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

Nakano, Shogo; Okazaki, Seiji; Tokiwa, Hiroaki; Asano, Yasuhisa

doi:10.1074/jbc.m113.540773

Cited by 19 publications

(43 citation statements)

References 37 publications

(51 reference statements)

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“…Loops analogous to the flexible Loop 1 identified in TbTDH have been highlighted in TDHs from other species (Yoneda et al, 2010;Nakano et al, 2014). Indeed, the aminoacid sequence corresponding to this loop appears to be a conserved feature among GalE-like TDHs.…”

Section: Substrate Binding and Catalytic Mechanism Of Actionmentioning

confidence: 90%

“…The NADH-and l-threonine-bound structure presented here (Fig. 7) is only accompanied in the literature by one other threonine-bound wild-type TDH structure (Nakano et al, 2014). Both structures provide valuable insights into the proposed mechanism of action of TDH, in which a hydride is transferred from the -carbon of l-threonine to the C4 atom of the nicotinamide ring of NAD + ; both l-threonine and the cofactor are bound in the necessary orientation for catalysis.…”

Section: Substrate Binding and Catalytic Mechanism Of Actionmentioning

confidence: 94%

“…Nakano and coworkers proposed a model whereby NAD + binding caused a rigidification of flexible regions in the NAD-binding domain, but the flexible loop remained open. Then, in the same model l-threonine binding causes Loop 1 to close over the active site and this accounts for the selectivity of the enzyme for l-threonine (Nakano et al, 2014).…”

Section: Substrate Binding and Catalytic Mechanism Of Actionmentioning

confidence: 97%

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Structure and function ofL-threonine-3-dehydrogenase from the parasitic protozoanTrypanosoma bruceirevealed by X-ray crystallography and geometric simulations

Adjogatse

Erskine

Wells

et al. 2018

Acta Crystallogr D Struct Biol

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Two of the world's most neglected tropical diseases, human African trypanosomiasis (HAT) and Chagas disease, are caused by protozoan parasites of the genus Trypanosoma. These organisms possess specialized metabolic pathways, frequently distinct from those in humans, which have potential to be exploited as novel drug targets. This study elucidates the structure and function of L-threonine-3-dehydrogenase (TDH) from T. brucei, the causative pathogen of HAT. TDH is a key enzyme in the metabolism of L-threonine, and an inhibitor of TDH has been shown to have trypanocidal activity in the procyclic form of T. brucei. TDH is a nonfunctional pseudogene in humans, suggesting that it may be possible to rationally design safe and specific therapies for trypanosomiasis by targeting this parasite enzyme. As an initial step, the TDH gene from T. brucei was expressed and the three-dimensional structure of the enzyme was solved by X-ray crystallography. In multiple crystallographic structures, T. brucei TDH is revealed to be a dimeric short-chain dehydrogenase that displays a considerable degree of conformational variation in its ligand-binding regions. Geometric simulations of the structure have provided insight into the dynamic behaviour of this enzyme. Furthermore, structures of TDH bound to its natural substrates and known inhibitors have been determined, giving an indication of the mechanism of catalysis of the enzyme. Collectively, these results provide vital details for future drug design to target TDH or related enzymes.

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Section: Substrate Binding and Catalytic Mechanism Of Actionmentioning

confidence: 90%

Section: Substrate Binding and Catalytic Mechanism Of Actionmentioning

confidence: 94%

Section: Substrate Binding and Catalytic Mechanism Of Actionmentioning

confidence: 97%

See 1 more Smart Citation

Structure and function ofL-threonine-3-dehydrogenase from the parasitic protozoanTrypanosoma bruceirevealed by X-ray crystallography and geometric simulations

Adjogatse

Erskine

Wells

et al. 2018

Acta Crystallogr D Struct Biol

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“…Prior to start productive MD simulation, simulated annealing procedure was applied to the system performing the same method as shown in previous study 39 . Then productive MD simulation was performed for 50 nsec.…”

Section: Methodsmentioning

confidence: 99%

Structural and computational analysis of peptide recognition mechanism of class-C type penicillin binding protein, alkaline D-peptidase from Bacillus cereus DF4-B

Nakano

Okazaki

Ishitsubo

et al. 2015

Sci Rep

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Alkaline D-peptidase from Bacillus cereus DF4-B, called ADP, is a D-stereospecific endopeptidase reacting with oligopeptides containing D-phenylalanine (D-Phe) at N-terminal penultimate residue. ADP has attracted increasing attention because it is useful as a catalyst for synthesis of D-Phe oligopeptides or, with the help of substrate mimetics, L-amino acid peptides and proteins. Structure and functional analysis of ADP is expected to elucidate molecular mechanism of ADP. In this study, the crystal structure of ADP (apo) form was determined at 2.1 Å resolution. The fold of ADP is similar to that of the class C penicillin-binding proteins of type-AmpH. Docking simulations and fragment molecular orbital analyses of two peptides, (D-Phe)4 and (D-Phe)2-(L-Phe)2, with the putative substrate binding sites of ADP indicated that the P1 residue of the peptide interacts with hydrophobic residues at the S1 site of ADP. Furthermore, molecular dynamics simulation of ADP for 50 nsec suggested that the ADP forms large cavity at the active site. Formation of the cavity suggested that the ADP has open state in the solution. For the ADP, having the open state is convenient to bind the peptides having bulky side chain, such as (D-Phe)4. Taken together, we predicted peptide recognition mechanism of ADP.

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“…In this study, TDH is utilized as a target protein to evaluate the PCD. TDH was chosen for the following reasons: (a) the effectiveness of the PCD method could be evaluated by comparing the results obtained by original procedures based on the CD method used in previous studies, , and (b) the enzymatic properties of the TDHs designed by PCD could be compared with those of many native TDHs. − Through biochemical and structural analysis of six artificial TDHs designed by PCD, we attempted to demonstrate the usefulness of PCD to design highly functional proteins and proposed a hypothesis that could contribute to advancing sequence-based protein design.…”

mentioning

confidence: 99%

Partial Consensus Design and Enhancement of Protein Function by Secondary-Structure-Guided Consensus Mutations

et al. 2021

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Consensus design (CD) is a representative sequence-based protein design method that enables the design of highly functional proteins by analyzing vast amounts of protein sequence data. This study proposes a partial consensus design (PCD) of a protein as a derivative approach of CD. The method replaces the target protein sequence with a consensus sequence in a secondary-structure-dependent manner (i.e., regionally dependent and divided into α-helix, β-sheet, and loop regions). In this study, we generated several artificial partial consensus L-threonine 3-dehydrogenases (PcTDHs) by PCD using the TDH from Cupriavidus necator (CnTDH) as a target protein. Structural and functional analysis of PcTDHs suggested that thermostability would be independently improved when consensus mutations are introduced into the loop region of TDHs. On the other hand, enzyme kinetic parameters (k cat / K m ) and average productivity would be synergistically enhanced by changing the combination of the mutationsreplacement of one region of CnTDH with a consensus sequence provided only negative effects, but the negative effects were nullified when the two regions were replaced simultaneously. Taken together, we propose the hypothesis that there are protein regions that encode individual protein properties, such as thermostability and activity, and that the introduction of consensus mutations into these regions could additively or synergistically modify their functions.

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

Cited by 19 publications

References 37 publications

Structure and function ofL-threonine-3-dehydrogenase from the parasitic protozoanTrypanosoma bruceirevealed by X-ray crystallography and geometric simulations

Structure and function ofL-threonine-3-dehydrogenase from the parasitic protozoanTrypanosoma bruceirevealed by X-ray crystallography and geometric simulations

Structural and computational analysis of peptide recognition mechanism of class-C type penicillin binding protein, alkaline D-peptidase from Bacillus cereus DF4-B

Partial Consensus Design and Enhancement of Protein Function by Secondary-Structure-Guided Consensus Mutations

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