9H5Q | pdb_00009h5q

Crystal structure of Thermoanaerobacterales bacterium monoamine oxidase in complex with spermidine and its oxidation products


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.189 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.155 (Depositor) 

Starting Model: experimental
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Literature

Altering substrate specificity of a thermostable bacterial monoamine oxidase by structure-based mutagenesis.

Basile, L.Poli, C.Santema, L.L.Lesenciuc, R.C.Fraaije, M.W.Binda, C.

(2024) Arch Biochem Biophys 764: 110276-110276

  • DOI: https://doi.org/10.1016/j.abb.2024.110276
  • Primary Citation of Related Structures:  
    9H5P, 9H5Q, 9H5Z, 9H64

  • PubMed Abstract: 

    Bacterial monoamine oxidases (MAOs) are FAD-dependent proteins catalyzing a relevant reaction for many industrial biocatalytic applications, ranging from production of enantiomerically pure building blocks for pharmaceutical synthesis to biosensors for monitoring food and beverage quality. The thermostable MAO enzyme from Thermoanaerobacterales bacterium (MAO Tb ) is about 36 % identical to both putrescine oxidase and human MAOs and can be efficiently produced in Escherichia coli. MAO Tb preferentially acts on n-alkyl monoamines but shows detectable activity also on polyamines and aromatic monoamines. The crystal structures of MAO Tb in complex with putrescine, benzylamine, spermidine and n-heptylamine at resolution ranging from 1.6 to 2.3 Å resolution revealed the binding mode of substrates to the enzyme. The MAO Tb active site is highly conserved in the inner part of the cavity in front of the flavin ring (re face), where the presence of two tyrosine residues creates the substrate amine binding site that is found also in human MAOs. Instead, more distantly from the flavin, the entrance of the catalytic site is much more open in MAO Tb and features a different arrangement of amino acids. Site-directed mutagenesis targeting residues Ala168, Thr199 and Val324 allowed the identification of key residues in ligand binding to alter substrate specificity. The A168D variant showed a higher activity on putrescine than wild-type, whereas by replacing either Thr199 or Val324 to Trp a marked enhancement in k cat /K M values was found on n-alkyl-monoamines and on aromatic amines.


  • Organizational Affiliation

    Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Monoamine oxidase
A, B
474Thermoanaerobacterales bacteriumMutation(s): 0 
UniProt
Find proteins for A0AAJ6N6J2 (Thermoanaerobacterales bacterium)
Explore A0AAJ6N6J2 
Go to UniProtKB:  A0AAJ6N6J2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAJ6N6J2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
SPD (Subject of Investigation/LOI)
Query on SPD

Download Ideal Coordinates CCD File 
I [auth B]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
4HA (Subject of Investigation/LOI)
Query on 4HA

Download Ideal Coordinates CCD File 
F [auth A]4-HYDROXYBUTAN-1-AMINIUM
C4 H12 N O
BLFRQYKZFKYQLO-UHFFFAOYSA-O
13D
Query on 13D

Download Ideal Coordinates CCD File 
E [auth A]1,3-DIAMINOPROPANE
C3 H10 N2
XFNJVJPLKCPIBV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
M [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.189 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.155 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.335α = 90
b = 94.456β = 90
c = 127.74γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Ministry of EducationItalyMUR PNRR NODES

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release