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1.
Annu Rev Biochem ; 82: 531-50, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23746262

RESUMO

Methylamine dehydrogenase (MADH) catalyzes the oxidative deamination of methylamine to formaldehyde and ammonia. Tryptophan tryptophylquinone (TTQ) is the protein-derived cofactor of MADH required for this catalytic activity. TTQ is biosynthesized through the posttranslational modification of two tryptophan residues within MADH, during which the indole rings of two tryptophan side chains are cross-linked and two oxygen atoms are inserted into one of the indole rings. MauG is a c-type diheme enzyme that catalyzes the final three reactions in TTQ formation. In total, this is a six-electron oxidation process requiring three cycles of MauG-dependent two-electron oxidation events using either H2O2 or O2. The MauG redox form responsible for the catalytic activity is an unprecedented bis-Fe(IV) species. The amino acids of MADH that are modified are ≈ 40 Å from the site where MauG binds oxygen, and the reaction proceeds by a hole hopping electron transfer mechanism. This review addresses these highly unusual aspects of the long-range catalytic reaction mediated by MauG.


Assuntos
Heme/metabolismo , Indolquinonas/biossíntese , Oxirredutases atuantes sobre Doadores de Grupo CH-NH/metabolismo , Paracoccus denitrificans/enzimologia , Processamento de Proteína Pós-Traducional/fisiologia , Triptofano/análogos & derivados , Triptofano/metabolismo , Catálise , Transporte de Elétrons , Oxirredução , Paracoccus denitrificans/genética , Paracoccus denitrificans/metabolismo , Triptofano/biossíntese
2.
Genes Dev ; 28(16): 1758-71, 2014 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-25128496

RESUMO

The dynamic reversible methylation of lysine residues on histone proteins is central to chromatin biology. Key components are demethylase enzymes, which remove methyl moieties from lysine residues. KDM2A, a member of the Jumonji C domain-containing histone lysine demethylase family, specifically targets lower methylation states of H3K36. Here, structural studies reveal that H3K36 specificity for KDM2A is mediated by the U-shaped threading of the H3K36 peptide through a catalytic groove within KDM2A. The side chain of methylated K36 inserts into the catalytic pocket occupied by Ni(2+) and cofactor, where it is positioned and oriented for demethylation. Key residues contributing to K36me specificity on histone H3 are G33 and G34 (positioned within a narrow channel), P38 (a turn residue), and Y41 (inserts into its own pocket). Given that KDM2A was found to also bind the H3K36me3 peptide, we postulate that steric constraints could prevent α-ketoglutarate from undergoing an "off-line"-to-"in-line" transition necessary for the demethylation reaction. Furthermore, structure-guided substitutions of residues in the KDM2A catalytic pocket abrogate KDM2A-mediated functions important for suppression of cancer cell phenotypes. Together, our results deduce insights into the molecular basis underlying KDM2A regulation of the biologically important methylated H3K36 mark.


Assuntos
Histonas/metabolismo , Histona Desmetilases com o Domínio Jumonji/química , Histona Desmetilases com o Domínio Jumonji/metabolismo , Modelos Moleculares , Animais , Sítios de Ligação , Linhagem Celular , Instabilidade Genômica , Histona Desmetilases com o Domínio Jumonji/genética , Metilação , Camundongos , Mutação , Ligação Proteica , Estrutura Quaternária de Proteína
3.
J Am Chem Soc ; 141(10): 4398-4405, 2019 03 13.
Artigo em Inglês | MEDLINE | ID: mdl-30811189

RESUMO

Understanding the biosynthesis of cofactors is fundamental to the life sciences, yet to date a few important pathways remain unresolved. One example is the redox cofactor pyrroloquinoline quinone (PQQ), which is critical for C1 metabolism in many microorganisms, a disproportionate number of which are opportunistic human pathogens. While the initial and final steps of PQQ biosynthesis, involving PqqD/E and PqqC, have been elucidated, the precise nature and order of the remaining transformations in the pathway are unknown. Here we show evidence that the remaining essential biosynthetic enzyme PqqB is an iron-dependent hydroxylase catalyzing oxygen-insertion reactions that are proposed to produce the quinone moiety of the mature PQQ cofactor. The demonstrated reactions of PqqB are unprecedented within the metallo ß-lactamase protein family and expand the catalytic repertoire of nonheme iron hydroxylases. These new findings also generate a nearly complete description of the PQQ biosynthetic pathway.


Assuntos
Proteínas de Bactérias/química , Di-Hidroxifenilalanina/análogos & derivados , Oxigenases de Função Mista/química , Catálise , Di-Hidroxifenilalanina/química , Hidroxilação , Ferro/química , Methylobacterium extorquens/enzimologia , Modelos Químicos , Zinco/química
4.
Biochemistry ; 57(8): 1306-1315, 2018 02 27.
Artigo em Inglês | MEDLINE | ID: mdl-29405700

RESUMO

The Radical SAM (RS) enzyme PqqE catalyzes the first step in the biosynthesis of the bacterial cofactor pyrroloquinoline quinone, forming a new carbon-carbon bond between two side chains within the ribosomally synthesized peptide substrate PqqA. In addition to the active site RS 4Fe-4S cluster, PqqE is predicted to have two auxiliary Fe-S clusters, like the other members of the SPASM domain family. Here we identify these sites and examine their structure using a combination of X-ray crystallography and Mössbauer and electron paramagnetic resonance (EPR) spectroscopies. X-ray crystallography allows us to identify the ligands to each of the two auxiliary clusters at the C-terminal region of the protein. The auxiliary cluster nearest the RS site (AuxI) is in the form of a 2Fe-2S cluster ligated by four cysteines, an Fe-S center not seen previously in other SPASM domain proteins; this assignment is further supported by Mössbauer and EPR spectroscopies. The second, more remote cluster (AuxII) is a 4Fe-4S center that is ligated by three cysteine residues and one aspartate residue. In addition, we examined the roles these ligands play in catalysis by the RS and AuxII clusters using site-directed mutagenesis coupled with EPR spectroscopy. Lastly, we discuss the possible functional consequences that these unique AuxI and AuxII clusters may have in catalysis for PqqE and how these may extend to additional RS enzymes catalyzing the post-translational modification of ribosomally encoded peptides.


Assuntos
Proteínas de Bactérias/química , Endopeptidases/química , Proteínas Ferro-Enxofre/química , Methylobacterium extorquens/química , Cristalografia por Raios X , Espectroscopia de Ressonância de Spin Eletrônica , Modelos Moleculares , Conformação Proteica , Temperatura
5.
Biochem J ; 474(23): 3871-3886, 2017 11 10.
Artigo em Inglês | MEDLINE | ID: mdl-29025976

RESUMO

In the interest of decreasing dependence on fossil fuels, microbial hydrocarbon biosynthesis pathways are being studied for renewable, tailored production of specialty chemicals and biofuels. One candidate is long-chain olefin biosynthesis, a widespread bacterial pathway that produces waxy hydrocarbons. Found in three- and four-gene clusters, oleABCD encodes the enzymes necessary to produce cis-olefins that differ by alkyl chain length, degree of unsaturation, and alkyl chain branching. The first enzyme in the pathway, OleA, catalyzes the Claisen condensation of two fatty acyl-coenzyme A (CoA) molecules to form a ß-keto acid. In this report, the mechanistic role of Xanthomonas campestris OleA Glu117 is investigated through mutant enzymes. Crystal structures were determined for each mutant as well as their complex with the inhibitor cerulenin. Complemented by substrate modeling, these structures suggest that Glu117 aids in substrate positioning for productive carbon-carbon bond formation. Analysis of acyl-CoA substrate hydrolysis shows diminished activity in all mutants. When the active site lacks an acidic residue in the 117 position, OleA cannot form condensed product, demonstrating that Glu117 has a critical role upstream of the essential condensation reaction. Profiling of pH dependence shows that the apparent pKa for Glu117 is affected by mutagenesis. Taken together, we propose that Glu117 is the general base needed to prime condensation via deprotonation of the second, non-covalently bound substrate during turnover. This is the first example of a member of the thiolase superfamily of condensing enzymes to contain an active site base originating from the second monomer of the dimer.


Assuntos
Proteínas de Bactérias/química , Ligases/química , Xanthomonas campestris/enzimologia , Acil Coenzima A/química , Acil Coenzima A/genética , Alcenos/química , Alcenos/metabolismo , Substituição de Aminoácidos , Proteínas de Bactérias/genética , Cristalografia por Raios X , Ácido Glutâmico/química , Ácido Glutâmico/genética , Ligases/genética , Mutação de Sentido Incorreto , Xanthomonas campestris/genética
6.
J Bacteriol ; 199(9)2017 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-28223313

RESUMO

Bacteria from different phyla produce long-chain olefinic hydrocarbons derived from an OleA-catalyzed Claisen condensation of two fatty acyl coenzyme A (acyl-CoA) substrates, followed by reduction and oxygen elimination reactions catalyzed by the proteins OleB, OleC, and OleD. In this report, OleA, OleB, OleC, and OleD were individually purified as soluble proteins, and all were found to be essential for reconstituting hydrocarbon biosynthesis. Recombinant coexpression of tagged OleABCD proteins from Xanthomonas campestris in Escherichia coli and purification over His6 and FLAG columns resulted in OleA separating, while OleBCD purified together, irrespective of which of the four Ole proteins were tagged. Hydrocarbon biosynthetic activity of copurified OleBCD assemblies could be reconstituted by adding separately purified OleA. Immunoblots of nondenaturing gels using anti-OleC reacted with X. campestris crude protein lysate indicated the presence of a large protein assembly containing OleC in the native host. Negative-stain electron microscopy of recombinant OleBCD revealed distinct large structures with diameters primarily between 24 and 40 nm. Assembling OleB, OleC, and OleD into a complex may be important to maintain stereochemical integrity of intermediates, facilitate the movement of hydrophobic metabolites between enzyme active sites, and protect the cell against the highly reactive ß-lactone intermediate produced by the OleC-catalyzed reaction.IMPORTANCE Bacteria biosynthesize hydrophobic molecules to maintain a membrane, store carbon, and for antibiotics that help them survive in their niche. The hydrophobic compounds are often synthesized by a multidomain protein or by large multienzyme assemblies. The present study reports on the discovery that long-chain olefinic hydrocarbons made by bacteria from different phyla are produced by multienzyme assemblies in X. campestris The OleBCD multienzyme assemblies are thought to compartmentalize and sequester olefin biosynthesis from the rest of the cell. This system provides additional insights into how bacteria control specific biosynthetic pathways.


Assuntos
Alcenos/metabolismo , Vias Biossintéticas , Hidrocarbonetos/metabolismo , Complexos Multienzimáticos/metabolismo , Xanthomonas campestris/metabolismo , Proteínas de Bactérias/genética , Domínio Catalítico , Escherichia coli/genética , Complexos Multienzimáticos/química , Complexos Multienzimáticos/isolamento & purificação , Especificidade por Substrato , Xanthomonas campestris/química
7.
Biochemistry ; 56(21): 2735-2746, 2017 05 30.
Artigo em Inglês | MEDLINE | ID: mdl-28481092

RESUMO

Biosynthesis of the ribosomally synthesized and post-translationally modified peptide (RiPP), pyrroloquinoline quinone (PQQ), is initiated when the precursor peptide, PqqA, is recognized and bound by the RiPP precursor peptide recognition element (RRE), PqqD, for presentation to the first enzyme in the pathway, PqqE. Unlike other RiPP-producing, postribosomal peptide synthesis (PRPS) pathways in which the RRE is a component domain of the first enzyme, PqqD is predominantly a separate scaffolding protein that forms a ternary complex with the precursor peptide and first tailoring enzyme. As PqqD is a stable, independent RRE, this makes the PQQ pathway an ideal PRPS model system for probing RRE interactions using nuclear magnetic resonance (NMR). Herein, we present both the solution NMR structure of Methylobacterium extorquens PqqD and results of 1H-15N HSQC binding experiments that identify the PqqD residues involved in binding the precursor peptide, PqqA, and the enzyme, PqqE. The reported structural model for an independent RRE, along with the mapped binding surfaces, will inform future efforts both to understand and to manipulate PRPS pathways.


Assuntos
Proteínas de Bactérias/metabolismo , Methylobacterium extorquens/enzimologia , Chaperonas Moleculares/metabolismo , Ressonância Magnética Nuclear Biomolecular , Oxirredutases/metabolismo , Cofator PQQ/biossíntese , Proteínas de Bactérias/química , Sítios de Ligação , Methylobacterium extorquens/metabolismo , Modelos Moleculares , Chaperonas Moleculares/química , Oxirredutases/química , Cofator PQQ/química , Cofator PQQ/metabolismo , Conformação Proteica
8.
Biochemistry ; 56(2): 348-351, 2017 Jan 17.
Artigo em Inglês | MEDLINE | ID: mdl-28029240

RESUMO

The first ß-lactone synthetase enzyme is reported, creating an unexpected link between the biosynthesis of olefinic hydrocarbons and highly functionalized natural products. The enzyme OleC, involved in the microbial biosynthesis of long-chain olefinic hydrocarbons, reacts with syn- and anti-ß-hydroxy acid substrates to yield cis- and trans-ß-lactones, respectively. Protein sequence comparisons reveal that enzymes homologous to OleC are encoded in natural product gene clusters that generate ß-lactone rings, suggesting a common mechanism of biosynthesis.


Assuntos
Proteínas de Bactérias/genética , Coenzima A Ligases/genética , Regulação Bacteriana da Expressão Gênica , Lactonas/metabolismo , Micrococcus luteus/genética , Stenotrophomonas maltophilia/genética , Streptomyces/genética , Alcenos/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/metabolismo , Produtos Biológicos/metabolismo , Coenzima A Ligases/metabolismo , Hidroxiácidos , Micrococcus luteus/enzimologia , Família Multigênica , Óperon , Homologia de Sequência de Aminoácidos , Stenotrophomonas maltophilia/enzimologia , Streptomyces/enzimologia
9.
J Biol Chem ; 291(52): 26698-26706, 2016 Dec 23.
Artigo em Inglês | MEDLINE | ID: mdl-27815501

RESUMO

Phylogenetically diverse microbes that produce long chain, olefinic hydrocarbons have received much attention as possible sources of renewable energy biocatalysts. One enzyme that is critical for this process is OleA, a thiolase superfamily enzyme that condenses two fatty acyl-CoA substrates to produce a ß-ketoacid product and initiates the biosynthesis of long chain olefins in bacteria. Thiolases typically utilize a ping-pong mechanism centered on an active site cysteine residue. Reaction with the first substrate produces a covalent cysteine-thioester tethered acyl group that is transferred to the second substrate through formation of a carbon-carbon bond. Although the basics of thiolase chemistry are precedented, the mechanism by which OleA accommodates two substrates with extended carbon chains and a coenzyme moiety-unusual for a thiolase-are unknown. Gaining insights into this process could enable manipulation of the system for large scale olefin production with hydrocarbon chains lengths equivalent to those of fossil fuels. In this study, mutagenesis of the active site cysteine in Xanthomonas campestris OleA (Cys143) enabled trapping of two catalytically relevant species in crystals. In the resulting structures, long chain alkyl groups (C12 and C14) and phosphopantetheinate define three substrate channels in a T-shaped configuration, explaining how OleA coordinates its two substrates and product. The C143A OleA co-crystal structure possesses a single bound acyl-CoA representing the Michaelis complex with the first substrate, whereas the C143S co-crystal structure contains both acyl-CoA and fatty acid, defining how a second substrate binds to the acyl-enzyme intermediate. An active site glutamate (Gluß117) is positioned to deprotonate bound acyl-CoA and initiate carbon-carbon bond formation.


Assuntos
Acetil-CoA C-Acetiltransferase/metabolismo , Acil Coenzima A/metabolismo , Alcenos/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Coenzima A/metabolismo , Xanthomonas campestris/enzimologia , Acetil-CoA C-Acetiltransferase/química , Acetil-CoA C-Acetiltransferase/genética , Proteínas de Bactérias/genética , Sítios de Ligação , Catálise , Domínio Catalítico , Cristalização , Cristalografia por Raios X , Cisteína/química , Cisteína/metabolismo , Modelos Moleculares , Proteínas Mutantes/química , Proteínas Mutantes/genética , Proteínas Mutantes/metabolismo , Mutação/genética , Conformação Proteica , Especificidade por Substrato , Xanthomonas campestris/genética
10.
J Biol Inorg Chem ; 22(7): 1089-1097, 2017 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-28825148

RESUMO

PqqB is an enzyme involved in the biosynthesis of pyrroloquinoline quinone and a distal member of the metallo-ß-lactamase (MBL) superfamily. PqqB lacks two residues in the conserved signature motif HxHxDH that makes up the key metal-chelating elements that can bind up to two metal ions at the active site of MBLs and other members of its superfamily. Here, we report crystal structures of PqqB bound to Mn2+, Mg2+, Cu2+, and Zn2+. These structures demonstrate that PqqB can still bind metal ions at the canonical MBL active site. The fact that PqqB can adapt its side chains to chelate a wide spectrum of metal ions with different coordination features on a uniform main chain scaffold demonstrates its metal-binding plasticity. This plasticity may provide insights into the structural basis of promiscuous activities found in ensembles of metal complexes within this superfamily. Furthermore, PqqB belongs to a small subclass of MBLs that contain an additional CxCxxC motif that binds a structural Zn2+. Our data support a key role for this motif in dimerization.


Assuntos
Proteínas de Bactérias/metabolismo , Metais/metabolismo , Pseudomonas putida/enzimologia , beta-Lactamases/metabolismo , Proteínas de Bactérias/química , Sítios de Ligação , Domínio Catalítico , Cristalografia por Raios X , Humanos , Metais/química , Modelos Moleculares , Cofator PQQ/metabolismo , Ligação Proteica , Conformação Proteica , Infecções por Pseudomonas/microbiologia , Pseudomonas putida/química , Pseudomonas putida/metabolismo , beta-Lactamases/química
11.
Biochim Biophys Acta ; 1847(8): 709-16, 2015 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-25896561

RESUMO

The diheme enzyme MauG catalyzes a six-electron oxidation required for posttranslational modification of a precursor of methylamine dehydrogenase (preMADH) to complete the biosynthesis of its protein-derived tryptophan tryptophylquinone (TTQ) cofactor. One heme is low-spin with ligands provided by His205 and Tyr294, and the other is high-spin with a ligand provided by His35. The side chain methyl groups of Thr67 and Leu70 are positioned at a distance of 3.4Å on either side of His35, maintaining a hydrophobic environment in the proximal pocket of the high-spin heme and restricting the movement of this ligand. Mutation of Thr67 to Ala in the proximal pocket of the high-spin heme prevented reduction of the low-spin heme by dithionite, yielding a mixed-valent state. The mutation also enhanced the stabilization of the charge-resonance-transition of the high-valent bis-FeIV state that is generated by addition of H2O2. The rates of electron transfer from TTQ biosynthetic intermediates to the high-valent form of T67A MauG were similar to that of wild-type MauG. These results are compared to those previously reported for mutation of residues in the distal pocket of the high-spin heme that also affected the redox properties and charge resonance transition stabilization of the high-valent state of the hemes. However, given the position of residue 67, the structure of the variant protein and the physical nature of the T67A mutation, the basis for the effects of the T67A mutation must be different from those of the mutations of the residues in the distal heme pocket.


Assuntos
Proteínas de Bactérias/química , Compostos Férricos/química , Compostos Ferrosos/química , Heme/química , Hemeproteínas/química , Mutação/genética , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Cristalografia por Raios X , Transporte de Elétrons , Compostos Férricos/metabolismo , Compostos Ferrosos/metabolismo , Heme/genética , Heme/metabolismo , Hemeproteínas/genética , Hemeproteínas/metabolismo , Indolquinonas/metabolismo , Modelos Moleculares , Oxirredução , Oxirredutases atuantes sobre Doadores de Grupo CH-NH/metabolismo , Paracoccus denitrificans/genética , Paracoccus denitrificans/crescimento & desenvolvimento , Paracoccus denitrificans/metabolismo , Processamento de Proteína Pós-Traducional , Rhodobacter sphaeroides/genética , Rhodobacter sphaeroides/crescimento & desenvolvimento , Rhodobacter sphaeroides/metabolismo , Análise Espectral Raman , Triptofano/análogos & derivados , Triptofano/metabolismo
12.
Proc Natl Acad Sci U S A ; 110(12): 4569-73, 2013 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-23487750

RESUMO

Despite the importance of tryptophan (Trp) radicals in biology, very few radicals have been trapped and characterized in a physiologically meaningful context. Here we demonstrate that the diheme enzyme MauG uses Trp radical chemistry to catalyze formation of a Trp-derived tryptophan tryptophylquinone cofactor on its substrate protein, premethylamine dehydrogenase. The unusual six-electron oxidation that results in tryptophan tryptophylquinone formation occurs in three discrete two-electron catalytic steps. Here the exact order of these oxidation steps in the processive six-electron biosynthetic reaction is determined, and reaction intermediates are structurally characterized. The intermediates observed in crystal structures are also verified in solution using mass spectrometry. Furthermore, an unprecedented Trp-derived diradical species on premethylamine dehydrogenase, which is an intermediate in the first two-electron step, is characterized using high-frequency and -field electron paramagnetic resonance spectroscopy and UV-visible absorbance spectroscopy. This work defines a unique mechanism for radical-mediated catalysis of a protein substrate, and has broad implications in the areas of applied biocatalysis and understanding of oxidative protein modification during oxidative stress.


Assuntos
Proteínas de Bactérias/química , Indolquinonas/biossíntese , Oxirredutases/química , Paracoccus denitrificans/enzimologia , Triptofano/análogos & derivados , Proteínas de Bactérias/metabolismo , Cristalografia por Raios X , Indolquinonas/química , Espectrometria de Massas , Oxirredução , Oxirredutases/metabolismo , Especificidade por Substrato , Triptofano/biossíntese , Triptofano/química
13.
Biochemistry ; 53(8): 1342-9, 2014 Mar 04.
Artigo em Inglês | MEDLINE | ID: mdl-24517455

RESUMO

The diheme enzyme MauG catalyzes a six-electron oxidation that is required for the posttranslational modification of a precursor of methylamine dehydrogenase (preMADH) to complete the biosynthesis of its protein-derived cofactor, tryptophan tryptophylquinone (TTQ). Crystallographic and computational studies have implicated Gln103 in stabilizing the Fe(IV)═O moiety of the bis-Fe(IV) state by hydrogen bonding. The role of Gln103 was probed by site-directed mutagenesis. Q103L and Q103E mutations resulted in no expression and very little expression of the protein, respectively. Q103A MauG exhibited oxidative damage when isolated. Q103N MauG was isolated at levels comparable to that of wild-type MauG and exhibited normal activity in catalyzing the biosynthesis of TTQ from preMADH. The crystal structure of the Q103N MauG-preMADH complex suggests that a water may mediate hydrogen bonding between the shorter Asn103 side chain and the Fe(IV)═O moiety. The Q103N mutation caused the two redox potentials associated with the diferric/diferrous redox couple to become less negative, although the redox cooperativity of the hemes of MauG was retained. Upon addition of H2O2, Q103N MauG exhibits changes in the absorbance spectrum in the Soret and near-IR regions consistent with formation of the bis-Fe(IV) redox state. However, the rate of spontaneous return of the spectrum in the Soret region was 4.5-fold greater for Q103N MauG than for wild-type MauG. In contrast, the rate of spontaneous decay of the absorbance at 950 nm, which is associated with charge-resonance stabilization of the high-valence state, was similar for wild-type MauG and Q103N MauG. This suggests that as a consequence of the mutation a different distribution of resonance structures stabilizes the bis-Fe(IV) state. These results demonstrate that subtle changes in the structure of the side chain of residue 103 can significantly affect the overall protein stability of MauG and alter the redox properties of the hemes.


Assuntos
Glutamina , Hemeproteínas/química , Hemeproteínas/metabolismo , Mutagênese Sítio-Dirigida , Paracoccus denitrificans/enzimologia , Cristalografia por Raios X , Estabilidade Enzimática , Hemeproteínas/genética , Ferro/metabolismo , Modelos Moleculares , Mutação , Oxirredução , Conformação Proteica
14.
J Biol Chem ; 288(39): 28409-17, 2013 Sep 27.
Artigo em Inglês | MEDLINE | ID: mdl-23940035

RESUMO

The mechanism of molecular oxygen activation is the subject of controversy in the copper amine oxidase family. At their active sites, copper amine oxidases contain both a mononuclear copper ion and a protein-derived quinone cofactor. Proposals have been made for the activation of molecular oxygen via both a Cu(II)-aminoquinol catalytic intermediate and a Cu(I)-semiquinone intermediate. Using protein crystallographic freeze-trapping methods under low oxygen conditions combined with single-crystal microspectrophotometry, we have determined structures corresponding to the iminoquinone and semiquinone forms of the enzyme. Methylamine reduction at acidic or neutral pH has revealed protonated and deprotonated forms of the iminoquinone that are accompanied by a bound oxygen species that is likely hydrogen peroxide. However, methylamine reduction at pH 8.5 has revealed a copper-ligated cofactor proposed to be the semiquinone form. A copper-ligated orientation, be it the sole identity of the semiquinone or not, blocks the oxygen-binding site, suggesting that accessibility of Cu(I) may be the basis of partitioning O2 activation between the aminoquinol and Cu(I).


Assuntos
Amina Oxidase (contendo Cobre)/química , Ascomicetos/metabolismo , Oxigênio/química , Catálise , Cobre/química , Cristalografia por Raios X , Transporte de Elétrons , Peróxido de Hidrogênio/química , Concentração de Íons de Hidrogênio , Hidroquinonas/química , Modelos Químicos , Oxirredução , Quinonas/química , Espectrofotometria
15.
Mol Genet Metab ; 111(2): 113-5, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24332804

RESUMO

The lack of methodological uniformity in enzyme assays has been a long-standing difficulty, a problem for bench researchers, for the interpretation of clinical diagnostic tests, and an issue for investigational drug review. Illustrative of the problem, α-L-iduronidase enzyme catalytic activity is frequently measured with the substrate 4-methylumbelliferyl-α-L-iduronide (4MU-iduronide); however, final substrate concentrations used in different assays vary greatly, ranging from 25 µM to 1425 µM (Km ≈ 180 µM) making it difficult to compare results between laboratories. In this study, α-L-iduronidase was assayed with 15 different substrate concentrations. The resulting activity levels from the same specimens varied greatly with different substrate concentrations but, as a group, obeyed the expectations of Michaelis-Menten kinetics. Therefore, for the sake of improved comparability, it is proposed that α-L-iduronidase enzyme assays should be conducted either (1) under substrate saturating conditions; or (2) when concentrations are significantly below substrate saturation, with results standardized by arithmetic adjustment that considers Michaelis-Menten kinetics. The approach can be generalized to many other enzyme assays.


Assuntos
Ensaios Enzimáticos/normas , Himecromona/análogos & derivados , Iduronidase/análise , Mucopolissacaridose I/enzimologia , Calibragem , Humanos , Himecromona/química , Himecromona/normas , Iduronidase/metabolismo , Cinética , Mucopolissacaridose I/diagnóstico , Mucopolissacaridose I/patologia , Controle de Qualidade
16.
Proc Natl Acad Sci U S A ; 108(41): 16956-61, 2011 Oct 11.
Artigo em Inglês | MEDLINE | ID: mdl-21969534

RESUMO

The diheme enzyme MauG catalyzes the posttranslational modification of the precursor protein of methylamine dehydrogenase (preMADH) to complete biosynthesis of its protein-derived tryptophan tryptophylquinone (TTQ) cofactor. Catalysis proceeds through a high valent bis-Fe(IV) redox state and requires long-range electron transfer (ET), as the distance between the modified residues of preMADH and the nearest heme iron of MauG is 19.4 Å. Trp199 of MauG resides at the MauG-preMADH interface, positioned midway between the residues that are modified and the nearest heme. W199F and W199K mutations did not affect the spectroscopic and redox properties of MauG, or its ability to stabilize the bis-Fe(IV) state. Crystal structures of complexes of W199F/K MauG with preMADH showed no significant perturbation of the MauG-preMADH structure or protein interface. However, neither MauG variant was able to synthesize TTQ from preMADH. In contrast, an ET reaction from diferrous MauG to quinone MADH, which does not require the bis-Fe(IV) intermediate, was minimally affected by the W199F/K mutations. W199F/K MauGs were able to oxidize quinol MADH to form TTQ, the putative final two-electron oxidation of the biosynthetic process, but with k(cat)/K(m) values approximately 10% that of wild-type MauG. The differential effects of the W199F/K mutations on these three different reactions are explained by a critical role for Trp199 in mediating multistep hopping from preMADH to bis-Fe(IV) MauG during the long-range ET that is required for TTQ biosynthesis.


Assuntos
Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Indolquinonas/biossíntese , Triptofano/análogos & derivados , Substituição de Aminoácidos , Proteínas de Bactérias/química , Cristalografia por Raios X , Precursores Enzimáticos/química , Precursores Enzimáticos/metabolismo , Modelos Moleculares , Complexos Multienzimáticos/química , Complexos Multienzimáticos/genética , Complexos Multienzimáticos/metabolismo , Mutagênese Sítio-Dirigida , Proteínas Mutantes/química , Proteínas Mutantes/genética , Proteínas Mutantes/metabolismo , Oxirredução , Oxirredutases atuantes sobre Doadores de Grupo CH-NH/química , Oxirredutases atuantes sobre Doadores de Grupo CH-NH/metabolismo , Paracoccus denitrificans/enzimologia , Paracoccus denitrificans/genética , Processamento de Proteína Pós-Traducional , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Espectrofotometria , Triptofano/biossíntese , Triptofano/química , Triptofano/genética
17.
Biochemistry ; 52(36): 6211-8, 2013 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-23952581

RESUMO

Hydroxylamine oxidoreductase (HAO) is a 24-heme homotrimeric enzyme that catalyzes the conversion of hydroxylamine to nitrite in nitrifying bacteria: a key reaction in the nitrogen cycle. One heme in each HAO monomer is a highly unusual heme P460 that is the site of catalysis. This was proposed to be a c-type heme that contained an additional porphyrin-tyrosine cross-link. Here, we report the crystal structure of HAO from Nitrosomonas europaea to 2.1 Å resolution that defines a different model compatible with the crystallographic and biochemical data. The structure reveals that heme P460 contains two covalent cross-links between the porphyrin and a Tyr residue. In addition, the enzyme was purified from source, and an unknown physiological HAO binding partner was present within the crystal (annotated in the genome as hypothetical protein NE1300). NE1300 may play a structural role in the ternary complex with cytochrome c554, the physiological electron acceptor of HAO.


Assuntos
Heme/análogos & derivados , Oxirredutases/química , Cristalografia por Raios X , Heme/química , Espectrometria de Massas , Modelos Moleculares , Simulação de Acoplamento Molecular , Nitrosomonas europaea/enzimologia , Oxirredutases/isolamento & purificação
18.
Biochemistry ; 52(38): 6662-71, 2013 Sep 24.
Artigo em Inglês | MEDLINE | ID: mdl-23980641

RESUMO

A family of dinuclear iron cluster-containing oxygenases that catalyze ß-hydroxylation tailoring reactions in natural product biosynthesis by nonribosomal peptide synthetase (NRPS) systems was recently described [Makris, T. M., Chakrabarti, M., Münck, E., and Lipscomb, J. D. (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 15391-15396]. Here, the 2.17 Å X-ray crystal structure of the archetypal enzyme from the family, CmlA, is reported. CmlA catalyzes ß-hydroxylation of l-p-aminophenylalanine during chloramphenicol biosynthesis. The fold of the N-terminal domain of CmlA is unlike any previously reported, but the C-terminal domain has the αßßα fold of the metallo-ß-lactamase (MBL) superfamily. The diiron cluster bound in the C-terminal domain is coordinated by an acetate, three His residues, two Asp residues, one Glu residue, and a bridging oxo moiety. One of the Asp ligands forms an unusual monodentate bridge. No other oxygen-activating diiron enzyme utilizes this ligation or the MBL protein fold. The N-terminal domain facilitates dimerization, but using computational docking and a sequence-based structural comparison to homologues, we hypothesize that it likely serves additional roles in NRPS recognition and the regulation of O2 activation.


Assuntos
Ferro/química , Oxigenases de Função Mista/química , Peptídeo Sintases/metabolismo , Sítios de Ligação , Cloranfenicol/biossíntese , Cristalografia por Raios X , Hidroxilação , Oxigenases de Função Mista/metabolismo , Modelos Moleculares
19.
Biochemistry ; 52(13): 2291-301, 2013 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-23452079

RESUMO

Copper amine oxidases (CAOs) are responsible for the oxidative deamination of primary amines to their corresponding aldehydes. The CAO catalytic mechanism can be divided into two half-reactions: a reductive half-reaction in which a primary amine substrate is oxidized to its corresponding aldehyde with the concomitant reduction of the organic cofactor 2,4,5-trihydroxyphenylalanine quinone (TPQ) and an oxidative half-reaction in which reduced TPQ is reoxidized with the reduction of molecular oxygen to hydrogen peroxide. The reductive half-reaction proceeds via Schiff base chemistry, in which the primary amine substrate first attacks the C5 carbonyl of TPQ, forming a series of covalent Schiff base intermediates. The X-ray crystal structures of copper amine oxidase-1 from the yeast Hansenula polymorpha (HPAO-1) in complex with ethylamine and benzylamine have been determined to resolutions of 2.18 and 2.25 Å, respectively. These structures reveal the two amine substrates bound at the back of the active site coincident with TPQ in its two-electron-reduced aminoquinol form. Rearrangements of particular amino acid side chains within the substrate channel and specific protein-substrate interactions provide insight into the substrate specificity of HPAO-1. These changes begin to account for this CAO's kinetic preference for small, aliphatic amines over the aromatic amines or whole peptides preferred by some of its homologues.


Assuntos
Amina Oxidase (contendo Cobre)/química , Amina Oxidase (contendo Cobre)/metabolismo , Pichia/enzimologia , Pichia/metabolismo , Benzilaminas/metabolismo , Domínio Catalítico , Cobre/metabolismo , Cristalografia por Raios X , Di-Hidroxifenilalanina/análogos & derivados , Di-Hidroxifenilalanina/metabolismo , Etilaminas/metabolismo , Cinética , Modelos Moleculares , Pichia/química , Ligação Proteica , Conformação Proteica , Especificidade por Substrato
20.
Biochemistry ; 52(37): 6358-67, 2013 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-23952537

RESUMO

The diheme enzyme MauG catalyzes a six-electron oxidation required for post-translational modification of a precursor of methylamine dehydrogenase (preMADH) to complete the biosynthesis of its protein-derived tryptophan tryptophylquinone (TTQ) cofactor. Crystallographic studies have implicated Glu113 in the formation of the bis-Fe(IV) state of MauG, in which one heme is Fe(IV)═O and the other is Fe(IV) with His-Tyr axial ligation. An E113Q mutation had no effect on the structure of MauG but significantly altered its redox properties. E113Q MauG could not be converted to the diferrous state by reduction with dithionite but was only reduced to a mixed valence Fe(II)/Fe(III) state, which is never observed in wild-type (WT) MauG. Addition of H2O2 to E113Q MauG generated a high valence state that formed more slowly and was less stable than the bis-Fe(IV) state of WT MauG. E113Q MauG exhibited no detectable TTQ biosynthesis activity in a steady-state assay with preMADH as the substrate. It did catalyze the steady-state oxidation of quinol MADH to the quinone, but 1000-fold less efficiently than WT MauG. Addition of H2O2 to a crystal of the E113Q MauG-preMADH complex resulted in partial synthesis of TTQ. Extended exposure of these crystals to H2O2 resulted in hydroxylation of Pro107 in the distal pocket of the high-spin heme. It is concluded that the loss of the carboxylic group of Glu113 disrupts the redox cooperativity between hemes that allows rapid formation of the diferrous state and alters the distribution of high-valence species that participate in charge-resonance stabilization of the bis-Fe(IV) redox state.


Assuntos
Compostos Férricos/química , Compostos Ferrosos/química , Ácido Glutâmico/química , Hemeproteínas/química , Indolquinonas/biossíntese , Oxirredutases atuantes sobre Doadores de Grupo CH-NH/química , Triptofano/análogos & derivados , Cristalografia por Raios X , Heme/química , Peróxido de Hidrogênio , Oxirredução , Oxirredutases atuantes sobre Doadores de Grupo CH-NH/metabolismo , Paracoccus denitrificans/enzimologia , Processamento de Proteína Pós-Traducional , Triptofano/biossíntese
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