Human mitochondrial aldehyde dehydrogenase complexed with crotonaldehyde, NAD(H) and Mg2+

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.175 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Coenzyme isomerization is integral to catalysis in aldehyde dehydrogenase

Perez-Miller, S.J.Hurley, T.D.

(2003) Biochemistry 42: 7100-7109

  • DOI: https://doi.org/10.1021/bi034182w
  • Primary Citation of Related Structures:  
    1NZW, 1NZX, 1NZZ, 1O00, 1O01, 1O02, 1O04

  • PubMed Abstract: 

    Crystal structures of many enzymes in the aldehyde dehydrogenase superfamily determined in the presence of bound NAD(P)(+) have exhibited conformational flexibility for the nicotinamide half of the cofactor. This has been hypothesized to be important in catalysis because one conformation would block the second half of the reaction, but no firm evidence has been put forth which shows whether the oxidized and reduced cofactors preferentially occupy the two observed conformations. We present here two structures of the wild type and two structures of a Cys302Ser mutant of human mitochondrial aldehyde dehydrogenase in binary complexes with NAD(+) and NADH. These structures, including the Cys302Ser mutant in complex with NAD(+) at 1.4 A resolution and the wild-type enzyme in complex with NADH at 1.9 A resolution, provide strong evidence that bound NAD(+) prefers an extended conformation ideal for hydride transfer and bound NADH prefers a contracted conformation ideal for acyl-enzyme hydrolysis. Unique interactions between the cofactor and the Rossmann fold make isomerization possible while allowing the remainder of the active site complex to remain intact. In addition, these structures clarify the role of magnesium in activating the human class 2 enzyme. Our data suggest that the presence of magnesium may lead to selection of particular conformations and speed isomerization of the reduced cofactor following hydride transfer.

  • Organizational Affiliation

    Program in Medical Biophysics and Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldehyde dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H
500Homo sapiensMutation(s): 0 
Gene Names: ALDH2 OR ALDM
UniProt & NIH Common Fund Data Resources
Find proteins for P05091 (Homo sapiens)
Explore P05091 
Go to UniProtKB:  P05091
GTEx:  ENSG00000111275 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05091
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
BB [auth H]
EA [auth D]
KA [auth E]
L [auth A]
Q [auth B]
BB [auth H],
EA [auth D],
KA [auth E],
L [auth A],
Q [auth B],
QA [auth F],
WA [auth G],
X [auth C]
C21 H27 N7 O14 P2
Query on CRD

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AA [auth D]
HA [auth E]
NA [auth F]
O [auth B]
T [auth C]
AA [auth D],
HA [auth E],
NA [auth F],
O [auth B],
T [auth C],
TA [auth G]
C4 H6 O
Query on EDO

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AB [auth H]
CA [auth D]
DA [auth D]
JA [auth E]
PA [auth F]
AB [auth H],
CA [auth D],
DA [auth D],
JA [auth E],
PA [auth F],
V [auth C],
VA [auth G],
W [auth C]
C2 H6 O2
Query on GAI

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BA [auth D]
IA [auth E]
K [auth A]
OA [auth F]
P [auth B]
BA [auth D],
IA [auth E],
K [auth A],
OA [auth F],
P [auth B],
U [auth C],
UA [auth G],
ZA [auth H]
C H5 N3
Query on MG

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FA [auth E]
I [auth A]
LA [auth F]
M [auth B]
R [auth C]
FA [auth E],
I [auth A],
LA [auth F],
M [auth B],
R [auth C],
RA [auth G],
XA [auth H],
Y [auth D]
Query on NA

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GA [auth E]
J [auth A]
MA [auth F]
N [auth B]
S [auth C]
GA [auth E],
J [auth A],
MA [auth F],
N [auth B],
S [auth C],
SA [auth G],
YA [auth H],
Z [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.133α = 90
b = 150.571β = 90
c = 176.782γ = 90
Software Package:
Software NamePurpose
DENZOdata 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: 2003-06-24
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description