2AGY

Crystal structure of the Schiff base intermediate in the reductive half-reaction of aromatic amine dehydrogenase (AADH) with tryptamine. Monoclinic form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Atomic description of an enzyme reaction dominated by proton tunneling

Masgrau, L.Roujeinikova, A.Johannissen, L.O.Hothi, P.Basran, J.Ranaghan, K.E.Mulholland, A.J.Sutcliffe, M.J.Scrutton, N.S.Leys, D.

(2006) Science 312: 237-241

  • DOI: 10.1126/science.1126002
  • Primary Citation of Related Structures:  
    2AH0, 2AGL, 2AGW, 2AH1, 2AGZ, 2AGY, 2AGX

  • PubMed Abstract: 
  • We present an atomic-level description of the reaction chemistry of an enzyme-catalyzed reaction dominated by proton tunneling. By solving structures of reaction intermediates at near-atomic resolution, we have identified the reaction pathway for try ...

    We present an atomic-level description of the reaction chemistry of an enzyme-catalyzed reaction dominated by proton tunneling. By solving structures of reaction intermediates at near-atomic resolution, we have identified the reaction pathway for tryptamine oxidation by aromatic amine dehydrogenase. Combining experiment and computer simulation, we show proton transfer occurs predominantly to oxygen O2 of Asp(128)beta in a reaction dominated by tunneling over approximately 0.6 angstroms. The role of long-range coupled motions in promoting tunneling is controversial. We show that, in this enzyme system, tunneling is promoted by a short-range motion modulating proton-acceptor distance and no long-range coupled motion is required.


    Organizational Affiliation

    Manchester Interdisciplinary Biocentre, University of Manchester, Jackson's Mill, Post Office Box 88, Manchester M60 1QD, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aromatic amine dehydrogenaseD, H135Alcaligenes 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 dehydrogenaseA, B361Alcaligenes 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
TSH
Query on TSH

Download CCD File 
D, H
2-(1H-INDOL-3-YL)ETHANIMINE
C10 H10 N2
DCXUMIPCJIGNQW-WDZFZDKYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TRQ
Query on TRQ
D,HL-PEPTIDE LINKINGC11 H10 N2 O4TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.144 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.703α = 90
b = 88.373β = 90.19
c = 79.709γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-25
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance