3PGB | pdb_00003pgb

Crystal structure of Aspergillus nidulans amine oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.254 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.211 (Depositor) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history

Literature

Structure and Activity of Aspergillus nidulans Copper Amine Oxidase

McGrath, A.P.Mithieux, S.M.Collyer, C.A.Bakhuis, J.G.van den Berg, M.Sein, A.Heinz, A.Schmelzer, C.Weiss, A.S.Guss, J.M.

(2011) Biochemistry 50: 5718-5730

  • DOI: https://doi.org/10.1021/bi200555c
  • Primary Citation Related Structures: 
    3PGB

  • PubMed Abstract: 

    Aspergillus nidulans amine oxidase (ANAO) has the unusual ability among the family of copper and trihydroxyphenylalanine quinone-containing amine oxidases of being able to oxidize the amine side chains of lysine residues in large peptides and proteins. We show here that in common with the related enzyme from the yeast Pichia pastoris, ANAO can promote the cross-linking of tropoelastin and oxidize the lysine residues in α-casein proteins and tropoelastin. The crystal structure of ANAO, the first for a fungal enzyme in this family, has been determined to a resolution of 2.4 Å. The enzyme is a dimer with the archetypal fold of a copper-containing amine oxidase. The active site is the most open of any of those of the structurally characterized enzymes in the family and provides a ready explanation for its lysine oxidase-like activity.


  • Organizational Affiliation
    • School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia.

Macromolecule Content 

  • Total Structure Weight: 92.63 kDa 
  • Atom Count: 6,367 
  • Modeled Residue Count: 740 
  • Deposited Residue Count: 797 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative uncharacterized protein797Aspergillus nidulansMutation(s): 0 
Gene Names: AN6092.2
EC: 1.4.3.6 (PDB Primary Data), 1.4.3 (UniProt)
UniProt
Find proteins for Q5B038 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Explore Q5B038 
Go to UniProtKB:  Q5B038
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5B038
Glycosylation
Glycosylation Sites: 5
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPQ
Query on TPQ
A
L-PEPTIDE LINKINGC9 H9 N O5TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.254 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.211 (Depositor) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.861α = 90
b = 179.861β = 90
c = 148.178γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-13
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary