2PNC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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 su ...

    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 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
    • 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
    • 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.,Sect.D 59: 727
    • 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


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Copper amine oxidase, liver isozyme
A, B
746Bos taurusMutation(s): 0 
EC: 1.4.3.21
Find proteins for Q29437 (Bos taurus)
Go to UniProtKB:  Q29437
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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Download CCD File 
A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CLU
Query on CLU

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Download CCD File 
A, B
2,6-DICHLORO-N-IMIDAZOLIDIN-2-YLIDENEANILINE
CLONIDINE
C9 H9 Cl2 N3
GJSURZIOUXUGAL-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPQ
Query on TPQ
A, B
L-PEPTIDE LINKINGC9 H9 N O5TYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CLUKi: 466000 nM BINDINGMOAD
CLUKi: 466000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.360α = 90.00
b = 131.956β = 90.00
c = 134.159γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.2: 2012-07-25
    Type: Other