3HIG

Crystal structure of human diamine oxidase in complex with the inhibitor berenil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and inhibition of human diamine oxidase

McGrath, A.P.Hilmer, K.M.Collyer, C.A.Shepard, E.M.Elmore, B.O.Brown, D.E.Dooley, D.M.Guss, J.M.

(2009) Biochemistry 48: 9810-9822

  • DOI: 10.1021/bi9014192
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Humans have three functioning genes that encode copper-containing amine oxidases. The product of the AOC1 gene is a so-called diamine oxidase (hDAO), named for its substrate preference for diamines, particularly histamine. hDAO has been cloned and ex ...

    Humans have three functioning genes that encode copper-containing amine oxidases. The product of the AOC1 gene is a so-called diamine oxidase (hDAO), named for its substrate preference for diamines, particularly histamine. hDAO has been cloned and expressed in insect cells and the structure of the native enzyme determined by X-ray crystallography to a resolution of 1.8 A. The homodimeric structure has the archetypal amine oxidase fold. Two active sites, one in each subunit, are characterized by the presence of a copper ion and a topaquinone residue formed by the post-translational modification of a tyrosine. Although hDAO shares 37.9% sequence identity with another human copper amine oxidase, semicarbazide sensitive amine oxidase or vascular adhesion protein-1, its substrate binding pocket and entry channel are distinctly different in accord with the different substrate specificities. The structures of two inhibitor complexes of hDAO, berenil and pentamidine, have been refined to resolutions of 2.1 and 2.2 A, respectively. They bind noncovalently in the active-site channel. The inhibitor binding suggests that an aspartic acid residue, conserved in all diamine oxidases but absent from other amine oxidases, is responsible for the diamine specificity by interacting with the second amino group of preferred diamine substrates.


    Organizational Affiliation

    School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Amiloride-sensitive amine oxidase
A, B
731Homo sapiensMutation(s): 1 
Gene Names: AOC1 (ABP1, DAO1)
EC: 1.4.3.22
Find proteins for P19801 (Homo sapiens)
Go to Gene View: AOC1
Go to UniProtKB:  P19801
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BRN
Query on BRN

Download SDF File 
Download CCD File 
A, B
BERENIL
DIMINAZINE ACETURATE; 1,3-TRIS-(4'AMIDINOPHENYL)TRIAZINE
C14 H15 N7
XNYZHCFCZNMTFY-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-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
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 %)
BRNKi: 13 nM BINDINGMOAD
BRNKi: 13 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 92.662α = 90.00
b = 94.884β = 90.00
c = 196.411γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description