1KSI

CRYSTAL STRUCTURE OF A EUKARYOTIC (PEA SEEDLING) COPPER-CONTAINING AMINE OXIDASE AT 2.2A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1KSI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pisum sativum
• Mutation(s): Yes 


• Deposited: 1996-07-20 Released: 1997-12-24 
• Deposition Author(s): Wilce, M.C.J., Kumar, V., Freeman, H.C., Guss, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 0.181 

Literature

Crystal structure of a eukaryotic (pea seedling) copper-containing amine oxidase at 2.2 A resolution.

Kumar, V., Dooley, D.M., Freeman, H.C., Guss, J.M., Harvey, I., McGuirl, M.A., Wilce, M.C., Zubak, V.M.

(1996) Structure 4: 943-955

• PubMed: 8805580 
• DOI: https://doi.org/10.1016/s0969-2126(96)00101-3
• Primary Citation of Related Structures:  
  1KSI


• PubMed Abstract: 
  

  Copper-containing amine oxidases catalyze the oxidative deamination of primary amines to aldehydes, in a reaction that requires free radicals. These enzymes are important in many biological processes, including cell differentiation and growth, would healing, detoxification and signalling. The catalytic reaction requires a redox cofactor, topa quinone (TPQ), which is derived by post-translational modification of an invariant tyrosine residue. Both the biogenesis of the TPQ cofactor and the reaction catalyzed by the enzyme require the presence of a copper atom at the active site. The crystal structure of a prokaryotic copper amine oxidase from E. coli (ECAO) has recently been reported.

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Organizational Affiliation: 

School of Chemistry, University of Sydney, NSW 2006, Australia.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 147.63 kDa 
• Atom Count: 10,995 
• Modelled Residue Count: 1,284 
• Deposited Residue Count: 1,284 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COPPER AMINE OXIDASE	A, B	642	Pisum sativum	Mutation(s): 1  EC: 1.4.3.6
UniProt
Find proteins for Q43077 (Pisum sativum) Explore Q43077  Go to UniProtKB:  Q43077

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CU	F [auth A], I [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
MN	G [auth A], J [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPQ	A, B	L-PEPTIDE LINKING	C9 H9 N O5		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.37	α = 90
b = 114.64	β = 90
c = 199.94	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CCP4	model building
PROLSQ	refinement
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-12-24 
Deposition Author(s): Wilce, M.C.J., Kumar, V., Freeman, H.C., Guss, J.M.

Revision History  

• Version 1.0: 1997-12-24
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary