Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 107.74 kDa 
• Atom Count: 8572 
• Modelled Residue Count: 945 
• Deposited Residue Count: 970 
• Unique protein chains: 2

2Q7Q

Crystal structure of Alcaligenes faecalis AADH in complex with p-chlorobenzylamine.

• DOI: 10.2210/pdb2Q7Q/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Alcaligenes faecalis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-06-07 Released: 2007-07-31 
• Deposition Author(s): Roujeinikova, A., Leys, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.193 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

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

• PubMed: 17636875 
• 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). 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aralkylamine dehydrogenase light chain	D, H	124	Alcaligenes faecalis	Mutation(s): 1  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aralkylamine dehydrogenase heavy chain	A, B	361	Alcaligenes faecalis	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2B	D, H	1-(4-CHLOROPHENYL)METHANAMINE C7 H8 Cl N YMVFJGSXZNNUDW-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TRQ	D,H	L-PEPTIDE LINKING	C11 H10 N2 O4		TRP

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
C2B	Kd :  5000   nM  PDBBind
C2B	Kd:  5000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.193 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.541	α = 90
b = 96.762	β = 90
c = 120.13	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-06-07 
• Released Date: 2007-07-31 
Deposition Author(s): Roujeinikova, A., Leys, D.

Revision History  

• Version 1.0: 2007-07-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description