Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 126.79 kDa 
• Atom Count: 8765 
• Modelled Residue Count: 1090 
• Deposited Residue Count: 1120 
• Unique protein chains: 1

1E8H

STRUCTURE OF THE H61T MUTANT OF THE FLAVOENZYME VANILLYL-ALCOHOL OXIDASE IN THE APO FORM COMPLEXED BY ADP

• PDB DOI: 10.2210/pdb1E8H/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Penicillium simplicissimum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-09-20 Released: 2000-09-21 
• Deposition Author(s): Mattevi, A., Fraaije, M.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.303 
• R-Value Work: 0.237 
• R-Value Observed: 0.237 

Literature

Structural Analysis of Flavinylation in Vanillyl-Alcohol Oxidase

Fraaije, M.W., Van Der Heuvel, R.H.H., Van Berkel, W.J.H., Mattevi, A.

(2001) J Biol Chem 275: 38654

• PubMed: 10984479 
• DOI: 10.1074/jbc.M004753200
• Primary Citation of Related Structures:  
  1E8F, 1E8G, 1E8H


• PubMed Abstract: 
  

Vanillyl-alcohol oxidase (VAO) is member of a newly recognized flavoprotein family of structurally related oxidoreductases. The enzyme contains a covalently linked FAD cofactor. To study the mechanism of flavinylation we have created a design point mutation (His-61 --> Thr). In the mutant enzyme the covalent His-C8alpha-flavin linkage is not formed, while the enzyme is still able to bind FAD and perform catalysis. The H61T mutant displays a similar affinity for FAD and ADP (K(d) = 1.8 and 2.1 microm, respectively) but does not interact with FMN. H61T is about 10-fold less active with 4-(methoxymethyl)phenol) (k(cat) = 0.24 s(-)(1), K(m) = 40 microm) than the wild-type enzyme. The crystal structures of both the holo and apo form of H61T are highly similar to the structure of wild-type VAO, indicating that binding of FAD to the apoprotein does not require major structural rearrangements. These results show that covalent flavinylation is an autocatalytical process in which His-61 plays a crucial role by activating His-422. Furthermore, our studies clearly demonstrate that in VAO, the FAD binds via a typical lock-and-key approach to a preorganized binding site.

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Organizational Affiliation: 

Department of Biomolecular Sciences, Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VANILLYL-ALCOHOL OXIDASE	A, B	560	Penicillium simplicissimum	Mutation(s): 1  Gene Names: VAOA EC: 1.1.3.7 (PDB Primary Data), 1.1.3.38 (UniProt)
UniProt
Find proteins for P56216 (Penicillium simplicissimum) Explore P56216  Go to UniProtKB:  P56216

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], D [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ADP	PDBBind:  1E8H	Kd: 2100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.303 
• R-Value Work: 0.237 
• R-Value Observed: 0.237 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.34	α = 90
b = 130.34	β = 90
c = 134	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-09-20 
• Released Date: 2000-09-21 
Deposition Author(s): Mattevi, A., Fraaije, M.W.

Revision History  

• Version 1.0: 2000-09-21
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance