4OU2

A 2.15 Angstroms X-ray crystal structure of E268A 2-aminomuconate 6-semialdehyde dehydrogenase catalytic intermediate from Pseudomonas fluorescens

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

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: 10.1038/ncomms6935
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-aminomuconate 6-semialdehyde dehydrogenase
A, B, C, D
483Pseudomonas fluorescensMutation(s): 1 
Gene Names: nbaE
Find proteins for Q83V33 (Pseudomonas fluorescens)
Go to UniProtKB:  Q83V33
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD
Download SDF File 
Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
6OA
Query on 6OA
Download SDF File 
Download CCD File 
A, B, C, D
(2Z,4E)-2,6-dihydroxyhexa-2,4-dienoic acid
C6 H8 O4
YRYDCWGBHNTXLE-WFTYEQLWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.571α = 90.00
b = 141.556β = 90.00
c = 174.630γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2014-02-14 
  • Released Date: 2014-12-24 
  • Deposition Author(s): Huo, L., Liu, A.

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2015-01-21
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description