2.00 Angstroms X-ray crystal structure of NAD- and substrate-bound 2-aminomuconate 6-semialdehyde dehydrogenase from Pseudomonas fluorescens

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 

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This is version 1.3 of the entry. See complete history


Crystallographic and spectroscopic snapshots reveal a dehydrogenase in action.

Huo, L.Davis, I.Liu, F.Andi, B.Esaki, S.Iwaki, H.Hasegawa, Y.Orville, A.M.Liu, A.

(2015) Nat Commun 6: 5935-5935

  • DOI: https://doi.org/10.1038/ncomms6935
  • Primary Citation of Related Structures:  
    4I1W, 4I25, 4I26, 4I2R, 4NPI, 4OE2, 4OU2, 4OUB

  • PubMed Abstract: 

    Aldehydes are ubiquitous intermediates in metabolic pathways and their innate reactivity can often make them quite unstable. There are several aldehydic intermediates in the metabolic pathway for tryptophan degradation that can decay into neuroactive compounds that have been associated with numerous neurological diseases. An enzyme of this pathway, 2-aminomuconate-6-semialdehyde dehydrogenase, is responsible for 'disarming' the final aldehydic intermediate. Here we show the crystal structures of a bacterial analogue enzyme in five catalytically relevant forms: resting state, one binary and two ternary complexes, and a covalent, thioacyl intermediate. We also report the crystal structures of a tetrahedral, thiohemiacetal intermediate, a thioacyl intermediate and an NAD(+)-bound complex from an active site mutant. These covalent intermediates are characterized by single-crystal and solution-state electronic absorption spectroscopy. The crystal structures reveal that the substrate undergoes an E/Z isomerization at the enzyme active site before an sp(3)-to-sp(2) transition during enzyme-mediated oxidation.

  • Organizational Affiliation

    1] Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA [2] Molecular Basis of Disease Area of Focus Program, Georgia State University, Atlanta, Georgia 30303, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-aminomuconate 6-semialdehyde dehydrogenase
A, B, C, D
500Pseudomonas fluorescensMutation(s): 0 
Gene Names: nbaE
Find proteins for Q83V33 (Pseudomonas fluorescens)
Explore Q83V33 
Go to UniProtKB:  Q83V33
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ83V33
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
K [auth C],
N [auth D]
C21 H27 N7 O14 P2
Query on 6OD

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
M [auth C],
P [auth D]
(2E,4E)-2-amino-6-oxohexa-2,4-dienoic acid
C6 H7 N O3
Query on NA

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
L [auth C],
O [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.253α = 90
b = 142.932β = 90
c = 175.125γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SERGUIdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2015-01-21
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description