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 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    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 ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-aminomuconate 6-semialdehyde dehydrogenaseA, B, C, D483Pseudomonas fluorescensMutation(s): 1 
Gene Names: nbaE
UniProt
Find proteins for Q83V33 (Pseudomonas fluorescens)
Explore Q83V33 
Go to UniProtKB:  Q83V33
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ83V33
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.571α = 90
b = 141.556β = 90
c = 174.63γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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  (Full details and data files)

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