4FR8

Crystal structure of human aldehyde dehydrogenase-2 in complex with nitroglycerin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Vascular Bioactivation of Nitroglycerin by Aldehyde Dehydrogenase-2: REACTION INTERMEDIATES REVEALED BY CRYSTALLOGRAPHY AND MASS SPECTROMETRY.

Lang, B.S., Gorren, A.C., Oberdorfer, G., Wenzl, M.V., Furdui, C.M., Poole, L.B., Mayer, B., Gruber, K.

(2012) J Biol Chem 287: 38124-38134

  • DOI: 10.1074/jbc.M112.371716
  • Primary Citation of Related Structures:  
    4FQF, 4FR8

  • PubMed Abstract: 

    • Aldehyde dehydrogenase-2 (ALDH2) catalyzes the bioactivation of nitroglycerin (glyceryl trinitrate, GTN) in blood vessels, resulting in vasodilation by nitric oxide (NO) or a related species. Because the mechanism of this reaction is still unclear we determined the three-dimensional structures of wild-type (WT) ALDH2 and of a triple mutant of the protein that exhibits low denitration activity (E268Q/C301S/C303S) in complex with GTN ...

    Aldehyde dehydrogenase-2 (ALDH2) catalyzes the bioactivation of nitroglycerin (glyceryl trinitrate, GTN) in blood vessels, resulting in vasodilation by nitric oxide (NO) or a related species. Because the mechanism of this reaction is still unclear we determined the three-dimensional structures of wild-type (WT) ALDH2 and of a triple mutant of the protein that exhibits low denitration activity (E268Q/C301S/C303S) in complex with GTN. The structure of the triple mutant showed that GTN binds to the active site via polar contacts to the oxyanion hole and to residues 268 and 301 as well as by van der Waals interactions to hydrophobic residues of the catalytic pocket. The structure of the GTN-soaked wild-type protein revealed a thionitrate adduct to Cys-302 as the first reaction intermediate, which was also found by mass spectrometry (MS) experiments. In addition, the MS data identified sulfinic acid as the irreversibly inactivated enzyme species. Assuming that the structures of the triple mutant and wild-type ALDH2 reflect binding of GTN to the catalytic site and the first reaction step, respectively, superposition of the two structures indicates that denitration of GTN is initiated by nucleophilic attack of Cys-302 at one of the terminal nitrate groups, resulting in formation of the observed thionitrate intermediate and release of 1,2-glyceryl dinitrate. Our results shed light on the molecular mechanism of the GTN denitration reaction and provide useful information on the structural requirements for high affinity binding of organic nitrates to the catalytic site of ALDH2.

    Organizational Affiliation: 

    Department of Pharmacology and Toxicology, University of Graz, 8010 Graz, Austria.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aldehyde dehydrogenase, mitochondrial
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
500Homo sapiensMutation(s): 3 
Gene Names: ALDH2, ALDM
EC: 1.2.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P05091 (Homo sapiens)
Explore P05091 
Go to UniProtKB:  P05091
PHAROS:  P05091
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05091
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD
Download Ideal Coordinates CCD File 
EA [auth F],
J [auth A],
R [auth C],
W [auth D]		NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N		 Ligand Interaction
ADP
Query on ADP
Download Ideal Coordinates CCD File 
AA [auth E],
HA [auth G],
LA [auth H],
N [auth B]		ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
TNG
Query on TNG
Download Ideal Coordinates CCD File 
I [auth A]propane-1,2,3-triyl trinitrate
C3 H5 N3 O9
SNIOPGDIGTZGOP-UHFFFAOYSA-N		 Ligand Interaction
BTB
Query on BTB
Download Ideal Coordinates CCD File 
KA [auth G]2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N		 Ligand Interaction
URE
Query on URE
Download Ideal Coordinates CCD File 
DA [auth E],
L [auth A],
P [auth B],
T [auth C],
V [auth C],
DA [auth E],
L [auth A],
P [auth B],
T [auth C],
V [auth C],
Y [auth D]
UREA
C H4 N2 O
XSQUKJJJFZCRTK-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
BA [auth E],
FA [auth F],
IA [auth G],
K [auth A],
MA [auth H],
BA [auth E],
FA [auth F],
IA [auth G],
K [auth A],
MA [auth H],
O [auth B],
S [auth C],
X [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
CA [auth E],
GA [auth F],
JA [auth G],
M [auth A],
NA [auth H],
CA [auth E],
GA [auth F],
JA [auth G],
M [auth A],
NA [auth H],
Q [auth B],
U [auth C],
Z [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.663α = 90
b = 175.916β = 95.01
c = 102.296γ = 90
Software Package:
Software NamePurpose
EDNAdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-26
    Type: Initial release
  • Version 1.1: 2012-11-21
    Changes: Database references