenase that acts as a cellular oxygen sensor in humans by hydroxylating the target residue Asn(803), found in the C-terminal transactivation domain (CTAD) of hypoxia inducible factor-1. FIH-Gln(239) makes two hydrogen bonds with CTAD-Asn(803), positioning this target residue over the Fe(II). We hypothesized the positioning of the side chain of CTAD-Asn(803) by FIH-Gln(239) was critical for stimulating O2 activation and subsequent substrate hydroxylation. The steady-state characterization of five FIH-Gln(239) variants (Ala, Asn, Glu, His, and Leu) tested the role of hydrogen bonding potential and sterics near the target residue. Each variant exhibited a 20-1200-fold decrease in kcat and kcat/KM(CTAD), but no change in KM(CTAD), indicating that the step after CTAD binding was affected by point mutation. Uncoupled O2 activation was prominent in these variants, as shown by large coupling ratios (C = [succinate]/[CTAD-OH] = 3-5) for each of the FIH-Gln(239) → X variants. The coupling ratios decreased in D2O, indicating an isotope-sensitive inactivation for variants, not observed in the wild type. The data presented indicate that the proper positioning of CTAD-Asn(803) by FIH-Gln(239) is necessary to suppress uncoupled turnover and to support substrate hydroxylation, suggesting substrate positioning may be crucial for directing O2 reactivity within the broader class of αKG hydroxylases.


Assuntos
Glicina/metabolismo , Oxigenases de Função Mista/metabolismo , Proteínas Repressoras/metabolismo , Sequência de Aminoácidos , Cinética , Oxigenases de Função Mista/química , Dados de Sequência Molecular , Proteínas Repressoras/química , Espectrometria de Fluorescência , Especificidade por Substrato
15.
J Inorg Biochem ; 133: 63-72, 2014 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-24468676

RESUMO

The ability to sense and adapt to changes in pO2 is crucial for basic metabolism in most organisms, leading to elaborate pathways for sensing hypoxia (low pO2). This review focuses on the mechanisms utilized by mammals and bacteria to sense hypoxia. While responses to acute hypoxia in mammalian tissues lead to altered vascular tension, the molecular mechanism of signal transduction is not well understood. In contrast, chronic hypoxia evokes cellular responses that lead to transcriptional changes mediated by the hypoxia inducible factor (HIF), which is directly controlled by post-translational hydroxylation of HIF by the non-heme Fe(II)/αKG-dependent enzymes FIH and PHD2. Research on PHD2 and FIH is focused on developing inhibitors and understanding the links between HIF binding and the O2 reaction in these enzymes. Sulfur speciation is a putative mechanism for acute O2-sensing, with special focus on the role of H2S. This sulfur-centered model is discussed, as are some of the directions for further refinement of this model. In contrast to mammals, bacterial O2-sensing relies on protein cofactors that either bind O2 or oxidatively decompose. The sensing modality for bacterial O2-sensors is either via altered DNA binding affinity of the sensory protein, or else due to the actions of a two-component signaling cascade. Emerging data suggests that proteins containing a hemerythrin-domain, such as FBXL5, may serve to connect iron sensing to O2-sensing in both bacteria and humans. As specific molecular machinery becomes identified, these hypoxia sensing pathways present therapeutic targets for diseases including ischemia, cancer, or bacterial infection.


Assuntos
Hipóxia/metabolismo , Oxigênio/metabolismo , Transdução de Sinais/genética , Animais , Bactérias/metabolismo , Heme/metabolismo , Humanos , Hipóxia/genética , Fator 1 Induzível por Hipóxia/genética , Fator 1 Induzível por Hipóxia/metabolismo , Prolina Dioxigenases do Fator Induzível por Hipóxia/metabolismo , Mamíferos/metabolismo
16.
Dalton Trans ; 43(4): 1505-8, 2014 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-24292428

RESUMO

Non-heme Fe(II) enzymes exhibit a general mechanistic strategy where binding all cosubstrates opens a coordination site on the Fe(II) for O2 activation. This study shows that strong-donor ligands, steric interactions with the substrate and second-sphere H-bonding to the facial triad carboxylate allow for five-coordinate site formation in this enzyme superfamily.


Assuntos
Enzimas/química , Compostos Ferrosos/química , Heme/química , Especificidade por Substrato
17.
J Am Chem Soc ; 135(26): 9665-74, 2013 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-23742069

RESUMO

Factor inhibiting hypoxia-inducible factor (FIH) is an α-ketoglutarate (αKG)-dependent enzyme which catalyzes hydroxylation of residue Asn803 in the C-terminal transactivation domain (CAD) of hypoxia-inducible factor 1α (HIF-1α) and plays an important role in cellular oxygen sensing and hypoxic response. Circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature, variable-field (VTVH) MCD spectroscopies are used to determine the geometric and electronic structures of FIH in its (Fe(II)), (Fe(II)/αKG), and (Fe(II)/αKG/CAD) forms. (Fe(II))FIH and (Fe(II)/αKG)FIH are found to be six-coordinate (6C), whereas (Fe(II)/αKG/CAD)FIH is found to be a 5C/6C mixture. Thus, FIH follows the general mechanistic strategy of non-heme Fe(II) enzymes. Modeling shows that, when Arg238 of FIH is removed, the facial triad carboxylate binds to Fe(II) in a bidentate mode with concomitant lengthening of the Fe(II)/αKG carbonyl bond, which would inhibit the O2 reaction. Correlations over α-keto acid-dependent enzymes and with the extradiol dioxygenases show that members of these families (where both the electron source and O2 bind to Fe(II)) have a second-sphere residue H-bonding to the terminal oxygen of the carboxylate, which stays monodentate. Alternatively, structures of the pterin-dependent and Rieske dioxygenases, which do not have substrate binding to Fe(II), lack H-bonds to the carboxylate and thus allow its bidentate coordination which would direct O2 reactivity. Finally, vis-UV MCD spectra show an unusually high-energy Fe(II) → αKG π* metal-to-ligand charge transfer transition in (Fe(II)/αKG)FIH which is red-shifted upon CAD binding. This red shift indicates formation of H-bonds to the αKG that lower the energy of its carbonyl LUMO, activating it for nucleophilic attack by the Fe-O2 intermediate formed along the reaction coordinate.


Assuntos
Oxigenases de Função Mista/química , Proteínas Repressoras/química , Dicroísmo Circular , Cristalografia por Raios X , Humanos , Oxigenases de Função Mista/metabolismo , Modelos Moleculares , Teoria Quântica , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Proteínas Repressoras/metabolismo , Espectroscopia de Luz Próxima ao Infravermelho
18.
J Inorg Biochem ; 126: 55-60, 2013 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-23787140

RESUMO

HIF prolyl-4-hydroxylase 2 (PHD2) is a non-heme Fe, 2-oxoglutarate (2OG) dependent dioxygenase that regulates the hypoxia inducible transcription factor (HIF) by hydroxylating two conserved prolyl residues in N-terminal oxygen degradation domain (NODD) and C-terminal oxygen degradation domain (CODD) of HIF-1α. Prior studies have suggested that the substrate preference of PHD2 arises from binding contacts with the ß2ß3 loop of PHD2. In this study we tested the substrate selectivity of PHD2 by kinetic competition assays, varied ionic strength, and global protein flexibility using amide H/D exchange (HDX). Our results revealed that PHD2 preferred CODD by 20-fold over NODD and that electrostatics influenced this effect. Global HDX monitored by mass spectrometry indicated that binding of Fe(II) and 2OG stabilized the overall protein structure but the saturating concentrations of either NODD or CODD caused an identical change in protein flexibility. These observations imply that both substrates stabilize the ß2ß3 loop to the same extent. Under unsaturated substrate conditions NODD led to a higher HDX rate than CODD due to its lower binding affinity to PHD2. Our results suggest that loop closure is the dominant contributor to substrate selectivity in PHD2.


Assuntos
Subunidade alfa do Fator 1 Induzível por Hipóxia/química , Prolina Dioxigenases do Fator Induzível por Hipóxia/química , Ferro/química , Ácidos Cetoglutáricos/química , Modelos Moleculares , Sítios de Ligação , Ligação Competitiva , Cátions Bivalentes , Escherichia coli/genética , Humanos , Hidroxilação , Subunidade alfa do Fator 1 Induzível por Hipóxia/genética , Prolina Dioxigenases do Fator Induzível por Hipóxia/genética , Cinética , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Estrutura Secundária de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Eletricidade Estática , Especificidade por Substrato , Termodinâmica
19.
Metallomics ; 5(4): 287-301, 2013 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-23446356

RESUMO

The Fe(ii)/αketoglutarate (αKG) dependent oxygenases catalyze a diverse range of reactions significant in biological processes such as antibiotic biosynthesis, lipid metabolism, oxygen sensing, and DNA and RNA repair. Although functionally diverse, the eight-stranded ß-barrel (cupin) and HX(D/E)XnH facial triad motifs are conserved in this super-family of enzymes. Crystal structure analysis of 25 αKG oxygenases reveals two stereoisomers of the Fe cofactor, Anti and Clock, which differ in the relative position of the exchangeable ligand position and the primary substrate. Herein, we discuss the relationship between the chemical mechanism and the secondary coordination sphere of the αKG oxygenases, within the constraints of the stereochemistry of the Fe cofactor. Sequence analysis of the cupin barrel indicates that a small subset of positions constitute the second coordination sphere, which has significant ramifications for the structure of the ferryl intermediate. The competence of both Anti and Clock stereoisomers of Fe points to a ferryl intermediate that is 5 coordinate. The small number of conserved close contacts within the active sites of αKG oxygenases can be extended to chemically related enzymes, such as the αKG-dependent halogenases SyrB2 and CytC3, and the non-αKG dependent dioxygenases isopenicillin N synthase (IPNS) and cysteine dioxygenase (CDO).


Assuntos
Metais/química , Oxigenases/química , Oxigenases/metabolismo , Sequência de Aminoácidos , Ácidos Cetoglutáricos , Metais/metabolismo , Dados de Sequência Molecular , Estrutura Secundária de Proteína , Estereoisomerismo , Especificidade por Substrato
20.
Biochemistry ; 52(9): 1594-602, 2013 Mar 05.
Artigo em Inglês | MEDLINE | ID: mdl-23351038

RESUMO

Oxygen homeostasis plays a critical role in angiogenesis, erythropoiesis, and cell metabolism. Oxygen homeostasis is set by the hypoxia inducible factor-1α (HIF-1α) pathway, which is controlled by factor inhibiting HIF-1α (FIH). FIH is a non-heme Fe(II), α-ketoglutarate (αKG)-dependent dioxygenase that inhibits HIF-1α by hydroxylating the C-terminal transactivation domain (CTAD) of HIF-1α at HIF-Asn(803). A tight coupling between CTAD binding and O2 activation is essential for hypoxia sensing, making changes in the coordination geometry of Fe(II) upon CTAD encounter a crucial feature of this enzyme. Although the consensus chemical mechanism for FIH proposes that CTAD binding triggers O2 activation by causing the Fe(II) cofactor to release an aquo ligand, experimental evidence of this has been absent. More broadly, this proposed coordination change at Fe(II) has not been observed during steady-state turnover in any αKG oxygenase to date. In this work, solvent isotope effects (SIEs) were used as a direct mechanistic probe of substrate-triggered aquo release in FIH, as inverse SIEs (SIE < 1) are signatures for pre-equilibrium aquo release from metal ions. Our mechanistic studies of FIH have revealed inverse solvent isotope effects in the steady-state rate constants at limiting concentrations of CTAD or αKG [(D2O)kcat/KM(CTAD) = 0.40 ± 0.07, and (D2O)kcat/KM(αKG) = 0.32 ± 0.08], providing direct evidence of aquo release during steady-state turnover. Furthermore, the SIE at saturating concentrations of CTAD and αKG was inverse ((D2O)kcat = 0.51 ± 0.07), indicating that aquo release occurs after CTAD binds. The inverse kinetic SIEs observed in the steady state for FIH can be explained by a strong Fe-OH2 bond. The stable Fe-OH2 bond plays an important part in FIH's regulatory role over O2 homeostasis in humans and points toward a strategy for tightly coupling O2 activation with CTAD hydroxylation that relies on substrate triggering.


Assuntos
Óxido de Deutério/metabolismo , Subunidade alfa do Fator 1 Induzível por Hipóxia/metabolismo , Ácidos Cetoglutáricos/metabolismo , Oxigenases de Função Mista/metabolismo , Proteínas Repressoras/metabolismo , Sequência de Aminoácidos , Humanos , Subunidade alfa do Fator 1 Induzível por Hipóxia/química , Cinética , Oxigenases de Função Mista/química , Dados de Sequência Molecular , Oxigênio/metabolismo , Estrutura Terciária de Proteína , Proteínas Repressoras/química , Especificidade por Substrato
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