1ASQ

X-RAY STRUCTURES AND MECHANISTIC IMPLICATIONS OF THREE FUNCTIONAL DERIVATIVES OF ASCORBATE OXIDASE FROM ZUCCHINI: REDUCED-, PEROXIDE-, AND AZIDE-FORMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

X-ray structures and mechanistic implications of three functional derivatives of ascorbate oxidase from zucchini. Reduced, peroxide and azide forms.

Messerschmidt, A.Luecke, H.Huber, R.

(1993) J Mol Biol 230: 997-1014

  • DOI: 10.1006/jmbi.1993.1215
  • Primary Citation of Related Structures:  
    1ASQ, 1ASP, 1ASO

  • PubMed Abstract: 
  • The X-ray structures of three functional derivatives of ascorbate oxidase (EC 1.10.3.3) from Zucchini have been determined and are compared to the "native" oxidized form. The fully reduced form of ascorbate oxidase has been refined to a crystallographic R-factor of 19 ...

    The X-ray structures of three functional derivatives of ascorbate oxidase (EC 1.10.3.3) from Zucchini have been determined and are compared to the "native" oxidized form. The fully reduced form of ascorbate oxidase has been refined to a crystallographic R-factor of 19.6% for all reflections between 8.0 A and 2.2 A resolution. The geometry at the type-1 copper (CU1) is unchanged compared to the oxidized form, but the oxygen ligand bridging the copper ions CU2 and CU3 (spectroscopic type-3 copper pair) is released and the copper ions move apart yielding a trigonal planar co-ordination with their ligating histidine residues. The co-ordination at the copper ion CU4 (spectroscopic type-2 copper) is not affected. The copper-copper distances increase from an average 3.7 A in the native form to 5.1 A for CU2-CU3, 4.4 A for CU2-CU4 and 4.1 A for CU3-CU4. The peroxide derivative of ascorbate oxidase has been refined to a crystallographic R-factor of 16.0% for all reflections between 8.0 A and 2.59 A resolution. The geometry at the type-1 copper site is not changed compared to the oxidized form. The oxygen ligand bridging copper atoms CU2 and CU3 is lost, too. The peroxide binds terminally to the copper ion CU2 as hydroperoxide. Copper ion CU2 is fourfold co-ordinated to the NE2 atoms of the three histidine residues and to the oxygen atom of the terminally bound peroxide molecule in a distorted tetrahedral geometry. Copper ion CU3 is threefold co-ordinated as in the reduced form and co-ordination around copper atom CU4 is unaltered. The copper-copper distances increase to 4.8 A for CU2-CU3 and 4.5 A for CU2-CU4. The distance CU3-CU4 remains 3.7 A. Treatment with peroxide causes a partial depletion of copper ion CU2. The refinement for the azide derivative of ascorbate oxidase converged at a crystallographic R-factor of 17.8% for all reflections between 8.0 A and 2.32 A. There are no significant structural changes at the type-1 copper site. The oxygen ligand bridging copper ions CU2 and CU3 is again released. Two azide molecules bind terminally to copper ion CU2. Copper ion CU2 is fivefold co-ordinated to the NE2 atoms of the three histidine residues and to both terminally bound azide molecules in a trigonal-bipyramidal manner. Copper-copper distances increase to 5.1 A for CU2-CU3 and 4.6 A for CU2-CU4. The distance CU3-CU4 is decreased to 3.6 A.(ABSTRACT TRUNCATED AT 400 WORDS)


    Related Citations: 
    • Refined Crystal Structure of Ascorbate Oxidase at 1.9 Angstroms Resolution
      Messerschmidt, A., Ladenstein, R., Huber, R., Bolognesi, M., Avigliano, L., Petruzzelli, R., Rossi, A., Finazzi-Agro, A.
      (1992) J Mol Biol 224: 179
    • X-Ray Crystal Structure of the Blue Oxidase Ascorbate Oxidase from Zucchini. Analysis of the Polypeptide Fold and Model of the Copper Sites and Ligands
      Messerschmidt, A., Rossi, A., Ladenstein, R., Huber, R., Bolognesi, M., Gatti, G., Marchesini, A., Petruzzelli, R., Finazzi-Agro, A.
      (1989) J Mol Biol 206: 513

    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Martinsried, FRG.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ASCORBATE OXIDASEA, B552Cucurbita pepo var. melopepoMutation(s): 0 
EC: 1.10.3.3
UniProt
Find proteins for P37064 (Cucurbita pepo var. melopepo)
Explore P37064 
Go to UniProtKB:  P37064
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A], L [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
D [auth A] , E [auth A] , F [auth A] , G [auth A] , K [auth A] , M [auth B] , N [auth B] , O [auth B] , 
D [auth A],  E [auth A],  F [auth A],  G [auth A],  K [auth A],  M [auth B],  N [auth B],  O [auth B],  P [auth B]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
AZI
Query on AZI

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], R [auth B], S [auth B]AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
OH
Query on OH

Download Ideal Coordinates CCD File 
H [auth A], Q [auth B]HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.32α = 90
b = 105.28β = 90
c = 113γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary