2HJB

Crystal structure of Alcaligenes faecalis AADH in complex with p-methoxybenzylamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Isotope effects reveal that para-substituted benzylamines are poor reactivity probes of the quinoprotein mechanism for aromatic amine dehydrogenase.

Hothi, P.Roujeinikova, A.Khadra, K.A.Lee, M.Cullis, P.Leys, D.Scrutton, N.S.

(2007) Biochemistry 46: 9250-9259

  • DOI: 10.1021/bi7007239
  • Primary Citation of Related Structures:  
    2Q7Q, 2HJ4, 2HJB

  • PubMed Abstract: 
  • Structure-activity correlations have been employed previously in the mechanistic interpretation of TTQ-dependent amine dehydrogenases using a series of para-substituted benzylamines. However, by combining the use of kinetic isotope effects (KIEs) and crystallographic analysis, in conjunction with structure-reactivity correlation studies, we show that para-substituted benzylamines are poor reactivity probes for TTQ-dependent aromatic amine dehydrogenase (AADH) ...

    Structure-activity correlations have been employed previously in the mechanistic interpretation of TTQ-dependent amine dehydrogenases using a series of para-substituted benzylamines. However, by combining the use of kinetic isotope effects (KIEs) and crystallographic analysis, in conjunction with structure-reactivity correlation studies, we show that para-substituted benzylamines are poor reactivity probes for TTQ-dependent aromatic amine dehydrogenase (AADH). Stopped-flow kinetic studies of the reductive half-reaction, with para-substituted benzylamines and their dideuterated counterparts, demonstrate that C-H or C-D bond breakage is not fully rate limiting (KIEs approximately unity). Contrary to previous reports, Hammett plots exhibit a poor correlation of structure-reactivity data with electronic substituent effects for para-substituted benzylamines and phenylethylamines. Crystallographic studies of enzyme-substrate complexes reveal that the observed structure-reactivity correlations are not attributed to distinct binding modes for para-substituted benzylamines in the active site, although two binding sites for p-nitrobenzylamine are identified. We identify structural rearrangements, prior to the H-transfer step, which are likely to limit the rate of TTQ reduction by benzylamines. This work emphasizes (i) the need for caution when applying structure-activity correlations to enzyme-catalyzed reactions and (ii) the added benefit of using both isotope effects and structural analysis, in conjunction with structure-reactivity relationships, to study chemical steps in enzyme reaction cycles.


    Organizational Affiliation

    Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aromatic amine dehydrogenase DH135Alcaligenes faecalisMutation(s): 0 
Gene Names: aauA
EC: 1.4.99.4 (PDB Primary Data), 1.4.9.2 (UniProt)
Find proteins for P84887 (Alcaligenes faecalis)
Explore P84887 
Go to UniProtKB:  P84887
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Aromatic amine dehydrogenase AB361Alcaligenes faecalisMutation(s): 0 
Gene Names: aauB
EC: 1.4.99.4 (PDB Primary Data), 1.4.9.2 (UniProt)
Find proteins for P84888 (Alcaligenes faecalis)
Explore P84888 
Go to UniProtKB:  P84888
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PZM
Query on PZM

Download Ideal Coordinates CCD File 
A, D
1-(4-METHOXYPHENYL)METHANAMINE
C8 H11 N O
IDPURXSQCKYKIJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TRQ
Query on TRQ
D,HL-PEPTIDE LINKINGC11 H10 N2 O4TRP
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PZMKd :  40300   nM  PDBBind
PZMKd:  40300   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.331α = 90
b = 96.602β = 90
c = 119.672γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description