2WOX

Betaine aldehyde dehydrogenase from Pseudomonas aeruginosa with NAD(P) H-catalytic thiol adduct.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Novel NADPH-cysteine covalent adduct found in the active site of an aldehyde dehydrogenase.

Diaz-Sanchez, A.G.Gonzalez-Segura, L.Rudino-Pinera, E.Lira-Rocha, A.Torres-Larios, A.Munoz-Clares, R.A.

(2011) Biochem J 439: 443-452

  • DOI: https://doi.org/10.1042/BJ20110376
  • Primary Citation of Related Structures:  
    2WOX, 3ZQA

  • PubMed Abstract: 

    PaBADH (Pseudomonas aeruginosa betaine aldehyde dehydrogenase) catalyses the irreversible NAD(P)+-dependent oxidation of betaine aldehyde to its corresponding acid, the osmoprotector glycine betaine. This reaction is involved in the catabolism of choline and in the response of this important pathogen to the osmotic and oxidative stresses prevalent in infection sites. The crystal structure of PaBADH in complex with NADPH showed a novel covalent adduct between the C2N of the pyridine ring and the sulfur atom of the catalytic cysteine residue, Cys286. This kind of adduct has not been reported previously either for a cysteine residue or for a low-molecular-mass thiol. The Michael addition of the cysteine thiolate in the 'resting' conformation to the double bond of the α,β-unsaturated nicotinamide is facilitated by the particular conformation of NADPH in the active site of PaBADH (also observed in the crystal structure of the Cys286Ala mutant) and by an ordered water molecule hydrogen bonded to the carboxamide group. Reversible formation of NAD(P)H-Cys286 adducts in solution causes reversible enzyme inactivation as well as the loss of Cys286 reactivity towards thiol-specific reagents. This novel covalent modification may provide a physiologically relevant regulatory mechanism of the irreversible PaBADH-catalysed reaction, preventing deleterious decreases in the intracellular NAD(P)+/NAD(P)H ratios.


  • Organizational Affiliation

    Departamento de Bioquímica, Universidad Nacional Autónoma de México, Ciudad Universitaria. clares@servidor.unam.mx


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETAINE ALDEHYDE DEHYDROGENASE
A, B, C, D
489Pseudomonas aeruginosaMutation(s): 0 
EC: 1.2.1.8
UniProt
Find proteins for Q9HTJ1 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HTJ1 
Go to UniProtKB:  Q9HTJ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HTJ1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
E [auth A],
GA [auth D],
M [auth B],
V [auth C]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
7PE
Query on 7PE

Download Ideal Coordinates CCD File 
EA [auth C],
I [auth A],
J [auth A],
S [auth B],
T [auth B]
2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL
C14 H30 O7
UKXKPKBTMYNOFS-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
H [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
H [auth A],
JA [auth D],
KA [auth D],
L [auth B],
LA [auth D],
MA [auth D],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
Y [auth C],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME
Query on BME

Download Ideal Coordinates CCD File 
FA [auth C],
K [auth A]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
HA [auth D]
IA [auth D]
N [auth B]
F [auth A],
G [auth A],
HA [auth D],
IA [auth D],
N [auth B],
U [auth B],
W [auth C],
X [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.164 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.749α = 90
b = 151.749β = 90
c = 242.053γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-10-26
    Changes: Database references
  • Version 2.0: 2019-01-23
    Changes: Advisory, Atomic model, Data collection, Database references, Source and taxonomy
  • Version 2.1: 2019-04-24
    Changes: Data collection, Derived calculations
  • Version 2.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description