4IJR | pdb_00004ijr

Crystal structure of Saccharomyces cerevisiae arabinose dehydrogenase Ara1 complexed with NADPH

• PDB DOI: https://doi.org/10.2210/pdb4IJR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-12-23 Released: 2013-11-27 
• Deposition Author(s): Hu, X.Q., Guo, P.C., Li, W.F., Zhou, C.Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

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

Hu, X.Q., Guo, P.C., Ma, J.D., Li, W.F.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 1190-1195

• PubMed: 24192347 
• DOI: https://doi.org/10.1107/S1744309113026857
• Primary Citation of Related Structures:  
  4IJC, 4IJR


• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 79.36 kDa 
• Atom Count: 5,655 
• Modelled Residue Count: 656 
• Deposited Residue Count: 688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-arabinose dehydrogenase [NAD(P)+] heavy chain	A, B [auth C]	344	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: ARA1, YBR1127, YBR149W EC: 1.1.1.117
UniProt
Find proteins for P38115 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38115  Go to UniProtKB:  P38115

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], D [auth C]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.369	α = 90
b = 90.568	β = 90.08
c = 69.823	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-27 
Deposition Author(s): Hu, X.Q., Guo, P.C., Li, W.F., Zhou, C.Z.

Revision History  

• Version 1.0: 2013-11-27
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description