Molecular and phylogenetic characterization of isopropylmalate dehydrogenase of a thermoacidophilic archaeon, Sulfolobus sp. strain 7

Suzuki, Toshiharu; Inoki, Y; Yamagishi, Akihiko; Iwasaki, Toshio; Wakagi, Takayoshi; Oshima, Tairo

doi:10.1128/jb.179.4.1174-1179.1997

Cited by 23 publications

(23 citation statements)

References 42 publications

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“…The IPMDH Mj is 44% identical to the crenarchaeal homolog from a Sulfolobus sp. (34). The two proteins have similar kinetic parameters for the oxidative decarboxylation of D-malate, although the Sulfolobus enzyme has a 20-fold-lower K m for ␤-isopropylmalate (Table 3).…”

Section: Discussionmentioning

confidence: 99%

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Enzymology and Evolution of the Pyruvate Pathway to 2-Oxobutyrate in Methanocaldococcus jannaschii

2007

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The archaeon Methanocaldococcus jannaschii uses three different 2-oxoacid elongation pathways, which extend the chain length of precursors in leucine, isoleucine, and coenzyme B biosyntheses. In each of these pathways an aconitase-type hydrolyase catalyzes an hydroxyacid isomerization reaction. The genome sequence of M. jannaschii encodes two homologs of each large and small subunit that forms the hydrolyase, but the genes are not cotranscribed. The genes are more similar to each other than to previously characterized isopropylmalate isomerase or homoaconitase enzyme genes. To identify the functions of these homologs, the four combinations of subunits were heterologously expressed in Escherichia coli, purified, and reconstituted to generate the iron-sulfur center of the holoenzyme. Only the combination of MJ0499 and MJ1277 proteins catalyzed isopropylmalate and citramalate isomerization reactions. This pair also catalyzed hydration half-reactions using citraconate and maleate. Another broad-specificity enzyme, isopropylmalate dehydrogenase (MJ0720), catalyzed the oxidative decarboxylation of ␤-isopropylmalate, ␤-methylmalate, and D-malate. Combined with these results, phylogenetic analysis suggests that the pyruvate pathway to 2-oxobutyrate (an alternative to threonine dehydratase in isoleucine biosynthesis) evolved several times in bacteria and archaea. The enzymes in the isopropylmalate pathway of leucine biosynthesis facilitated the evolution of 2-oxobutyrate biosynthesis through the introduction of a citramalate synthase, either by gene recruitment or gene duplication and functional divergence.

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Section: Discussionmentioning

confidence: 99%

“…Because the leucine biosynthetic IPMI from Saccharomyces cerevisiae also catalyzes the hydra-tion of citraconate (27), we predicted that the M. jannaschii IPMI could function in both leucine and isoleucine pathways. Similarly, the M. jannaschii IPMDH homolog could also catalyze the oxidative decarboxylation of ␤-methylmalate to produce 2-oxobutyrate (34).…”

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confidence: 99%

Enzymology and Evolution of the Pyruvate Pathway to 2-Oxobutyrate in Methanocaldococcus jannaschii

2007

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“…Thus, the fact that two hyperthermophilic ICDHs are dimeric indicates that tetramerization is not the only way to acquire elevated thermostability. In tetrameric StIPMDH, the hydrophobic residues that correspond to Val135, Tyr132, and Val141 in TtHICDH are conserved as Val135, Val131, and Ile141, respectively, indicating that this enzyme may have the similar hydrophobic dimer-dimer interactions to form a tetramer (27). The crystal structure of StIPMDH at a 2.8-Å res- olution (which has recently been deposited in the RCSB Protein Data Bank as 1WPW) indicates that StIPMDH is also stabilized by a dimer-dimer interaction like that of TtHICDH.…”

Section: Discussionmentioning

confidence: 99%

“…It is known that ICDH from Thermotoga maritima (26) and IPMDH from Sulfolobus tokodaii 7 (StIPMDH) (27,33) are also tetrameric ␤-decarboxylating dehydrogenases, although most ␤-decarboxylating dehydrogenases are dimers. Interestingly, the tetrameric ␤-decarboxylating dehydrogenases are found only in hyperthermophiles and not in mesophiles.…”

Section: Discussionmentioning

confidence: 99%

“…TtHICDH is a homotetramer, while most ␤-decarboxylating dehydrogenases are homodimers. Although a few members of ␤-decarboxylating dehydrogenases are reported to be tetramers (26,27,33), the interactions necessary for tetramer formation have not been elucidated at all. The third characteristic is the thermotolerance of TtHICDH, which is substantially higher than for IPMDH and ICDH from T. thermophilus.…”

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Crystal Structure of Tetrameric Homoisocitrate Dehydrogenase from an Extreme Thermophile, Thermus thermophilus : Involvement of Hydrophobic Dimer-Dimer Interaction in Extremely High Thermotolerance

et al. 2005

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The crystal structure of homoisocitrate dehydrogenase involved in lysine biosynthesis from Thermus thermophilus (TtHICDH) was determined at 1.85-Å resolution. Arg85, which was shown to be a determinant for substrate specificity in our previous study, is positioned close to the putative substrate binding site and interacts with Glu122. Glu122 is highly conserved in the equivalent position in the primary sequence of ICDH and archaeal 3-isopropylmalate dehydrogenase (IPMDH) but interacts with main-and side-chain atoms in the same domain in those paralogs. In addition, a conserved Tyr residue (Tyr125 in TtHICDH) which extends its side chain toward a substrate and thus has a catalytic function in the related ␤-decarboxylating dehydrogenases, is flipped out of the substrate-binding site. These results suggest the possibility that the conformation of the region containing Glu122-Tyr125 is changed upon substrate binding in TtHICDH. The crystal structure of TtHICDH also reveals that the arm region is involved in tetramer formation via hydrophobic interactions and might be responsible for the high thermotolerance. Mutation of Val135, located in the dimer-dimer interface and involved in the hydrophobic interaction, to Met alters the enzyme to a dimer (probably due to steric perturbation) and markedly decreases the thermal inactivation temperature. Both the crystal structure and the mutation analysis indicate that tetramer formation is involved in the extremely high thermotolerance of TtHICDH.Homoisocitrate dehydrogenase (HICDH) is the third enzyme involved in lysine biosynthesis through ␣-aminoadipate (19) and is a member of a family of ␤-decarboxylating dehydrogenases that includes isocitrate dehydrogenase (ICDH) in the tricarboxylic acid cycle, 3-isopropylmalate dehydrogenase (IPMDH) in leucine biosynthesis, and tartrate dehydrogenase in vitamin production (2). It has been suggested that these enzymes diverged from a common ancestral ␤-decarboxylating dehydrogenase (4, 9, 34).We have shown that in an extremely thermophilic bacterium, Thermus thermophilus HB27, lysine is synthesized through ␣-aminoadipate, although lysine is synthesized through diaminopimelate in most bacteria (13,18,20,22,23,31). We have previously characterized HICDH from T. thermophilus HB27 (TtHICDH) in detail and have shown that the enzyme has four unique features (19). The first is its substrate specificity. Although TtHICDH is essential for lysine biosynthesis in the bacterium, TtHICDH can catalyze the reaction with isocitrate as a substrate; isocitrate is the substrate of ICDH at a 20-fold-higher efficiency than toward the native substrate, homoisocitrate. This feature contrasts with HICDH from Saccharomyces cerevisiae, which utilizes only homoisocitrate as a substrate (19). Moreover, the substrate specificity is easily altered by a single mutation, Arg85Val, to lose activity for isocitrate but to acquire activity for 3-isopropylmalate, a substrate of IPMDH. The second feature is the unique subunit organization. TtHICDH is a homotetramer, while mo...

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Evolution of a Transition State: Role of Lys100 in the Active Site of Isocitrate Dehydrogenase

et al. 2014

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An active site lysine essential to catalysis in isocitrate dehydrogenase (IDH) is absent from related enzymes. As all family members catalyze the same oxidative β-decarboxylation at the 2R-malate core common to their substrates, it seems odd that an amino acid essential to one is not found in all. Ordinarily, hydride transfer to a nicotinamide C4 neutralizes the positive charge at N1 directly. In IDH the negatively charged C4-carboxylate of isocitrate stabilizes the ground state positive charge on the adjacent nicotinamide N1, opposing hydride transfer. The critical lysine is poised to stabilize – and perhaps even protonate – an oxyanion formed on the nicotinamide 3-carboxamide, thereby enabling the hydride to be transferred while the positive charge at N1 is maintained. IDH may catalyze the same overall reaction as other family members, but dehydrogenation proceeds through a distinct, though related, transition state. Partial activation of lysine mutants by K+ and NH4+ represents a throwback to the primordial state of the first substrate promiscuous family member.

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Molecular and phylogenetic characterization of isopropylmalate dehydrogenase of a thermoacidophilic archaeon, Sulfolobus sp. strain 7

Cited by 23 publications

References 42 publications

Enzymology and Evolution of the Pyruvate Pathway to 2-Oxobutyrate in Methanocaldococcus jannaschii

Enzymology and Evolution of the Pyruvate Pathway to 2-Oxobutyrate in Methanocaldococcus jannaschii

Crystal Structure of Tetrameric Homoisocitrate Dehydrogenase from an Extreme Thermophile, Thermus thermophilus : Involvement of Hydrophobic Dimer-Dimer Interaction in Extremely High Thermotolerance

Evolution of a Transition State: Role of Lys100 in the Active Site of Isocitrate Dehydrogenase

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