1TU5

Crystal structure of bovine plasma copper-containing amine oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

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This is version 2.0 of the entry. See complete history


Literature

Crystal structure of amine oxidase from bovine serum.

Lunelli, M.Di Paolo, M.L.Biadene, M.Calderone, V.Battistutta, R.Scarpa, M.Rigo, A.Zanotti, G.

(2005) J Mol Biol 346: 991-1004

  • DOI: 10.1016/j.jmb.2004.12.038
  • Primary Citation of Related Structures:  
    1TU5

  • PubMed Abstract: 
  • Copper-containing amine oxidase extracted from bovine serum (BSAO) was crystallized and its three-dimensional structure at 2.37A resolution is described. The biological unit of BSAO is a homodimer, formed by two monomers related to each other by a non-crystallographic 2-fold axis ...

    Copper-containing amine oxidase extracted from bovine serum (BSAO) was crystallized and its three-dimensional structure at 2.37A resolution is described. The biological unit of BSAO is a homodimer, formed by two monomers related to each other by a non-crystallographic 2-fold axis. Each monomer is composed of three domains, similar to those of other amine oxidases from lower species. The two monomers are structurally equivalent, despite some minor differences at the two active sites. A large funnel allows access of substrates to the active-site; another cavity, accessible to the solvent, is also present between the two monomers; this second cavity could allow the entrance of molecular oxygen necessary for the oxidative reaction. Some sugar residues, bound to Asn, were still present and visible in the electron density map, in spite of the exhaustive deglycosylation necessary to grow the crystals. The comparison of the BSAO structure with those of other resolved AO structures shows strong dissimilarities in the architecture and charge distribution of the cavities leading to the active-site, possibly explaining the differences in substrate specificity.


    Related Citations: 
    • Crystallization and preliminary X-ray data of amine oxidase from bovine serum
      Calderone, V., Di Paolo, M.L., Trabucco, M., Biadene, M., Battistutta, R., Rigo, A., Zanotti, G.
      (2003) Acta Crystallogr D Biol Crystallogr 59: 727
    • Crystal structure of a quinoenzyme: copper amine oxidase of Escherichia coli at 2 A resolution
      Parsons, M.R., Convery, M.A., Wilmot, C.M., Yadav, K.D., Blakeley, V., Corner, A.S., Phillips, S.E., McPherson, M.J., Knowles, P.F.
      (1995) Structure 3: 1171
    • 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
    • The crystal structure of Pichia pastoris lysyl oxidase
      Duff, A.P., Cohen, A.E., Ellis, P.J., Kuchar, J.A., Langley, D.B., Shepard, E.M., Dooley, D.M., Freeman, H.C., Guss, J.M.
      (2003) Biochemistry 42: 15148

    Organizational Affiliation

    Department of Biological Chemistry, University of Padua, Viale G. Colombo 3, 35121 Padua, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Copper amine oxidase, liver isozymeA, B746Bos taurusMutation(s): 1 
EC: 1.4.3.6 (PDB Primary Data), 1.4.3.21 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q29437 (Bos taurus)
Explore Q29437 
Go to UniProtKB:  Q29437
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ29437
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC, D 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G47362BJ
GlyCosmos:  G47362BJ
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPQ
Query on TPQ
A, B L-PEPTIDE LINKINGC9 H9 N O5TYR
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900017
Query on PRD_900017
C, Dtriacetyl-beta-chitotrioseOligosaccharide / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.68α = 90
b = 131.192β = 90
c = 134.001γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    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, Non-polymer description, Structure summary