Structure and function of the l-threonine dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis

Bowyer, A.; Mikolajek, Halina; Stuart, Jan; Wood, Steve; Jamil, Farrukh; Rashid, Naeem; Akhtar, Muhammad; Cooper, J.B.

doi:10.1016/j.jsb.2009.07.011

Cited by 23 publications

(25 citation statements)

References 52 publications

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“…An 11 ϫ 10 ϫ 11-nm 3 cuboid box was prepared after completion of protonation. Protonated CnThrDH (holo, with NAD ϩ ) was moved to the center of the box, and TIP3P water molecules were solvated into the box at a solvent density of 1.0 g/cm 3 . Energy minimization of the system was performed using the Charmm27 force field as follows: first, energy minimization was performed by constraining the backbone atoms of CnThrDH, and then the constraint was turned off.…”

Section: Methodsmentioning

confidence: 99%

“…L-ThrDH utilizes oxidized NAD ϩ as a coenzyme to catalyze dehydrogenation of the 3Ј carbon atom of L-Thr. The product 2-amino 3-keto butyrate is decomposed rapidly to aminoacetone and CO 2 (2) or converted to glycine by 2-amino 3-keto butyrate CoA ligase (3). The structures of two types of L-ThrDH enzymes have been reported.…”

mentioning

confidence: 99%

“…The structures of two types of L-ThrDH enzymes have been reported. One type is classified within the medium chain dehydrogenase/reductase (MDR) superfamily, and is similar to alcohol dehydrogenase (ADH) (3,4). MDR has ϳ350 amino acid residues and contains a Rossmann fold domain in its C-terminal region (5).…”

mentioning

confidence: 99%

“…The functions of MDR family members are divergent (6), and this type of L-ThrDH is classified as a zinc-dependent MDR as well as an ADH. Several biochemical and structural studies have been performed on this type of L-ThrDH (3,(7)(8)(9)(10). The other type is classified within the extended short chain dehydrogenase/reductase (SDR) (4) and is similar to UDP-galactose 4-epimerase (GalE).…”

mentioning

confidence: 99%

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Binding of NAD+ and l-Threonine Induces Stepwise Structural and Flexibility Changes in Cupriavidus necator l-Threonine Dehydrogenase

Nakano

Okazaki

Tokiwa

et al. 2014

Journal of Biological Chemistry

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Section: Methodsmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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confidence: 99%

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Binding of NAD+ and l-Threonine Induces Stepwise Structural and Flexibility Changes in Cupriavidus necator l-Threonine Dehydrogenase

Nakano

Okazaki

Tokiwa

et al. 2014

Journal of Biological Chemistry

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“…The latter was observed only in KGDH1. It is most likely that the activities toward Thr/Ser derive from the threonine 3-dehydrogenase of T. kodakarensis, encoded by TK0916 (52,53). The enzyme has been characterized, has been shown to be dependent on NAD ϩ , and displays a low level of activity toward Ser.…”

Section: Discussionmentioning

confidence: 99%

Genetic Examination of Initial Amino Acid Oxidation and Glutamate Catabolism in the Hyperthermophilic Archaeon Thermococcus kodakarensis

et al. 2013

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dAmino acid catabolism in Thermococcales is presumed to proceed via three steps: oxidative deamination of amino acids by glutamate dehydrogenase (GDH) or aminotransferases, oxidative decarboxylation by 2-oxoacid:ferredoxin oxidoreductases (KOR), and hydrolysis of acyl-coenzyme A (CoA) by ADP-forming acyl-CoA synthetases (ACS). Here, we performed a genetic examination of enzymes involved in Glu catabolism in Thermococcus kodakarensis. Examination of amino acid dehydrogenase activities in cell extracts of T. kodakarensis KUW1 (⌬pyrF ⌬trpE) revealed high NADP-dependent GDH activity, along with lower levels of NAD-dependent activity. NADP-dependent activities toward Gln/Ala/Val/Cys and an NAD-dependent threonine dehydrogenase activity were also detected. In KGDH1, a gene disruption strain of T. kodakarensis GDH (Tk-GDH), only threonine dehydrogenase activity was detected, indicating that all other activities were dependent on Tk-GDH. KGDH1 could not grow in a medium in which growth was dependent on amino acid catabolism, implying that Tk-GDH is the only enzyme that can discharge the electrons (to NADP ؉ /NAD ؉ ) released from amino acids in their oxidation to 2-oxoacids. In a medium containing excess pyruvate, KGDH1 displayed normal growth, but higher degrees of amino acid catabolism were observed compared to those for KUW1, suggesting that Tk-GDH functions to suppress amino acid oxidation and plays an anabolic role under this condition. We further constructed disruption strains of 2-oxoglutarate:ferredoxin oxidoreductase and succinyl-CoA synthetase. The two strains displayed growth defects in both media compared to KUW1. Succinate generation was not observed in these strains, indicating that the two enzymes are solely responsible for Glu catabolism among the multiple KOR and ACS enzymes in T. kodakarensis.

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An overview of 25 years of research on Thermococcus kodakarensis, a genetically versatile model organism for archaeal research

Rashid

Aslam

2019

Folia Microbiol

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Structure and function of the l-threonine dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis

Cited by 23 publications

References 52 publications

Binding of NAD+ and l-Threonine Induces Stepwise Structural and Flexibility Changes in Cupriavidus necator l-Threonine Dehydrogenase

Binding of NAD+ and l-Threonine Induces Stepwise Structural and Flexibility Changes in Cupriavidus necator l-Threonine Dehydrogenase

Genetic Examination of Initial Amino Acid Oxidation and Glutamate Catabolism in the Hyperthermophilic Archaeon Thermococcus kodakarensis

An overview of 25 years of research on Thermococcus kodakarensis, a genetically versatile model organism for archaeal research

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