4IJR

Crystal structure of Saccharomyces cerevisiae arabinose dehydrogenase Ara1 complexed with NADPH

Summary for 4IJR

• Entry DOI: 10.2210/pdb4ijr/pdb
• Related: 4IJC
• Descriptor: D-arabinose dehydrogenase [NAD(P)+] heavy chain, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (3 entities in total)
• Functional Keywords: tim barrel, dehydrogenase, nadph binding, cytosol, oxidoreductase
• Biological source: Saccharomyces cerevisiae (yeast)
• Cellular location: Cytoplasm: P38115
• Total number of polymer chains: 2
• Total formula weight: 79355.73

Authors

Hu, X.Q.,Guo, P.C.,Li, W.F.,Zhou, C.Z. (deposition date: 2012-12-23, release date: 2013-11-27, Last modification date: 2023-11-08)

Primary citation

Hu, X.Q.,Guo, P.C.,Ma, J.D.,Li, W.F.
Structures of Saccharomyces cerevisiaeD-arabinose dehydrogenase Ara1 and its complex with NADPH: implications for cofactor-assisted substrate recognition
Acta Crystallogr.,Sect.F, 69:1190-1195, 2013

PubMed 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.

PubMed: 24192347
DOI: 10.1107/S1744309113026857

Experimental method

X-RAY DIFFRACTION (2 Å)