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1.
Structure ; 3(11): 1147-58, 1995 Nov 15.
Artículo en Inglés | MEDLINE | ID: mdl-8591026

RESUMEN

BACKGROUND: The hyperthermophile Pyrococcus furiosus is one of the most thermostable organisms known, with an optimum growth temperature of 100 degrees C. The proteins from this organism display extreme thermostability. We have undertaken the structure determination of glutamate dehydrogenase from P. furiosus in order to gain further insights into the relationship between molecular structure and thermal stability. RESULTS: The structure of P. furiosus glutamate dehydrogenase, a homohexameric enzyme, has been determined at 2.2 A resolution and compared with the structure of glutamate dehydrogenase from the mesophile Clostridium symbiosum. CONCLUSIONS: Comparison of the structures of these two enzymes has revealed one major difference: the structure of the hyperthermophilic enzyme contains a striking series of ion-pair networks on the surface of the protein subunits and buried at both interdomain and intersubunit interfaces. We propose that the formation of such extended networks may represent a major stabilizing feature associated with the adaptation of enzymes to extreme temperatures.


Asunto(s)
Archaea/enzimología , Proteínas Bacterianas/química , Glutamato Deshidrogenasa/química , Modelos Moleculares , Conformación Proteica , Secuencia de Aminoácidos , Fenómenos Químicos , Química Física , Enlace de Hidrógeno , Iones , Datos de Secuencia Molecular , Desnaturalización Proteica , Alineación de Secuencia , Temperatura
2.
FEMS Microbiol Rev ; 18(2-3): 105-17, 1996 May.
Artículo en Inglés | MEDLINE | ID: mdl-8639325

RESUMEN

The structure determination of the glutamate dehydrogenase from the hyperthermophile Pyrococcus furiosus has been completed at 2.2 A resolution. The structure has been compared with the glutamate dehydrogenases from the mesophiles Clostridium symbiosum, Escherichia coli and Neurospora crassa. This comparison has revealed that the hyperthermophilic enzyme contains a striking series of networks of ion-pairs which are formed by regions of the protein which contain a high density of charged residues. Such regions are not found in the mesophilic enzymes and the number and extent of ion-pair formation is much more limited. The ion-pair networks are clustered at both inter domain and inter subunit interfaces and may well represent a major stabilising feature associated with the adaptation of enzymes to extreme temperatures.


Asunto(s)
Archaea/enzimología , Glutamato Deshidrogenasa/química , Secuencia de Aminoácidos , Estabilidad de Enzimas , Calor , Datos de Secuencia Molecular , Conformación Proteica , Pliegue de Proteína
3.
Biochim Biophys Acta ; 1247(2): 231-8, 1995 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-7696313

RESUMEN

The positions of the intron-exon boundaries in the genes for glutamate dehydrogenase from Chlorella sorokiniana rat, and human have been located on the three-dimensional structure of the highly homologous enzyme from Clostridium symbiosum and analysed for their position in the protein structure. This analysis shows no correlation between the positions of these boundaries in the mammalian and Chlorella glutamate dehydrogenase genes and no correlation with units of function in the enzyme and suggests that the present day exons do not represent the protein modules of an ancestral glutamate dehydrogenase. There appears to be no clear preference for the residues at the splice junctions to be either buried or exposed to solvent. However, the frequency with which the introns appear in the loops linking elements of secondary structure, rather than in either the alpha-helical or beta-sheet segments, is higher than predicted on the basis of the proportion of residues in the loops. This is consistent with but not proof of a role for exon modification/exchange in protein evolution since changes at these positions are less likely to disturb the structure and hence maintain function.


Asunto(s)
Exones , Glutamato Deshidrogenasa/genética , Intrones , Animales , Chlorella , Humanos , Modelos Moleculares , Conformación Proteica , Estructura Secundaria de Proteína , Ratas
4.
Biochim Biophys Acta ; 1297(2): 149-58, 1996 Oct 17.
Artículo en Inglés | MEDLINE | ID: mdl-8917616

RESUMEN

By using site-directed mutagenesis, Phe-187, one of the amino-acid residues involved in hydrophobic interaction between the three identical dimers comprising the hexamer of Clostridium symbiosum glutamate dehydrogenase (GDH), has been replaced by an aspartic acid residue. Over-expression in Escherichia coli led to production of large amounts of a soluble protein which, though devoid of GDH activity, showed the expected subunit M(r) on SDS-PAGE, and cross-reacted with an anti-GDH antibody preparation in Western blots. The antibody was used to monitor purification of the inactive protein. F187D GDH showed altered mobility on non-denaturing electrophoresis, consistent with changed size and/or surface charge. Gel filtration on a calibrated column indicated an M(r) of 87000 +/- 3000. The mutant enzyme did not bind to the dye column routinely used in preparing wild-type GDH. Nevertheless suspicions of major misfolding were allayed by the results of chemical modification studies: as with wild-type GDH, NAD+ completely protected one-SH group against modification by DTNB, implying normal coenzyme binding. A significant difference, however, is that in the mutant enzyme both cysteine groups were modified by DTNB, rather than C320 only. The CD spectrum in the far-UV region indicated no major change in secondary structure in the mutant protein. The near-UV CD spectrum, however, was less intense and showed a pronounced Phe contribution, possibly reflecting the changed environment of Phe-199, which would be buried in the hexamer. Sedimentation velocity experiments gave corrected coefficients S20,W of 11.08 S and 5.29 S for the wild-type and mutant proteins. Sedimentation equilibrium gave weight average molar masses M(r,app) of 280000 +/- 5000 g/mol. consistent with the hexameric structure for the wild-type protein and 135000 +/- 3000 g/mol for F187D. The value for the mutant is intermediate between the values expected for a dimer (98000) and a trimer (147000). To investigate the basis of this, sedimentation equilibrium experiments were performed over a range of protein concentrations. M(r,app) showed a linear dependence on concentration and a value of 108 118 g/mol at infinite dilution. This indicates a rapid equilibrium between dimeric and hexameric forms of the mutant protein with an equilibrium constant of 0.13 l/g. An independent analysis of the radial absorption scans with Microcal Origin software indicated a threefold association constant of 0.11 l/g. Introduction of the F187D mutation thus appears to have been successful in producing a dimeric GDH species. Since this protein is inactive it is possible that activity requires subunit interaction around the 3-fold symmetry axis. On the other hand this mutation may disrupt the structure in a way that cannot be extrapolated to other dimers. This issue can only be resolved by making alternative dimeric mutants.


Asunto(s)
Clostridium/enzimología , Dimerización , Glutamato Deshidrogenasa/química , Ácido Aspártico/genética , Ácido Aspártico/metabolismo , Western Blotting , Dicroismo Circular , Clonación Molecular , Electroforesis en Gel de Poliacrilamida , Escherichia coli/genética , Glutamato Deshidrogenasa/genética , Modelos Moleculares , Mutagénesis Sitio-Dirigida/genética , Mutación/genética , Conformación Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/aislamiento & purificación , Proteínas Recombinantes/metabolismo , Ultracentrifugación
5.
Biochim Biophys Acta ; 1544(1-2): 10-7, 2001 Jan 12.
Artículo en Inglés | MEDLINE | ID: mdl-11341912

RESUMEN

Glutamate dehydrogenase from Clostridium symbiosum displays unusual kinetic behaviour at high pH when compared with other members of this enzyme family. Structural and sequence comparisons with GDHs from other organisms have indicated that the Asp residue at position 114 in the clostridial enzyme may account for these differences. By replacing this residue by Asn, a mutant protein has been created with altered functional properties at high pH. This mutant protein can be efficiently overexpressed in Escherichia coli, and several criteria, including mobility in non-denaturing electrophoresis, circular dichroism (CD) spectra and initial crystallisation studies, suggest a folding and an assembly comparable to those of the wild-type protein. The D114N mutant enzyme shows a higher optimum pH for activity than the wild-type enzyme, and both CD data and activity measurements show that the distinctive time-dependent reversible conformational inactivation seen at high pH in the wild-type enzyme is abolished in the mutant.


Asunto(s)
Ácido Aspártico/metabolismo , Clostridium/enzimología , Glutamato Deshidrogenasa/metabolismo , Secuencia de Bases , Sitios de Unión , Dicroismo Circular , Cartilla de ADN , Electroforesis en Gel de Poliacrilamida , Glutamato Deshidrogenasa/química , Glutamato Deshidrogenasa/genética , Concentración de Iones de Hidrógeno , Mutagénesis Sitio-Dirigida , Conformación Proteica
6.
Biochim Biophys Acta ; 1080(3): 191-7, 1991 Nov 15.
Artículo en Inglés | MEDLINE | ID: mdl-1954226

RESUMEN

The amino acid sequence is reported for CNBr and tryptic peptide fragments of the NAD(+)-dependent glutamate dehydrogenase of Clostridium symbiosum. Together with the N-terminal sequence, these make up about 75% of the total sequence. The sequence shows extensive similarity with that of the NADP(+)-dependent glutamate dehydrogenase of Escherichia coli (52% identical residues out of the 332 compared) allowing confident placing of the peptide fragments within the overall sequence. This demonstrated sequence similarity with the E. coli enzyme, despite different coenzyme specificity, is much greater than the similarity (31% identities) between the GDH's of C. symbiosum and Peptostreptococcus asaccharolyticus, both NAD(+)-linked. The evolutionary implications are discussed. In the 'fingerprint' region of the nucleotide binding fold the sequence Gly X Gly X X Ala is found, rather than Gly X Gly X X Gly. The sequence found here has previously been associated with NADP+ specificity and its finding in a strictly NAD(+)-dependent enzyme requires closer examination of the function of this structural motif.


Asunto(s)
Clostridium/enzimología , Glutamato Deshidrogenasa/química , Secuencia de Aminoácidos , Evolución Biológica , Bromuro de Cianógeno , Glutamato Deshidrogenasa/aislamiento & purificación , Datos de Secuencia Molecular , NAD/fisiología , Homología de Secuencia de Ácido Nucleico , Tripsina
7.
J Mol Biol ; 234(4): 1131-9, 1993 Dec 20.
Artículo en Inglés | MEDLINE | ID: mdl-8263917

RESUMEN

We have solved the structure of the binary complex of the glutamate dehydrogenase from Clostridium symbiosum with glutamate to 1.9 A resolution. In this complex, the glutamate side-chain lies in a pocket on the enzyme surface and a key determinant of the enzymic specificity is an interaction of the substrate gamma-carboxyl group with the amino group of Lys89. In the apo-enzyme, Lys113 from the catalytic domain forms an important hydrogen bond to Asn373, in the NAD(+)-binding domain. On glutamate binding, the side-chain of this lysine undergoes a significant movement in order to optimize its hydrogen bonding to the alpha-carboxyl group of the substrate. Despite this shift, the interaction between Lys113 and Asn373 is maintained by a large-scale conformational change that closes the cleft between the two domains. Modelling studies indicate that in this "closed" conformation the C-4 of the nicotinamide ring and the alpha-carbon atom of the amino acid substrate are poised for efficient hydride transfer. Examination of the structure has led to a proposal for the catalytic activity of the enzyme, which involves Asp165 as a general base, and an enzyme-bound water molecule, hydrogen-bonded to an uncharged lysine residue, Lys125, as an attacking nucleophile in the reaction.


Asunto(s)
Glutamato Deshidrogenasa/química , Proteínas Bacterianas/química , Proteínas Bacterianas/ultraestructura , Sitios de Unión , Catálisis , Clostridium/enzimología , Cristalografía por Rayos X , Glutamato Deshidrogenasa/ultraestructura , Glutamatos/química , Modelos Moleculares , Movimiento (Física) , NAD/química , Conformación Proteica , Especificidad por Sustrato , Agua
8.
J Mol Biol ; 234(4): 938-45, 1993 Dec 20.
Artículo en Inglés | MEDLINE | ID: mdl-8263939

RESUMEN

We have analysed the sequence homology between glutamate, leucine and phenylalanine dehydrogenases in the light of the solution of the structure of the glutamate dehydrogenase from Clostridium symbiosum. This analysis indicates that the elements of secondary structure comprising the core of the two domains in glutamate dehydrogenase are conserved in the other two enzymes. There is a striking conservation of the residues responsible for the recognition of the nicotinamide ring of the nucleotide cofactor and the backbone of the amino acid substrates. Furthermore, residues involved in a major conformational rearrangement on amino acid binding are preserved, as are those implicated in the catalytic chemistry. In contrast, the pattern of insertions/deletions between these enzymes is consistent with possible differences in quaternary structure. Differential substrate specificity between these enzymes is achieved by critical substitutions at the base of the binding pocket, which accommodates the side-chain of the amino acid substrate. This provides insights into the mutations necessary to produce new catalysts for the chiral synthesis of novel amino acids.


Asunto(s)
Aminoácido Oxidorreductasas/química , Glutamato Deshidrogenasa/química , Aminoácido Oxidorreductasas/genética , Aminoácido Oxidorreductasas/metabolismo , Secuencia de Aminoácidos , Bacillus/enzimología , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Evolución Biológica , Catálisis , Clostridium/enzimología , Glutamato Deshidrogenasa/genética , Glutamato Deshidrogenasa/metabolismo , Leucina-Deshidrogenasa , Micromonosporaceae/enzimología , Modelos Moleculares , Datos de Secuencia Molecular , Conformación Proteica , Estructura Terciaria de Proteína , Alineación de Secuencia , Homología de Secuencia de Aminoácido , Especificidad por Sustrato
9.
J Mol Biol ; 228(2): 662-71, 1992 Nov 20.
Artículo en Inglés | MEDLINE | ID: mdl-1453469

RESUMEN

The dinucleotide binding beta alpha beta motif in the crystal structures of seven different enzymes has been analysed in terms of their three-dimensional structures and primary sequences. We have identified that the hydrogen bonding of the adenine ribose to the glycine-rich turn containing the fingerprint sequence GXGXXG/A occurs via a direct or indirect mechanism, depending on the nature of the fingerprint sequence but independent of coenzyme specificity. The major determinant of the type of interaction is the nature of the residue occupying the last position of the above fingerprint. In the NAD(+)-linked dehydrogenases, an acidic residue is commonly used to form important hydrogen bonds to the adenine ribose hydroxyls and, hitherto, this residue has been thought to be an indicator of NAD+ specificity. However, on the basis of the three-dimensional structure of the NAD(+)-linked glutamate dehydrogenase (GDH) from Clostridium symbiosum we have demonstrated that this residue is not a universal requirement for the construction of an NAD+ binding site. Furthermore, considerations of sequence homology unambiguously identify an equivalent acidic residue in both NADP+ and dual specificity glutamate dehydrogenases. The conservation of this residue in these enzymes, coupled to its close proximity to the 2' phosphate implied by the necessary similarity in three-dimensional structure to C. symbiosum GDH, implicates this residue in the recognition of the 2' phosphate either via water-mediated or direct hydrogen-bonding schemes. Analysis of the latter has led us to suggest that two patterns of recognition for the 2' phosphate group of NADP(+)-binding enzymes may exist, which are distinguished by the ionization state of the 2' phosphate.


Asunto(s)
Enzimas/química , Adenosina Difosfato Ribosa/metabolismo , Secuencia de Aminoácidos , Animales , Enzimas/metabolismo , Glicina/química , Glicina/metabolismo , Humanos , Enlace de Hidrógeno , Datos de Secuencia Molecular , NAD/química , NAD/metabolismo , Conformación de Ácido Nucleico , Nucleótidos/metabolismo , Fosfatos/metabolismo , Conformación Proteica , Especificidad por Sustrato
10.
J Mol Biol ; 224(4): 1181-4, 1992 Apr 20.
Artículo en Inglés | MEDLINE | ID: mdl-1349042

RESUMEN

A new crystal form of the hexameric NAD(+)-linked glutamate dehydrogenase (GDH) from Clostridium symbiosum has been grown using the hanging drop method of vapour diffusion. The crystals are obtained either by using high concentrations of the amino acid substrate of the enzyme, glutamate, as the precipitant or by co-crystallization from ammonium sulphate in the presence of either p-chloromercuribenzene sulphonate or potassium tetracyanoplatinate. The crystals diffract well and X-ray photographs have established that they are in the space group R32. Considerations of the values of Vm indicate that the asymmetric unit of the R32 crystals contains a single subunit. Packing considerations based on the structure of the native enzyme determined from a different crystal form suggest that the molecule must undergo a significant conformational change in order to be accommodated in the new cell. Such a conformational rearrangement may represent an important step in the catalytic cycle.


Asunto(s)
Clostridium/enzimología , Glutamato Deshidrogenasa/ultraestructura , Cristalografía , Glutamato Deshidrogenasa/química , Glutamatos/metabolismo , Ácido Glutámico , Ligandos , NAD/metabolismo , Conformación Proteica , Relación Estructura-Actividad
11.
J Mol Biol ; 285(2): 875-85, 1999 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-9878450

RESUMEN

Comparisons of the structures of glutamate dehydrogenase (GluDH) and leucine dehydrogenase (LeuDH) have suggested that two substitutions, deep within the amino acid binding pockets of these homologous enzymes, from hydrophilic residues to hydrophobic ones are critical components of their differential substrate specificity. When one of these residues, K89, which hydrogen-bonds to the gamma-carboxyl group of the substrate l-glutamate in GluDH, was altered by site-directed mutagenesis to a leucine residue, the mutant enzyme showed increased substrate activity for methionine and norleucine but negligible activity with either glutamate or leucine. In order to understand the molecular basis of this shift in specificity we have determined the crystal structure of the K89L mutant of GluDH from Clostridium symbiosum. Analysis of the structure suggests that further subtle differences in the binding pocket prevent the mutant from using a branched hydrophobic substrate but permit the straight-chain amino acids to be used as substrates. The three-dimensional crystal structure of the GluDH from C. symbiosum has been previously determined in two distinct forms in the presence and absence of its substrate glutamate. A comparison of these two structures has revealed that the enzyme can adopt different conformations by flexing about the cleft between its two domains, providing a motion which is critical for orienting the partners involved in the hydride transfer reaction. It has previously been proposed that this conformational change is triggered by substrate binding. However, analysis of the K89L mutant shows that it adopts an almost identical conformation with that of the wild-type enzyme in the presence of substrate. Comparison of the mutant structure with both the wild-type open and closed forms has enabled us to separate conformational changes associated with substrate binding and domain motion and suggests that the domain closure may well be a property of the wild-type enzyme even in the absence of substrate.


Asunto(s)
Clostridium/enzimología , Glutamato Deshidrogenasa/química , Glutamato Deshidrogenasa/metabolismo , Leucina/metabolismo , Lisina/metabolismo , Conformación Proteica , Aminoácido Oxidorreductasas/metabolismo , Secuencia de Aminoácidos , Glutamato Deshidrogenasa/genética , Leucina/genética , Leucina-Deshidrogenasa , Lisina/genética , Datos de Secuencia Molecular , Mutagénesis Sitio-Dirigida , Relación Estructura-Actividad , Especificidad por Sustrato
12.
J Mol Biol ; 293(5): 1121-32, 1999 Nov 12.
Artículo en Inglés | MEDLINE | ID: mdl-10547290

RESUMEN

Glutamate dehydrogenase catalyses the oxidative deamination of glutamate to 2-oxoglutarate with concomitant reduction of NAD(P)(+), and has been shown to be widely distributed in nature across species ranging from psychrophiles to hyperthermophiles. Extensive characterisation of this enzyme isolated from hyperthermophilic organisms has led to its adoption as a model system for analysing the determinants of thermal stability. The crystal structure of the extremely thermostable glutamate dehydrogenase from Thermococcus litoralis has been determined at 2.5 A resolution, and has been compared to that from the hyperthermophile Pyrococcus furiosus. The two enzymes are 87 % identical in sequence, yet differ 16-fold in their half-lives at 104 degrees C. This is the first reported comparative analysis of the structures of a multisubunit enzyme from two closely related yet distinct hyperthermophilies. The less stable T. litoralis enzyme has a decreased number of ion pair interactions; modified patterns of hydrogen bonding resulting from isosteric sequence changes; substitutions that decrease packing efficiency; and substitutions which give rise to subtle but distinct shifts in both main-chain and side-chain elements of the structure. This analysis provides a rational basis to test ideas on the factors that confer thermal stability in proteins through a combination of mutagenesis, calorimetry, and structural studies.


Asunto(s)
Glutamato Deshidrogenasa/química , Pyrococcus furiosus/enzimología , Thermococcus/enzimología , Secuencia de Aminoácidos , Sustitución de Aminoácidos , Sitios de Unión , Cristalización , Cristalografía por Rayos X , Estabilidad de Enzimas , Glutamato Deshidrogenasa/metabolismo , Semivida , Enlace de Hidrógeno , Iones , Modelos Moleculares , Datos de Secuencia Molecular , Pliegue de Proteína , Estructura Secundaria de Proteína , Alineación de Secuencia , Eliminación de Secuencia , Electricidad Estática , Temperatura , Agua/química , Agua/metabolismo
13.
Protein Sci ; 7(4): 966-74, 1998 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-9568903

RESUMEN

The refolding of Clostridium symbiosum glutamate dehydrogenase (GDH) involves the formation of an inactive structured monomeric intermediate prior to its concentration-dependent association. The structured monomer obtained after removal of guanidinium chloride was stable and competent for reconstitution into active hexamers. Site-directed mutagenesis of C. symbiosum gdh gene was performed to replace the residues Arg-61 and Phe-187 which are involved in subunit-subunit interactions, as determined by three-dimensional structure analysis. Heterologous over-expression in Escherichia coli of the double mutant (R61E/F187D) led to the production of a soluble protein with a molecular mass consistent with the monomeric form of clostridial GDH. This protein is catalytically inactive but cross-reacts with an anti-wild-type GDH antibody preparation. The double mutant R61E/F187D does not assemble into hexamers. The physical properties and the stability toward guanidinium chloride and urea of R61E/F187D were studied and compared to those of the structured monomeric intermediate.


Asunto(s)
Clostridium/enzimología , Glutamato Deshidrogenasa/química , Pliegue de Proteína , Naftalenosulfonatos de Anilina/metabolismo , Sitios de Unión , Dicroismo Circular , Simulación por Computador , Escherichia coli/genética , Fluorescencia , Glutamato Deshidrogenasa/genética , Guanidina/farmacología , Peso Molecular , Mutagénesis Sitio-Dirigida/genética , Conformación Proteica , Desnaturalización Proteica/efectos de los fármacos , Ingeniería de Proteínas/métodos , Estructura Secundaria de Proteína , Proteínas Recombinantes/química , Ultracentrifugación , Urea/farmacología
14.
FEBS Lett ; 370(1-2): 93-6, 1995 Aug 14.
Artículo en Inglés | MEDLINE | ID: mdl-7649311

RESUMEN

Glycine-124 and leucine-307 of phenylalanine dehydrogenase from Bacillus sphaericus were altered by site-specific mutagenesis to the corresponding residues in leucine dehydrogenase: alanine and valine, respectively. These two residues have previously been implicated from molecular modelling as important in determining the substrate discrimination of the two enzymes. Single and double mutants displayed lower activities towards L-phenylalanine and enhanced activity towards almost all aliphatic amino acid substrates tested compared to the wild-type, thus confirming the predictions made from molecular modelling.


Asunto(s)
Aminoácido Oxidorreductasas/metabolismo , Bacillus/enzimología , Glicina , Leucina , Conformación Proteica , Aminoácido Oxidorreductasas/biosíntesis , Aminoácido Oxidorreductasas/química , Secuencia de Aminoácidos , Aminoácidos/metabolismo , Secuencia de Bases , Cinética , Leucina-Deshidrogenasa , Modelos Moleculares , Datos de Secuencia Molecular , Mutagénesis Sitio-Dirigida , Oligodesoxirribonucleótidos , Mutación Puntual , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Especificidad por Sustrato
15.
Nat Struct Biol ; 5(7): 593-601, 1998 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-9665174

RESUMEN

Opine dehydrogenases catalyze the NAD(P)H-dependent reversible reaction to form opines that contain two asymmetric centers exhibiting either (L,L) or (D,L) stereochemistry. The first structure of a (D,L) superfamily member, N-(1-D-carboxylethyl)-L-norvaline dehydrogenase (CENDH) from Arthrobacter sp. strain 1C, has been determined at 1.8 A resolution and the location of the bound nucleotide coenzyme has been identified. Six conserved residues cluster in the cleft between the enzyme's two domains, close to the nucleotide binding site, and are presumed to define the enzyme's catalytic machinery. Conservation of a His-Asp pair as part of this cluster suggests that the enzyme mechanism is related to the 2-hydroxy acid dehydrogenases. The pattern of sequence conservation and substitution between members of this enzyme family has permitted the tentative location of the residues that define their differential substrate specificities.


Asunto(s)
Arthrobacter/enzimología , Oxidorreductasas actuantes sobre Donantes de Grupo CH-NH/química , Estructura Secundaria de Proteína , Secuencia de Aminoácidos , Sitios de Unión , Secuencia Conservada , Cristalografía por Rayos X , Dimerización , Modelos Moleculares , Datos de Secuencia Molecular , NAD/química
16.
Eur J Biochem ; 209(3): 851-9, 1992 Nov 01.
Artículo en Inglés | MEDLINE | ID: mdl-1358610

RESUMEN

The family of glutamate dehydrogenases include a group of hexameric oligomers with a subunit M(r) of around 50,000, which are closely related in amino acid sequence and a smaller group of tetrameric oligomers based on a much larger subunit with M(r) 115,000. Sequence comparisons have indicated a low level of similarity between the C-terminal portion of the tetrameric enzymes and a substantial region of the polypeptide chain for the more widespread hexameric glutamate dehydrogenases. In the light of the solution of the three-dimensional structure of the hexameric NAD(+)-linked glutamate dehydrogenase from Clostridium symbiosum, we have undertaken a detailed examination of the alignment of the sequence for the C-terminal domain of the tetrameric Neurospora crassa glutamate dehydrogenase against the sequence and the molecular structure of that from C. symbiosum. This analysis reveals that the residues conserved between these two families are clustered in the three-dimensional structure and points to a remarkably similar layout of the glutamate-binding site and the active-site pocket, though with some differences in the mode of recognition of the nucleotide cofactor.


Asunto(s)
Glutamato Deshidrogenasa/química , Secuencia de Aminoácidos , Animales , Sitios de Unión , Bovinos , Clostridium/enzimología , Glutamato Deshidrogenasa/metabolismo , Glutamatos/metabolismo , Ácido Glutámico , Datos de Secuencia Molecular , Neurospora crassa/enzimología , Nucleótidos/metabolismo , Conformación Proteica , Alineación de Secuencia
17.
Protein Eng ; 8(2): 147-52, 1995 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-7630885

RESUMEN

Two residues, K89 and S380, thought to interact with the gamma-carboxyl group of the substrate L-glutamate, have been altered by site-directed mutagenesis of clostridial glutamate dehydrogenase (GDH). The single mutants K89L and S380V and the combined double mutant K89L/S380V were constructed. All three mutants were satisfactorily overproduced in soluble form. However, only the K89L mutant was retained by the dye column normally used in purifying the wild-type enzyme. All three mutant enzymes were purified to homogeneity and tested for substrate specificity with 24 amino acids. The single mutant S380V showed no detectable activity. The alternative single mutant K89L showed an activity towards L-glutamate that was decreased nearly 2000-fold compared with wild-type enzyme, whereas the activities towards the monocarboxylic substrates alpha-aminobutyrate and norvaline were increased 2- to 3-fold. A similar level of activity was obtained with methionine (0.005 U/mg) and norleucine (0.012 U/mg), neither of which give any activity with the wild-type enzyme under the same conditions. The double mutant showed decreased activity with all substrates compared with the wild-type GDH. In view of its novel activities, the K89L mutant was investigated in greater detail. A strictly linear relationship between reaction velocity and substrate concentration was observed up to 80 mM L-methionine and 200 mM L-norleucine, implying very high Km values. Values of kcat/Km for L-methionine and L-norleucine were 6.7 x 10(-2) and 0.15 s-1 M-1, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)


Asunto(s)
Aminoácidos/metabolismo , Clostridium/enzimología , Glutamato Deshidrogenasa/metabolismo , Lisina/química , Mutagénesis Sitio-Dirigida , Secuencia de Aminoácidos , Secuencia de Bases , Sitios de Unión , Escherichia coli , Expresión Génica , Glutamato Deshidrogenasa/genética , Ácido Glutámico/farmacología , Cinética , Lisina/genética , Modelos Moleculares , Datos de Secuencia Molecular , Conformación Proteica , Relación Estructura-Actividad , Especificidad por Sustrato
18.
J Biol Chem ; 273(15): 9023-30, 1998 Apr 10.
Artículo en Inglés | MEDLINE | ID: mdl-9535890

RESUMEN

A homology-based modeling study on the extremely halophilic glutamate dehydrogenase from Halobacterium salinarum has been used to provide insights into the molecular basis of salt tolerance. The modeling reveals two significant differences in the characteristics of the surface of the halophilic enzyme that may contribute to its stability in high salt. The first of these is that the surface is decorated with acidic residues, a feature previously seen in structures of halophilic enzymes. The second is that the surface displays a significant reduction in exposed hydrophobic character. The latter arises not from a loss of surface-exposed hydrophobic residues, as has previously been proposed, but from a reduction in surface-exposed lysine residues. This is the first report of such an observation.


Asunto(s)
Glutamato Deshidrogenasa/química , Halobacterium salinarum/enzimología , Estructura Secundaria de Proteína , Secuencia de Aminoácidos , Bacterias/enzimología , Simulación por Computador , Halobacterium salinarum/fisiología , Soluciones Hipertónicas , Modelos Moleculares , Datos de Secuencia Molecular , Alineación de Secuencia , Homología de Secuencia de Aminoácido , Programas Informáticos
19.
Acta Crystallogr D Biol Crystallogr ; 54(Pt 1): 124-6, 1998 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-9867431

RESUMEN

The novel NAD+-linked opine dehydrogenase from a soil isolate Arthrobacter sp. strain 1C belongs to an enzyme superfamily whose members exhibit quite diverse substrate specificities. Crystals of this opine dehydrogenase, obtained in the presence or absence of co-factor and substrates, have been shown to diffract to beyond 1.8 A resolution. X-ray precession photographs have established that the crystals belong to space group P21212, with cell parameters a = 104.9, b = 80.0, c = 45.5 A and a single subunit in the asymmetric unit. The elucidation of the three-dimensional structure of this enzyme will provide a structural framework for this novel class of dehydrogenases to enable a comparison to be made with other enzyme families and also as the basis for mutagenesis experiments directed towards the production of natural and synthetic opine-type compounds containing two chiral centres.


Asunto(s)
Arthrobacter/enzimología , NAD/química , Oxidorreductasas actuantes sobre Donantes de Grupo CH-NH/química , Cristalización , Cristalografía por Rayos X
20.
Eur J Biochem ; 268(22): 5791-9, 2001 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-11722565

RESUMEN

In earlier attempts to shift the substrate specificity of glutamate dehydrogenase (GDH) in favour of monocarboxylic amino-acid substrates, the active-site residues K89 and S380 were replaced by leucine and valine, respectively, which occupy corresponding positions in leucine dehydrogenase. In the GDH framework, however, the mutation S380V caused a steric clash. To avoid this, S380 has been replaced with alanine instead. The single mutant S380A and the combined double mutant K89L/S380A were satisfactorily overexpressed in soluble form and folded correctly as hexameric enzymes. Both were purified successfully by Remazol Red dye chromatography as routinely used for wild-type GDH. The S380A mutant shows much lower activity than wild-type GDH with glutamate. Activities towards monocarboxylic substrates were only marginally altered, and the pH profile of substrate specificity was not markedly altered. In the double mutant K89L/S380A, activity towards glutamate was undetectable. Activity towards L-methionine, L-norleucine and L-norvaline, however, was measurable at pH 7.0, 8.0 and 9.0, as for wild-type GDH. Ala163 is one of the residues that lines the binding pocket for the side chain of the amino-acid substrate. To explore its importance, the three mutants A163G, K89L/A163G and K89L/S380A/A163G were constructed. All three were abundantly overexpressed and showed chromatographic behaviour identical with that of wild-type GDH. With A163G, glutamate activity was lower at pH 7.0 and 8.0, but by contrast higher at pH 9.0 than with wild-type GDH. Activities towards five aliphatic amino acids were remarkably higher than those for the wild-type enzyme at pH 8.0 and 9.0. In addition, the mutant A163G used L-aspartate and L-leucine as substrates, neither of which gave any detectable activity with wild-type GDH. Compared with wild-type GDH, the A163 mutant showed lower catalytic efficiencies and higher K(m ) values for glutamate/2-oxoglutarate at pH 7.0, but a similar k(cat)/K(m) value and lower K(m) at pH 8.0, and a nearly 22-fold lower S(0.5) (substrate concentration giving half-saturation under conditions where Michaelis-Menten kinetics does not apply) at pH 9.0. Coupling the A163G mutation with the K89L mutation markedly enhanced activity (100-1000-fold) over that of the single mutant K89L towards monocarboxylic amino acids, especially L-norleucine and L-methionine. The triple mutant K89L/S380A/A163G retained a level of activity towards monocarboxylic amino acids similar to that of the double mutant K89L/A163G, but could no longer use glutamate as substrate. In terms of natural amino-acid substrates, the triple mutant represents effective conversion of a glutamate dehydrogenase into a methionine dehydrogenase. Kinetic parameters for the reductive amination reaction are also reported. At pH 7 the triple mutant and K89L/A163G show 5 to 10-fold increased catalytic efficiency, compared with K89L, towards the novel substrates. In the oxidative deamination reaction, it is not possible to estimate k(cat) and K(m) separately, but for reductive amination the additional mutations have no significant effect on k(cat) at pH 7, and the increase in catalytic efficiency is entirely attributable to the measured decrease in K(m). At pH 8 the enhancement of catalytic efficiency with the novel substrates was much more striking (e.g. for norleucine approximately 2000-fold compared with wild-type or the K89L mutant), but it was not established whether this is also exclusively due to more favourable Michaelis constants.


Asunto(s)
Aminoácido Oxidorreductasas/metabolismo , Glutamato Deshidrogenasa/metabolismo , Secuencia de Bases , Coenzimas/metabolismo , Cartilla de ADN , Formazáns/química , Glutamato Deshidrogenasa/genética , Indicadores y Reactivos/química , Cinética , Mutagénesis Sitio-Dirigida , Unión Proteica , Especificidad por Sustrato
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