2PNC

Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 

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This is version 2.0 of the entry. See complete history


Literature

Multiple binding sites for substrates and modulators of semicarbazide-sensitive amine oxidases: kinetic consequences

Holt, A.Smith, D.J.Cendron, L.Zanotti, G.Rigo, A.Di Paolo, M.L.

(2008) Mol Pharmacol 73: 525-538

  • DOI: 10.1124/mol.107.040964
  • Primary Citation of Related Structures:  
    2PNC

  • PubMed Abstract: 
  • Human semicarbazide-sensitive amine oxidase (SSAO) is a target for novel anti-inflammatory drugs that inhibit enzymatic activity. However, progress in developing such drugs has been hampered by an incomplete understanding of mechanisms involved in substrate turnover ...

    Human semicarbazide-sensitive amine oxidase (SSAO) is a target for novel anti-inflammatory drugs that inhibit enzymatic activity. However, progress in developing such drugs has been hampered by an incomplete understanding of mechanisms involved in substrate turnover. We report here results of a comparative study of human and bovine SSAO enzymes that reveal binding of substrates and other ligands to at least two (human) and up to four (bovine) distinct sites on enzyme monomers. Anaerobic spectroscopy reveals binding of substrates (spermidine and benzylamine) and of an imidazoline site ligand (clonidine) to the reduced active site of bovine SSAO, whereas interactions with oxidized enzyme are evident in kinetic assays and crystallization studies. Radioligand binding experiments with [(3)H]tetraphenylphosphonium, an inhibitor of bovine SSAO that binds to an anionic cavity outside the active site, reveal competition with spermidine, benzylamine, and clonidine, indicating that these ligands also bind to this second anionic region. Kinetic models of bovine SSAO are consistent with one spermidine molecule straddling the active and secondary sites on both oxidized and reduced enzyme, whereas these sites are occupied by two individual molecules of smaller substrates such as benzylamine. Clonidine and other imidazoline site ligands enhance or inhibit activity as a result of differing affinities for both sites on oxidized and reduced enzyme. In contrast, although analyses of kinetic data obtained with human SSAO are also consistent with ligands binding to oxidized and reduced enzyme, we observed no apparent requirement for substrate or modulator binding to any secondary site to model enzyme behavior.


    Related Citations: 
    • 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
    • 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 Pharmacology, Faculty of Medicine and Dentistry, 9-70 Medical Sciences Bldg., University of Alberta, Edmonton, AB, Canada. aholt@pmcol.ualberta.ca



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Copper amine oxidase, liver isozymeA, B746Bos taurusMutation(s): 0 
EC: 1.4.3.6 (PDB Primary Data), 1.4.3.21 (UniProt)
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

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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
Binding Affinity Annotations 
IDSourceBinding Affinity
CLU PDBBind:  2PNC Ki: 4.66e+5 (nM) from 1 assay(s)
Binding MOAD:  2PNC Ki: 4.66e+5 (nM) from 1 assay(s)
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: 2.40 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.36α = 90
b = 131.956β = 90
c = 134.159γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2012-07-25
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary