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1.
Chembiochem ; 24(14): e202300021, 2023 07 17.
Artículo en Inglés | MEDLINE | ID: mdl-36916316

RESUMEN

Adenosylcobalamin (AdoCbl), or coenzyme B12 , is a naturally occurring organometallic compound that serves as a cofactor for enzymes that catalyze intramolecular group-transfer reactions and ribonucleotide reduction in a wide variety of organisms from bacteria to animals. AdoCbl-dependent enzymes are radical enzymes that generate an adenosyl radical by homolysis of the coenzyme's cobalt-carbon (Co-C) bond for catalysis. How do the enzymes activate and cleave the Co-C bond to form the adenosyl radical? How do the enzymes utilize the high reactivity of the adenosyl radical for catalysis by suppressing undesirable side reactions? Our recent structural studies, which aimed to solve these problems with diol dehydratase and ethanolamine ammonia-lyase, established the crucial importance of the steric strain of the Co-C bond and conformational stabilization of the adenosyl radical for coenzyme B12 catalysis. We outline here our results obtained with these eliminating isomerases and compare them with those obtained with other radical B12 enzymes.


Asunto(s)
Carbono , Cobalto , Animales , Cobalto/química , Carbono/química , Modelos Moleculares , Cobamidas/química , Catálisis
2.
Chemistry ; 28(65): e202202196, 2022 Nov 21.
Artículo en Inglés | MEDLINE | ID: mdl-35974426

RESUMEN

The X-ray structures of coenzyme B12 (AdoCbl)-dependent eliminating isomerases complexed with adenosylmethylcobalamin (AdoMeCbl) have been determined. As judged from geometries, the Co-C bond in diol dehydratase (DD) is not activated even in the presence of substrate. In ethanolamine ammonia-lyase (EAL), the bond is elongated in the absence of substrate; in the presence of substrate, the complex likely exists in both pre- and post-homolysis states. The impacts of incorporating an extra CH2 group are different in the two enzymes: the DD active site is flexible, and AdoMeCbl binding causes large conformational changes that make DD unable to adopt the catalytic state, whereas the EAL active site is rigid, and AdoMeCbl binding does not induce significant conformational changes. Such flexibility and rigidity of the active sites might reflect the tightness of adenine binding. The structures provide good insights into the basis of the very low activity of AdoMeCbl in these enzymes.


Asunto(s)
Etanolamina Amoníaco-Liasa , Propanodiol Deshidratasa , Etanolamina Amoníaco-Liasa/química , Etanolamina Amoníaco-Liasa/metabolismo , Propanodiol Deshidratasa/química , Propanodiol Deshidratasa/metabolismo , Cobamidas/química , Cobamidas/metabolismo , Cinética
3.
Angew Chem Int Ed Engl ; 57(26): 7830-7835, 2018 06 25.
Artículo en Inglés | MEDLINE | ID: mdl-29797764

RESUMEN

The crystal structures of the B12 -dependent isomerases (eliminating) diol dehydratase and ethanolamine ammonia-lyase complexed with adenosylcobalamin were solved with and without substrates. The structures revealed that the peripheral a-acetamide side chain of the corrin ring directly interacts with the adenosyl group to maintain the group in the catalytic position, and that this side chain swings between the original and catalytic positions in a synchronized manner with the radical shuttling between the coenzyme and substrate/product. Mutations involving key residues that cooperatively participate in the positioning of the adenosyl group, directly or indirectly through the interaction with the a-side chain, decreased the turnover rate and increased the relative rate of irreversible inactivation caused by undesirable side reactions. These findings guide the engineering of enzymes for improved catalysis and producing useful chemicals by utilizing the high reactivity of radical species.


Asunto(s)
Cobamidas/química , Corrinoides/química , Sitios de Unión , Catálisis , Corrinoides/genética , Cristalografía por Rayos X , Enlace de Hidrógeno , Cinética , Modelos Moleculares , Conformación Proteica
4.
Biochem Biophys Res Commun ; 485(1): 41-46, 2017 03 25.
Artículo en Inglés | MEDLINE | ID: mdl-28174006

RESUMEN

Starfish oocytes are arrested at the prophase stage of the first meiotic division in the ovary and resume meiosis by the stimulus of 1-methyladenine (1-MeAde), the oocyte maturation-inducing hormone of starfish. Putative 1-MeAde receptors on the oocyte surface have been suggested, but not yet been biochemically characterized. Immunophotoaffinity labeling, i.e., photoaffinity labeling combined with immunochemical detection, was attempted to detect unknown 1-MeAde binders including putative maturation-inducing hormone receptors in starfish oocytes. When the oocyte crude membrane fraction or its Triton X-100/EDTA extract was incubated with N6-[6-(5-azido-2-nitrobenzoyl)aminohexyl]carboxamidomethyl-1-methyladenine and then photo-irradiated, followed by western blotting with antibody that was raised against a 1-MeAde hapten, a single band with Mr of 47.5 K was detected. The band was lost when extract was heated at 100 °C. A similar 47.5 K band was detected in the crude membrane fraction of testis as well. Upon labeling with whole cells, this band was detected in immature and maturing oocytes, but only faintly in mature oocytes. As judged from these results, this 1-MeAde binder might be a possible candidate of the starfish maturation-inducing hormone receptors.


Asunto(s)
Adenina/análogos & derivados , Western Blotting , Oocitos/metabolismo , Oogénesis , Etiquetas de Fotoafinidad/metabolismo , Estrellas de Mar/fisiología , Adenina/metabolismo , Animales , Western Blotting/métodos , Femenino , Oocitos/citología , Etiquetas de Fotoafinidad/síntesis química , Etiquetas de Fotoafinidad/química
5.
Biochem Biophys Res Commun ; 486(4): 1055-1061, 2017 05 13.
Artículo en Inglés | MEDLINE | ID: mdl-28366629

RESUMEN

Starfish oocytes are arrested at the prophase stage of the first meiotic division in the ovary. They resume meiosis by the stimulus of 1-methyladenine (1-MeAde), the maturation-inducing hormone for starfish oocytes. Putative 1-MeAde receptors have been suggested to be present on the oocyte surface, but not yet been characterized biochemically. As reported recently (T. Toraya, T. Kida, A. Kuyama, S. Matsuda, S. Tanaka, Y. Komatsu, T. Tsurukai, Biochem. Biophys. Res. Commun. 485 (2017) 41-46), it became possible to detect unknown 1-MeAde binders of starfish oocytes by immunophotoaffinity labeling, i.e., photoaffinity labeling combined with immunochemical detection. We designed and synthesized water-soluble and insoluble polymer-bound 1-MeAde derivatives. A water-soluble polymer-bound 1-MeAde derivative, in which 1-MeAde is bound to dextran through an N6-substituent, triggered the germinal-vesicle breakdown toward follicle-free oocytes, dejellied oocytes, and denuded oocytes. This is consistent with the idea that putative 1-MeAde receptors are located on the cell surface of starfish oocytes. A water-insoluble polymer-bound 1-MeAde derivative, in which 1-MeAde is bound to Sepharose 4B through an N6-substituent, served as an effective affinity adsorbent for the partial purification of a 1-MeAde binder with Mr of 47.5 K that might be a possible candidate of the maturation-inducing hormone receptors of starfish oocytes.


Asunto(s)
Adenina/análogos & derivados , Cromatografía de Afinidad/métodos , Excipientes/química , Oocitos/metabolismo , Estrellas de Mar/metabolismo , Adenina/química , Adenina/metabolismo , Animales , Células Cultivadas , Femenino , Oocitos/crecimiento & desarrollo , Oogénesis/fisiología
6.
Biochemistry ; 55(1): 69-78, 2016 Jan 12.
Artículo en Inglés | MEDLINE | ID: mdl-26704729

RESUMEN

Holoenzymes of adenosylcobalamin-dependent diol and glycerol dehydratases undergo mechanism-based inactivation by glycerol and O2 inactivation in the absence of substrate, which accompanies irreversible cleavage of the coenzyme Co-C bond. The inactivated holodiol dehydratase and the inactive enzyme·cyanocobalamin complex were (re)activated by incubation with NADH, ATP, and Mg(2+) (or Mn(2+)) in crude extracts of Klebsiella oxytoca, suggesting the presence of a reactivating system in the extract. The reducing system with NADH could be replaced by FMNH2. When inactivated holoenzyme or the enzyme·cyanocobalamin complex, a model of inactivated holoenzyme, was incubated with purified recombinant diol dehydratase-reactivase (DD-R) and an ATP:cob(I)alamin adenosyltransferase in the presence of FMNH2, ATP, and Mg(2+), diol dehydratase activity was restored. Among the three adenosyltransferases (PduO, EutT, and CobA) of this bacterium, PduO and CobA were much more efficient for the reactivation than EutT, although PduO showed the lowest adenosyltransfease activity toward free cob(I)alamin. These results suggest that (1) diol dehydratase activity is maintained through coenzyme recycling by a reactivating system for diol dehydratase composed of DD-R, PduO adenosyltransferase, and a reducing system, (2) the releasing factor DD-R is essential for the recycling of adenosycobalamin, a tightly bound, prosthetic group-type coenzyme, and (3) PduO is a specific adenosylating enzyme for the DD reactivation, whereas CobA and EutT exert their effects through free synthesized coenzyme. Although FMNH2 was mainly used as a reductant in this study, a natural reducing system might consist of PduS cobalamin reductase and NADH.


Asunto(s)
Proteínas Bacterianas/metabolismo , Cobamidas/metabolismo , Activación Enzimática , Klebsiella oxytoca/metabolismo , Propanodiol Deshidratasa/metabolismo , Adenosina Trifosfato/metabolismo , Transferasas Alquil y Aril/metabolismo , Mononucleótido de Flavina/metabolismo , Hidroquinonas/metabolismo , Klebsiella oxytoca/enzimología , Magnesio/metabolismo , NAD/metabolismo
7.
Biochemistry ; 53(16): 2661-71, 2014 Apr 29.
Artículo en Inglés | MEDLINE | ID: mdl-24735254

RESUMEN

Ethanolamine ammonia-lyase (EAL) catalyzes the adenosylcobalamin-dependent conversion of ethanolamine to acetaldehyde and ammonia. 1-OH of the substrate is hydrogen-bonded with Gluα287, Argα160, and Asnα193 and 2-NH2 with Gluα287, Glnα162, and Aspα362. The active site somewhat resembles that of diol dehydratase. All five residues were important for the high-affinity binding of the substrate and for catalysis. The -COO(-) group at residue α287 was absolutely required for activity and coenzyme Co-C bond cleavage, and there was a spatially optimal position for it, suggesting that Gluα287 contributes to Co-C bond homolysis, stabilizes the transition state for the migration of NH2 from C2 to C1 through partial deprotonation of spectator OH, and functions as a base in the elimination of ammonia. A positive charge and/or the hydrogen bond at position α160 and the hydrogen bonds at positions α162 and α193 with the substrate are important for catalysis and for preventing a radical intermediate from undergoing side reactions. Argα160 would stabilize the trigonal transition state in NH2 migration by electrostatic catalysis and hydrogen bonding with spectator OH. Asnα193 would contribute to maintaining the appropriate position and direction of the guanidinium group of Argα160, as well. Hydrogen bond acceptors were necessary at position α162, but hydrogen bond donors were rather harmful. Glnα162 might stabilize the trigonal transition state by accepting a hydrogen bond from migrating NH3(+). The activity was very sensitive to the position of -COO(-) at α362. Aspα362 would assist Co-C bond homolysis indirectly and stabilize the trigonal transition state by accepting a hydrogen bond from migrating NH3(+) and electrostatic interaction.


Asunto(s)
Etanolamina Amoníaco-Liasa/química , Etanolamina Amoníaco-Liasa/metabolismo , Sitios de Unión , Catálisis , Dominio Catalítico , Cobamidas/metabolismo , Espectroscopía de Resonancia por Spin del Electrón , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Etanolamina Amoníaco-Liasa/genética , Enlace de Hidrógeno , Mutagénesis Sitio-Dirigida
8.
Arch Biochem Biophys ; 544: 40-57, 2014 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-24269950

RESUMEN

Adenosylcobalamin, a coenzyme form of vitamin B12, is an organometallic compound that participates in about ten enzymatic reactions. These enzymes catalyze chemically challenging reactions by using a highly reactive primary carbon radical that is derived from homolysis of the coenzyme Co-C bond. Among them, diol dehydratases and ethanolamine ammonia-lyase have been most extensively studied to establish the general mechanism of adenosylcobalamin-assisted enzymatic catalysis and radical-catalyzed reactions. Another important point is that adenosylcobalamin-dependent radical enzymes are prone to mechanism-based irreversible inactivation during catalysis and have their own chaperones for the maintenance of catalytic activities. This review will highlight biochemical, structural, and computational studies with special emphases on radical catalysis and reactivating chaperones of these enzymes.


Asunto(s)
Etanolamina Amoníaco-Liasa/metabolismo , Hidroliasas/metabolismo , Vitamina B 12/metabolismo , Animales , Bacterias/química , Bacterias/enzimología , Cristalografía por Rayos X , Etanolamina Amoníaco-Liasa/química , Humanos , Hidroliasas/química , Modelos Moleculares , Vitamina B 12/química
9.
J Biochem ; 2024 Jul 11.
Artículo en Inglés | MEDLINE | ID: mdl-38987935

RESUMEN

3,3,3-Trifluoro-1,2-propanediol undergoes complete defluorination in two distinct steps: first, the conversion into 3,3,3-trifluoropropionaldehyde catalyzed by adenosylcobalamin (coenzyme B12)-dependent diol dehydratase; second, non-enzymatic elimination of all three fluorides from this aldehyde to afford malonic semialdehyde (3-oxopropanoic acid), which is decarboxylated to acetaldehyde. Diol dehydratase accepts 3,3,3-trifluoro-1,2-propanediol as a relatively poor substrate, albeit without significant mechanism-based inactivation of the enzyme during catalysis. Optical and EPR spectra revealed the steady-state formation of cob(II)alamin and a substrate-derived intermediate organic radical (3,3,3-trifluoro-1,2-dihydroxyprop-1-yl). The coenzyme undergoes Co-C bond homolysis initiating a sequence of reaction by the generally accepted pathway via intermediate radicals. However, the greater steric size of trifluoromethyl and especially its negative impact on the stability of an adjacent radical center compared to a methyl group has implications for the mechanism of the diol dehydratase reaction. Nevertheless, 3,3,3-trifluoropropionaldehyde is formed by the normal diol dehydratase pathway, but then undergoes non-enzymatic conversion into acetaldehyde, probably via 3,3-difluoropropenal and malonic semialdehyde.

10.
Biochemistry ; 52(48): 8677-86, 2013 Dec 03.
Artículo en Inglés | MEDLINE | ID: mdl-24229359

RESUMEN

Diol dehydratase-reactivase (DD-R) is a molecular chaperone that reactivates inactivated holodiol dehydratase (DD) by cofactor exchange. Its ADP-bound and ATP-bound forms are high-affinity and low-affinity forms for DD, respectively. Among DD-Rs mutated at the nucleotide-binding site, neither the Dα8N nor Dα413N mutant was effective as a reactivase. Although Dα413N showed ATPase activity, it did not mediate cyanocobalamin (CN-Cbl) release from the DD·CN-Cbl complex in the presence of ATP or ADP and formed a tight complex with apoDD even in the presence of ATP, suggesting the involvement of Aspα413 in the nucleotide switch. In contrast, Dα8N showed very low ATPase activity and did not mediate CN-Cbl release from the complex in the presence of ATP, but it did cause about 50% release in the presence of ADP. The complex formation of this mutant with DD was partially reversed by ATP, suggesting that Aspα8 is involved in the ATPase activity but only partially in the nucleotide switch. Among DD-Rs mutated at the Mg(2+)-binding site, only Eß31Q was about 30% as active as wild-type DD-R and formed a tight complex with apoDD, indicating that the DD-R ß subunit is not absolutely required for reactivation. If subunit swapping occurs between the DD-R ß and DD ß subunits, Gluß97 of DD would coordinate to Mg(2+). The complex of Eß97Q DD with CN-Cbl was not activated by wild-type DD-R. No complex was formed between this mutant and wild-type DD-R, indicating that the coordination of Gluß97 to Mg(2+) is essential for subunit swapping and therefore for (re)activation.


Asunto(s)
Chaperonas Moleculares/química , Nucleótidos/metabolismo , Propanodiol Deshidratasa/química , Secuencia de Aminoácidos , Proteínas Bacterianas/química , Proteínas Bacterianas/fisiología , Sitios de Unión , Reactivadores Enzimáticos/química , Humanos , Cinética , Klebsiella oxytoca/enzimología , Metales/química , Modelos Moleculares , Datos de Secuencia Molecular , Unión Proteica , Dominios y Motivos de Interacción de Proteínas/fisiología
11.
Biochemistry ; 51(45): 9202-10, 2012 Nov 13.
Artículo en Inglés | MEDLINE | ID: mdl-23098175

RESUMEN

Inactivation of diol dehydratase during the glycerol dehydration reaction is studied on the basis of quantum mechanical/molecular mechanical calculations. Glycerol is not a chiral compound but contains a prochiral carbon atom. Once it is bound to the active site, the enzyme adopts two binding conformations. One is predominantly responsible for the product-forming reaction (G(R) conformation), and the other primarily contributes to inactivation (G(S) conformation). Reactant radical is converted into a product and byproduct in the product-forming reaction and inactivation, respectively. The OH group migrates from C2 to C1 in the product-forming reaction, whereas the transfer of a hydrogen from the 3-OH group of glycerol to C1 takes place during the inactivation. The activation barrier of the hydrogen transfer does not depend on the substrate-binding conformation. On the other hand, the activation barrier of OH group migration is sensitive to conformation and is 4.5 kcal/mol lower in the G(R) conformation than in the G(S) conformation. In the OH group migration, Glu170 plays a critical role in stabilizing the reactant radical in the G(S) conformation. Moreover, the hydrogen bonding interaction between Ser301 and the 3-OH group of glycerol lowers the activation barrier in G(R)-TS2. As a result, the difference in energy between the hydrogen transfer and the OH group migration is reduced in the G(S) conformation, which shows that the inactivation is favored in the G(S) conformation.


Asunto(s)
Glicerol/metabolismo , Hidrógeno/química , Propanodiol Deshidratasa/química , Propanodiol Deshidratasa/metabolismo , Modelos Moleculares , Propanodiol Deshidratasa/antagonistas & inhibidores , Conformación Proteica , Teoría Cuántica
12.
Biosci Biotechnol Biochem ; 76(9): 1661-71, 2012.
Artículo en Inglés | MEDLINE | ID: mdl-22972351

RESUMEN

To determine whether and if so how a DNA methylation-dependent epigenetic mechanism for transcriptional gene silencing functions in Echinoderms, we cloned and sequenced dnmt1 and dnmt3 cDNAs of the starfish Asterina pectinifera. Since the Strongylocentrotus purpuratus genome has only two loci of DNA (cytosine-5)-methyltransferase genes encoding Dnmt1 and Dnmt3, they might constitute a sufficient set of dnmt genes in Echinoderms. The starfish Dnmt3 whose cDNA we cloned showed highest homology to a mammalian Dnmt3a2 splicing variant. Essentially all the characteristic motifs and sequences of the mammalian counterparts were found in the starfish Dnmts as well, except that a typical PCNA binding domain motif was lacking in the starfish Dnmt1. RT-PCR analysis indicated that the dnmt1 mRNA exists in both ovary and oocytes, but its levels in other tissues were very low or almost negligible. In contrast, the dnmt3 mRNA was detected only in the ovary, and not at all in the oocytes. The size of a dnmt1 transcript was about 6.5 kb on Northern blot analysis. On heterologous expression, the starfish Dnmt1 protein was expressed in insect cells in catalytically active form.


Asunto(s)
Asterina/genética , ADN (Citosina-5-)-Metiltransferasas/genética , Oocitos/enzimología , Ovario/enzimología , Secuencias de Aminoácidos , Animales , Asterina/enzimología , Clonación Molecular , ADN (Citosina-5-)-Metiltransferasas/metabolismo , Escherichia coli/genética , Femenino , Biblioteca de Genes , Isoenzimas/genética , Isoenzimas/metabolismo , Datos de Secuencia Molecular , Especificidad de Órganos , Filogenia , Estructura Terciaria de Proteína , Proteínas Recombinantes de Fusión/genética , Proteínas Recombinantes de Fusión/metabolismo , Alineación de Secuencia , Homología de Secuencia de Aminoácido , Células Sf9/metabolismo , Strongylocentrotus purpuratus/enzimología , Strongylocentrotus purpuratus/genética
13.
Methods Enzymol ; 668: 243-284, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35589195

RESUMEN

Adenosylcobalamin (AdoCbl) or coenzyme B12-dependent enzymes tend to undergo mechanism-based inactivation during catalysis or inactivation in the absence of substrate. Such inactivation may be inevitable because they use a highly reactive radical for catalysis, and side reactions of radical intermediates result in the damage of the coenzyme. How do living organisms address such inactivation when enzymes are inactivated by undesirable side reactions? We discovered reactivating factors for radical B12 eliminases. They function as releasing factors for damaged cofactor(s) from enzymes and thus mediate their exchange for intact AdoCbl. Since multiple turnovers and chaperone functions were demonstrated, they were renamed "reactivases" or "reactivating chaperones." They play an essential role in coenzyme recycling as part of the activity-maintaining systems for B12 enzymes. In this chapter, we describe our investigations on reactivating chaperones, including their discovery, gene cloning, preparation, characterization, activity assays, and mechanistic studies, that have been conducted using a wide range of biochemical and structural methods that we have developed.


Asunto(s)
Etanolamina Amoníaco-Liasa , Propanodiol Deshidratasa , Cobamidas/química , Coenzimas , Etanolamina Amoníaco-Liasa/química , Glicerol , Hidroliasas , Chaperonas Moleculares , Fosfotreonina/análogos & derivados , Propanodiol Deshidratasa/química , Propanodiol Deshidratasa/genética
14.
Methods Enzymol ; 668: 181-242, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35589194

RESUMEN

Adenosylcobalamin (AdoCbl) or coenzyme B12-dependent enzymes catalyze intramolecular group-transfer reactions and ribonucleotide reduction in a wide variety of organisms from bacteria to animals. They use a super-reactive primary-carbon radical formed by the homolysis of the coenzyme's Co-C bond for catalysis and thus belong to the larger class of "radical enzymes." For understanding the general mechanisms of radical enzymes, it is of great importance to establish the general mechanism of AdoCbl-dependent catalysis using enzymes that catalyze the simplest reactions-such as diol dehydratase, glycerol dehydratase and ethanolamine ammonia-lyase. These enzymes are often called "eliminases." We have studied AdoCbl and eliminases for more than a half century. Progress has always been driven by the development of new experimental methodologies. In this chapter, we describe our investigations on these enzymes, including their metabolic roles, gene cloning, preparation, characterization, activity assays, and mechanistic studies, that have been conducted using a wide range of biochemical and structural methodologies we have developed.


Asunto(s)
Etanolamina Amoníaco-Liasa , Animales , Cobamidas/química , Cobamidas/metabolismo , Etanolamina Amoníaco-Liasa/química , Etanolamina Amoníaco-Liasa/metabolismo , Glicerol , Hidroliasas , Fosfotreonina/análogos & derivados
15.
Biochemistry ; 50(4): 591-8, 2011 Feb 01.
Artículo en Inglés | MEDLINE | ID: mdl-21142024

RESUMEN

Coenzyme B(12)-dependent ethanolamine ammonia-lyase acts on both enantiomers of the substrate 2-amino-1-propanol [Diziol, P., et al. (1980) Eur. J. Biochem. 106, 211-224]. To rationalize this apparent lack of stereospecificity and the enantiomer-specific stereochemical courses of the deamination, we analyzed the X-ray structures of enantiomer-bound forms of the enzyme-cyanocobalamin complex. The lower affinity for the (R)-enantiomer may be due to the conformational change of the Valα326 side chain of the enzyme. In a manner consistent with the reported experimental results, we can predict that the pro-S hydrogen atom on C1 is abstracted by the adenosyl radical from both enantiomeric substrates, because it is the nearest one in both enantiomer-bound forms. We also predicted that the NH(2) group migrates from C2 to C1 by a suprafacial shift, with inversion of configuration at C1 for both enantiomeric substrates, although the absolute configuration of the 1-amino-1-propanol intermediate is not yet known. Reported labeling experiments demonstrate that (R)-2-amino-1-propanol is deaminated by the enzyme with inversion of configuration at C2, whereas the (S)-enantiomer is deaminated with retention. By taking these results into consideration, we can predict the rotameric radical intermediate from the (S)-enantiomer undergoes flipping to the rotamer from the (R)-enantiomer before the hydrogen back-abstraction. This suggests the preference of the enzyme active site for the rotamer from the (R)-enantiomer in equilibration. This preference might be explained in terms of the steric repulsion of the (S)-enantiomer-derived product radical at C3 with the Pheα329 and Leuα402 residues.


Asunto(s)
Cobamidas/química , Etanolamina Amoníaco-Liasa/química , Propanolaminas/química , Dominio Catalítico , Cobamidas/metabolismo , Cristalografía por Rayos X , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Etanolamina Amoníaco-Liasa/metabolismo , Valor Predictivo de las Pruebas , Estereoisomerismo , Relación Estructura-Actividad , Especificidad por Sustrato
16.
J Biol Chem ; 285(34): 26484-93, 2010 Aug 20.
Artículo en Inglés | MEDLINE | ID: mdl-20519496

RESUMEN

N-terminal truncation of the Escherichia coli ethanolamine ammonia-lyase beta-subunit does not affect the catalytic properties of the enzyme (Akita, K., Hieda, N., Baba, N., Kawaguchi, S., Sakamoto, H., Nakanishi, Y., Yamanishi, M., Mori, K., and Toraya, T. (2010) J. Biochem. 147, 83-93). The binary complex of the truncated enzyme with cyanocobalamin and the ternary complex with cyanocobalamin or adeninylpentylcobalamin and substrates were crystallized, and their x-ray structures were analyzed. The enzyme exists as a trimer of the (alphabeta)(2) dimer. The active site is in the (beta/alpha)(8) barrel of the alpha-subunit; the beta-subunit covers the lower part of the cobalamin that is bound in the interface of the alpha- and beta-subunits. The structure complexed with adeninylpentylcobalamin revealed the presence of an adenine ring-binding pocket in the enzyme that accommodates the adenine moiety through a hydrogen bond network. The substrate is bound by six hydrogen bonds with active-site residues. Argalpha(160) contributes to substrate binding most likely by hydrogen bonding with the O1 atom. The modeling study implies that marked angular strains and tensile forces induced by tight enzyme-coenzyme interactions are responsible for breaking the coenzyme Co-C bond. The coenzyme adenosyl radical in the productive conformation was modeled by superimposing its adenine ring on the adenine ring-binding site followed by ribosyl rotation around the N-glycosidic bond. A major structural change upon substrate binding was not observed with this particular enzyme. Glualpha(287), one of the substrate-binding residues, has a direct contact with the ribose group of the modeled adenosylcobalamin, which may contribute to the substrate-induced additional labilization of the Co-C bond.


Asunto(s)
Cobamidas/química , Proteínas de Escherichia coli/química , Etanolamina Amoníaco-Liasa/química , Dominio Catalítico , Cobamidas/metabolismo , Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Etanolamina Amoníaco-Liasa/metabolismo , Enlace de Hidrógeno , Compuestos Organometálicos/química , Compuestos Organometálicos/metabolismo , Unión Proteica , Subunidades de Proteína , Especificidad por Sustrato , Vitamina B 12/química , Vitamina B 12/metabolismo
17.
Inorg Chem ; 50(7): 2944-52, 2011 Apr 04.
Artículo en Inglés | MEDLINE | ID: mdl-21388166

RESUMEN

Functions of the metal ion in the substrate-binding site of diol dehydratase are studied on the basis of quantum mechanical/molecular mechanical (QM/MM) calculations. The metal ion directly coordinates to substrate and is essential for structural retention and substrate binding. The metal ion has been originally assigned to the K(+) ion; however, QM/MM computations indicate that Ca(2+) ion is more reasonable as the metal ion because calculated Ca-O distances better fit to the coordination distances in X-ray crystal structures rather than calculated K-O distances. The activation energy for the OH group migration, which is essential in the conversion of diols to corresponding aldehydes, is sensitive to the identity of the metal ion. For example, the spectator OH group of substrate is fully deprotonated by Glu170 in the transition state for the OH group migration in the Ca-contained QM/MM model, and therefore the barrier height is significantly decreased in the model having Ca(2+) ion. On the other hand, the deprotonation of the spectator OH group cannot effectively be triggered by the K(+) ion. Moreover, in the hydrogen recombination, the most energy-demanding step is more favorable in the Ca-contained model. The proposal that the Ca(2+) ion should be involved in the substrate-binding site is consistent with an observed large deuterium kinetic isotope effect of 10, which indicates that C-H bond activation is involved in the rate-determining step. Asp335 is found to have a strong anticatalytic effect on the OH group migration despite its important role in substrate binding. The synergistic interplay of the O-C bond cleavage by Ca(2+) ion and the deprotonation of the spectator OH group by Glu170 is required to overcome the anticatalytic effect of Asp335.


Asunto(s)
Calcio/metabolismo , Compuestos Organometálicos/metabolismo , Propanodiol Deshidratasa/metabolismo , Teoría Cuántica , Vitamina B 12/metabolismo , Sitios de Unión , Biocatálisis , Calcio/química , Cristalografía por Rayos X , Iones/química , Iones/metabolismo , Modelos Moleculares , Estructura Molecular , Compuestos Organometálicos/química , Propanodiol Deshidratasa/química , Vitamina B 12/química
18.
Biochemistry ; 49(33): 7210-7, 2010 Aug 24.
Artículo en Inglés | MEDLINE | ID: mdl-20712378

RESUMEN

The X-ray analyses of coenzyme B(12)-dependent diol dehydratase revealed two kinds of electron densities that correspond to metal ions in the active site. One is directly coordinated by substrate [Shibata, N., et al. (1999) Structure 7, 997-1008] and the other located near the adenine ring of the coenzyme adenosyl group [Masuda, J., et al. (2000) Structure 8, 775-788]. Both have been assigned as potassium ions, although the coordination distances of the former are slightly shorter than expected. We examined the possibility that the enzyme is a metalloenzyme. Apodiol dehydratase was strongly inhibited by incubation with EDTA and EGTA in the absence of substrate. The metal analysis revealed that the enzyme contains approximately 2 mol of tightly bound calcium per mole of enzyme. The calcium-deprived, EDTA-free apoenzyme was obtained by the EDTA treatment, followed by ultrafiltration. The activity of the calcium-deprived apoenzyme was dependent on Ca(2+) when assayed with 1 mM substrate. The K(m) for Ca(2+) evaluated in reconstitution experiments was 0.88 muM. These results indicate that the calcium is essential for catalysis. Ca(2+) showed a significant stabilizing effect on the calcium-deprived apoenzyme as well. It was thus concluded that the substrate-coordinated metal ion is not potassium but calcium. The potassium ion bound near the adenine ring would be the essential one for the diol dehydratase catalysis. Therefore, this enzyme can be considered to be a metal-activated metalloenzyme.


Asunto(s)
Calcio/metabolismo , Klebsiella oxytoca/enzimología , Metaloproteínas/química , Propanodiol Deshidratasa/química , Calcio/química , Dominio Catalítico , Cristalografía por Rayos X , Ácido Edético/metabolismo , Ácido Egtácico/metabolismo , Estabilidad de Enzimas , Metaloproteínas/metabolismo , Metales/química , Metales/metabolismo , Modelos Moleculares , Propanodiol Deshidratasa/antagonistas & inhibidores , Propanodiol Deshidratasa/metabolismo , Unión Proteica , Especificidad por Sustrato , Vitamina B 12/metabolismo
20.
Artículo en Inglés | MEDLINE | ID: mdl-20516606

RESUMEN

Ethanolamine ammonia-lyase (EAL) catalyzes the adenosylcobalamin-dependent conversion of ethanolamine to acetaldehyde and ammonia. The wild-type enzyme shows a very low solubility. N-terminal truncation of the Escherichia coli EAL beta-subunit dramatically increases the solubility of the enzyme without altering its catalytic properties. Two deletion mutants of the enzyme [EAL(betaDelta4-30) and EAL(betaDelta4-43)] have been overexpressed, purified and crystallized using the sitting-drop vapour-diffusion method. Crystals of EAL(betaDelta4-30) and EAL(betaDelta4-43) diffracted to approximately 8.0 and 2.1 A resolution, respectively.


Asunto(s)
Escherichia coli/enzimología , Etanolamina Amoníaco-Liasa/química , Cristalización , Cristalografía por Rayos X , Etanolamina Amoníaco-Liasa/genética , Expresión Génica , Mutación
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