Crystal Structure Analysis of ω-Amino Acid: Pyruvate Aminotransferase with a Newly Developed Weissenberg Camera and an Imaging Plate Using Synchrotron Radiation1

Watanabe, Nobuhisa; Sakabe, K.; Sakabe, Noriyoshi; Higashi, Tsuneyuki; Sasaki, Kyoyu; Aibara, Shigeo; Morita, Yuhei; Yonaha, Kazuo; Toyama, Seizen; Fukutani, Hirohito

doi:10.1093/oxfordjournals.jbchem.a122600

Cited by 69 publications

(43 citation statements)

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“…A prokaryotic aminotransferase, the o-aminoacid :pyruvate aminotransferase from Pseudomonas spec. F-126, was found to be a tetramer of 43 kDa polypeptides (Morita et al, 1979;Soda, 1985;Watanabe et al, 1989). Far-reaching similarity of the native molecular mass and the subunit stoichiometry may be deduced from 2,2-dialkylglycine decarboxylase, isolated from Pseudomonas cepacia.…”

Section: Resultsmentioning

confidence: 99%

High‐resolution Electron Microscopic Studies on the Quaternary Structure of Ornithine Aminotransferase from Pig Kidney

Lünsdorf

Hecht

Tsai

1994

European Journal of Biochemistry

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The ornithine aminotransferase (OAT) from pig kidney has been studied on the basis of highresolution electron microscopy and the morphological appearance of the apoenzyme and holoenzyme have been examined. The quaternary structure of the OAT molecules in the presence of 5 mM pyridoxal 5'-phosphate could be established. The enzyme molecule appears to be built up of two morphological units, called M1. The native holoenzyme, termed morphological unit M2, measures . 10.9 nm in length and 5.8 nm in width and its molecular mass is approximately 168 kDa, based on electron microscopical calculations. Since the enzyme is composed of only one type of 45-kDa subunit, the holoenzyme is a homotetramer. Each M1 is composed of two subunits and, as seen in top-view projection, has an oval to triangular shape. Upon tilting to 40" the triangular shape changes into three distinct centers of mass. This morphological differentiation reflects the inner organization of M1, i.e. the shape of the individual subunit deviates from strictly globular proteins. This observation is compatible with the notion that the 45-kDa subunit consists of one large and one small domain. By tilting to 40", both large domains in M1 represent two of the three centers of mass, while the third center of mass is attributed to the superposition of both small domains. Thus, the four domains of both subunits in M1, in accordance with the triangular top-view projection, are quasi-tetrahedrally arranged. Since the change in shape of M1 upon tilting is only obvious in one of the two halves of the native OAT, it suggests that both morphological units of M2 are oriented asymmetrically relative to one another.

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Section: Resultsmentioning

confidence: 99%

High‐resolution Electron Microscopic Studies on the Quaternary Structure of Ornithine Aminotransferase from Pig Kidney

Lünsdorf

Hecht

Tsai

1994

European Journal of Biochemistry

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“…The possible evolutionary relationship between the a and y family (Table 3) must be confirmed by further investigation, in particular by determination of the three-dimensional structure of a member of the y family. Three-dimensional structures have been reported for o-amino acid aminotransferase (Watanabe et al, 1989), 2,2-dialkylglycine decarboxylase (Toney et al, 1993) and phosphoserine aminotransferase (preliminary partial structure; Stark et al, 1991) which, all belong to the a family (Table 4). Indeed, the folding patterns of the polypeptide chain of these enzymes, at least in the large domain, are similar to that of aspartate ami-…”

Section: Discussionmentioning

confidence: 99%

Evolutionary relationships among pyridoxal‐5′‐phosphate‐dependent enzymes

Alexander

Sandmeier

Mehta

et al. 1994

European Journal of Biochemistry

357

290

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Pyridoxal-5'-phosphate-dependent enzymes catalyze manifold reactions in the metabolism of amino acids. A comprehensive comparison of amino acid sequences has shown that most of these enzymes can be assigned to one of three different families of homologous proteins. The sequences of the enzymes of each family were aligned and their homology confirmed by profile analysis. Scrutiny of the reactions catalyzed by the enzymes showed that their affiliation with one of the three structurally defined families correlates in most cases with their regio-specificity.In the largest family, the covalency changes of the substrate occur at the same carbon atom that carries the amino group forming the irnine linkage with the coenzyme. This family was thus named a family. It comprises glycine hydroxymethyltransferase, glycine C-acetyltransferase, 5-aminulevulinate synthase, 8-amino-7-oxononanoate synthase, all aminotransferases (with the possible exception of subgroup 111), a number of other enzymes relatively closely related with the aminotransferases and very likely a certain group of amino acid decarboxylases as well as tryptophanase and tyrosine phenol-lyase which, however, catalyze p-elimination reactions. The p family includes L-and Dserine dehydratase, threonine dehydratase, the /? subunit of tryptophan synthase, threonine synthase and cysteine synthase. These enzymes catalyze p-replacement or p-elimination reactions. The y family incorporates 0-succinylhomoserine (thio1)-lyase, 0-acetylhomoserine (thio1)-lyase, and cystathionine y-lyase, which catalyze y-replacement or y-elimination reactions, as well as cystathionine P-lyase.The a and y family might be distantly related with one another, but are clearly not homologous with the / 3 family. Apparently, the primordial pyridoxal-5'-phosphate-dependent enzymes were regio-specific catalysts, which first specialized for reaction specificity and then for substrate specificity. The following pyridoxal-5'-phosphate-dependent enzymes seem to be unrelated with the a, /? or y family by the criterion of profile analysis: alanine racemase, selenocysteine synthase, and many amino acid decarboxylases. These enzymes may represent yet other families of B, enzymes.Pyridoxal-5'-phosphate-dependent enzymes (B, enzymes) catalyze such a wide variety of transformations of amino acids that they are found in no fewer than four out of the total six EC classes of enzymes (Enzyme Nomenclature, 1992). This paper is part of a study on the evolutionary relationships among these multifarious enzymes. Previously, we have found that most if not all aminotransferases constitute a group of homologous proteins . Profile analysis, an algorithm for the detection of distant relationships between amino acid sequences (Gribskov et al., 1990), showed, however, that the evolutionary relationships extend beyond the group of aminotransferases and include other B, enzymes Mehta and Christen, 1994). This study compares the currently known amino acid sequences of B, enzymes and shows that many of them belong to one of th...

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“…The fold of the enzyme is roughly similar to the well-studied aspartate aminotransferase (6), which is a member of evolutionary subgroup I of aminotransferases (7). DGD is a representative member of evolutionary subgroup II (8), and its fold is closely similar to the other known structures of subgroup II enzymes (9,10). The active site structure of DGD is similar to that of aspartate aminotransferase in that the interactions made between coenzyme and protein are highly conserved (5).…”

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confidence: 91%

Reactions of Alternate Substrates Demonstrate Stereoelectronic Control of Reactivity in Dialkylglycine Decarboxylase

1998

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Kinetic and product analyses of the reactions of dialkylglycine decarboxylase with several alternative substrates are presented. Rate constants for the reactions of amino and keto acids of several substrates decrease logarithmically with increasing side-chain size. Conversely, k cat for L-amino acid decarboxylation increases with side-chain size. These and other data confirm a proposed model for three binding subsites in the active site. In this model, bond making and breaking in both the decarboxylation and transamination half-reactions occurs at the "A" subsite, which maintains the scissile bond aligned with the p orbitals of the conjugated aldimine and thus maximizes stereoelectronic effects. This strongly supports the proposal by Dunathan (Proc. Natl. Acad. Sci. U.S.A. 55,[712][713][714][715][716]) that PLP-dependent enzymes can largely control reaction specificity by specific orientation about C R in the external aldimine intermediate. The "B" subsite can accept either an alkyl or a carboxylate group, while the "C" subsite accepts only small alkyl groups. This model predicts the existence of nonproductive binding modes for amino acids, which is proposed to be the ultimate origin of the k cat increase with side-chain size for L-amino acid decarboxylation. The specificity of the 2-aminoisobutyrate decarboxylation half-reaction toward oxidative decarboxylation is very high (<1 in 10 5 turnovers yields nonoxidative decarboxylation). The origin of this specificity is explored with the reactions of amino-and methylaminomalonate. These substrates exhibit high yields of nonoxidative decarboxylation, providing support for a model in which the interaction between a carboxylate group in the B subsite and Arg406 is a prerequisite to proton donation to and removal from C R .Dialkylglycine decarboxylase (DGD) 1,2 from Pseudomonas cepacia is a PLP dependent enzyme that catalyzes the oxidative decarboxylation of 2,2-dialkylglycines, yielding CO 2 , a ketone, and the PMP form of the enzyme (Scheme 1). The catalytic cycle is completed by transamination of an R-keto acid, preferentially pyruvate (1-3). The overall reaction catalyzed by DGD is shown below. The unusual ability of DGD to catalyze rapidly two classical PLPdependent reactions has rekindled an interest in this enzyme.The X-ray structure of DGD has been determined to 2.1-Å resolution (4, 5). The fold of the enzyme is roughly similar to the well-studied aspartate aminotransferase (6), which is a member of evolutionary subgroup I of aminotransferases (7). DGD is a representative member of evolutionary subgroup II (8), and its fold is closely similar to the other known structures of subgroup II enzymes (9, 10). The active site structure of DGD is similar to that of aspartate aminotransferase in that the interactions made between coenzyme and protein are highly conserved (5).Toney et al. (5) proposed a structurally based model of the active site of DGD in which there are three binding subsites (A-C) that differ in their functional group specificities. One of t...

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Crystal Structure Analysis of ω-Amino Acid: Pyruvate Aminotransferase with a Newly Developed Weissenberg Camera and an Imaging Plate Using Synchrotron Radiation1

Cited by 69 publications

References 0 publications

High‐resolution Electron Microscopic Studies on the Quaternary Structure of Ornithine Aminotransferase from Pig Kidney

High‐resolution Electron Microscopic Studies on the Quaternary Structure of Ornithine Aminotransferase from Pig Kidney

Evolutionary relationships among pyridoxal‐5′‐phosphate‐dependent enzymes

Reactions of Alternate Substrates Demonstrate Stereoelectronic Control of Reactivity in Dialkylglycine Decarboxylase

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