Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 45.69 kDa 
• Atom Count: 4187 
• Modelled Residue Count: 418 
• Deposited Residue Count: 422 
• Unique protein chains: 1

2VFR

Alditol Oxidase from Streptomyces coelicolor A3(2): Native Enzyme

• DOI: 10.2210/pdb2VFR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces coelicolor A3(2)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-11-05 Released: 2008-01-08 
• Deposition Author(s): Forneris, F., Mattevi, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.165 
• R-Value Work: 0.139 
• R-Value Observed: 0.140 

Literature

Structural Analysis of the Catalytic Mechanism and Stereoselectivity in Streptomyces Coelicolor Alditol Oxidase.

Forneris, F., Heuts, D.P.H.M., Delvecchio, M., Rovida, S., Fraaije, M.W., Mattevi, A.

(2008) Biochemistry 47: 978

• PubMed: 18154360 
• DOI: 10.1021/bi701886t
• Primary Citation of Related Structures:  
  2VFR, 2VFS, 2VFT, 2VFU, 2VFV


• PubMed Abstract: 
  

Alditol oxidase (AldO) from Streptomyces coelicolor A3(2) is a soluble monomeric flavin-dependent oxidase that performs selective oxidation of the terminal primary hydroxyl group of several alditols. Here, we report the crystal structure of the recombinant enzyme in its native state and in complex with both six-carbon (mannitol and sorbitol) and five-carbon substrates (xylitol). AldO shares the same folding topology of the members of the vanillyl-alcohol oxidase family of flavoenzymes and exhibits a covalently linked FAD which is located at the bottom of a funnel-shaped pocket that forms the active site. The high resolution of the three-dimensional structures highlights a well-defined hydrogen-bonding network that tightly constrains the substrate in the productive conformation for catalysis. Substrate binding occurs through a lock-and-key mechanism and does not induce conformational changes with respect to the ligand-free protein. A network of charged residues is proposed to favor catalysis through stabilization of the deprotonated form of the substrate. A His side chain acts as back door that "pushes" the substrate-reactive carbon atom toward the N5-C4a locus of the flavin. Analysis of the three-dimensional structure reveals possible pathways for diffusion of molecular oxygen and a small cavity on the re side of the flavin that may host oxygen during FAD reoxidation. These features combined with the tight shape of the catalytic site provide insights into the mechanism of AldO-mediated regioselective oxidation reactions and its substrate specificity.

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Organizational Affiliation: 

Department of Genetics and Microbiology, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XYLITOL OXIDASE	A	422	Streptomyces coelicolor A3(2)	Mutation(s): 0  Gene Names: xyoA, SCO6147, SC1A9.11c EC: 1.1.3.41
Find proteins for Q9ZBU1 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9ZBU1  Go to UniProtKB:  Q9ZBU1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.165 
• R-Value Work: 0.139 
• R-Value Observed: 0.140 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.023	α = 90
b = 68.614	β = 95.15
c = 57.977	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-11-05 
• Released Date: 2008-01-08 
Deposition Author(s): Forneris, F., Mattevi, A.

Revision History  

• Version 1.0: 2008-01-08
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance