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Structures of Saccharomyces cerevisiae D-arabinose dehydrogenase Ara1 and its complex with NADPH: implications for cofactor-assisted substrate recognition.

Hu XQ, Guo PC, Ma JD, Li WF - Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. (2013)

Bottom Line: The primary role of yeast Ara1, previously mis-annotated as a D-arabinose dehydrogenase, is to catalyze the reduction of a variety of toxic α,β-dicarbonyl compounds using NADPH as a cofactor at physiological pH levels.Ara1 exists as a homodimer, each subunit of which adopts an (α/β)8-barrel structure and has a highly conserved cofactor-binding pocket.Structural comparison revealed that induced fit upon NADPH binding yielded an intact active-site pocket that recognizes the substrate.

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Affiliation: College of Life and Environment Science, Huangshan University, Huangshan, Anhui 245041, People's Republic of China.

ABSTRACT
The primary role of yeast Ara1, previously mis-annotated as a D-arabinose dehydrogenase, is to catalyze the reduction of a variety of toxic α,β-dicarbonyl compounds using NADPH as a cofactor at physiological pH levels. Here, crystal structures of Ara1 in apo and NADPH-complexed forms are presented at 2.10 and 2.00 Å resolution, respectively. Ara1 exists as a homodimer, each subunit of which adopts an (α/β)8-barrel structure and has a highly conserved cofactor-binding pocket. Structural comparison revealed that induced fit upon NADPH binding yielded an intact active-site pocket that recognizes the substrate. Moreover, the crystal structures combined with computational simulation defined an open substrate-binding site to accommodate various substrates that possess a dicarbonyl group.

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Related in: MedlinePlus

Overall structure. Schematic representation of (a) the Ara1 dimer and (b) the Ara1 monomer. (c) Cartoon representation and (d) molecular surface of the Ara1–NADPH complex. NADPH is shown as green sticks. All figures were drawn using PyMOL.
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fig1: Overall structure. Schematic representation of (a) the Ara1 dimer and (b) the Ara1 monomer. (c) Cartoon representation and (d) molecular surface of the Ara1–NADPH complex. NADPH is shown as green sticks. All figures were drawn using PyMOL.

Mentions: The asymmetric unit contains a dimer of Ara1 with an interface area of 1030 Å2. The two subunits are very similar, with an overall root-mean-square deviation (r.m.s.d.) of 0.13 Å over 296 Cα atoms (Fig. 1 ▶a). Gel-filtration chromatography also indicated the existence of Ara1 as a dimer in solution. The dimeric interface is mainly mediated by strands βA, βB and two loops (Met15–Tyr24 and Lys91–Leu96) in each subunit and contains eight hydrogen bonds and 111 non-bonded contacts, which include hydrophobic interactions and salt bridges.


Structures of Saccharomyces cerevisiae D-arabinose dehydrogenase Ara1 and its complex with NADPH: implications for cofactor-assisted substrate recognition.

Hu XQ, Guo PC, Ma JD, Li WF - Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. (2013)

Overall structure. Schematic representation of (a) the Ara1 dimer and (b) the Ara1 monomer. (c) Cartoon representation and (d) molecular surface of the Ara1–NADPH complex. NADPH is shown as green sticks. All figures were drawn using PyMOL.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3818031&req=5

fig1: Overall structure. Schematic representation of (a) the Ara1 dimer and (b) the Ara1 monomer. (c) Cartoon representation and (d) molecular surface of the Ara1–NADPH complex. NADPH is shown as green sticks. All figures were drawn using PyMOL.
Mentions: The asymmetric unit contains a dimer of Ara1 with an interface area of 1030 Å2. The two subunits are very similar, with an overall root-mean-square deviation (r.m.s.d.) of 0.13 Å over 296 Cα atoms (Fig. 1 ▶a). Gel-filtration chromatography also indicated the existence of Ara1 as a dimer in solution. The dimeric interface is mainly mediated by strands βA, βB and two loops (Met15–Tyr24 and Lys91–Leu96) in each subunit and contains eight hydrogen bonds and 111 non-bonded contacts, which include hydrophobic interactions and salt bridges.

Bottom Line: The primary role of yeast Ara1, previously mis-annotated as a D-arabinose dehydrogenase, is to catalyze the reduction of a variety of toxic α,β-dicarbonyl compounds using NADPH as a cofactor at physiological pH levels.Ara1 exists as a homodimer, each subunit of which adopts an (α/β)8-barrel structure and has a highly conserved cofactor-binding pocket.Structural comparison revealed that induced fit upon NADPH binding yielded an intact active-site pocket that recognizes the substrate.

View Article: PubMed Central - HTML - PubMed

Affiliation: College of Life and Environment Science, Huangshan University, Huangshan, Anhui 245041, People's Republic of China.

ABSTRACT
The primary role of yeast Ara1, previously mis-annotated as a D-arabinose dehydrogenase, is to catalyze the reduction of a variety of toxic α,β-dicarbonyl compounds using NADPH as a cofactor at physiological pH levels. Here, crystal structures of Ara1 in apo and NADPH-complexed forms are presented at 2.10 and 2.00 Å resolution, respectively. Ara1 exists as a homodimer, each subunit of which adopts an (α/β)8-barrel structure and has a highly conserved cofactor-binding pocket. Structural comparison revealed that induced fit upon NADPH binding yielded an intact active-site pocket that recognizes the substrate. Moreover, the crystal structures combined with computational simulation defined an open substrate-binding site to accommodate various substrates that possess a dicarbonyl group.

Show MeSH
Related in: MedlinePlus