2ONM

Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, complexed with NAD+

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

Structural and functional consequences of coenzyme binding to the inactive asian variant of mitochondrial aldehyde dehydrogenase: roles of residues 475 and 487.

Larson, H.N., Zhou, J., Chen, Z., Stamler, J.S., Weiner, H., Hurley, T.D.

(2007) J Biol Chem 282: 12940-12950

  • DOI: 10.1074/jbc.M607959200
  • Primary Citation of Related Structures:  
    2ONM, 2ONN, 2ONO, 2ONP

  • PubMed Abstract: 

    • The common mitochondrial aldehyde dehydrogenase (ALDH2) ALDH2(*)2 polymorphism is associated with impaired ethanol metabolism and decreased efficacy of nitroglycerin treatment. These physiological effects are due to the substitution of Lys for Glu-487 that reduces the k(cat) for these processes and increases the K(m) for NAD(+), as compared with ALDH2 ...

    The common mitochondrial aldehyde dehydrogenase (ALDH2) ALDH2(*)2 polymorphism is associated with impaired ethanol metabolism and decreased efficacy of nitroglycerin treatment. These physiological effects are due to the substitution of Lys for Glu-487 that reduces the k(cat) for these processes and increases the K(m) for NAD(+), as compared with ALDH2. In this study, we sought to understand the nature of the interactions that give rise to the loss of structural integrity and low activity in ALDH2(*)2 even when complexed with coenzyme. Consequently, we have solved the crystal structure of ALDH2(*)2 complexed with coenzyme to 2.5A(.) We have also solved the structures of a mutated form of ALDH2 where Arg-475 is replaced by Gln (R475Q). The structural and functional properties of the R475Q enzyme are intermediate between those of wild-type and the ALDH2(*)2 enzymes. In both cases, the binding of coenzyme restores most of the structural deficits observed in the apoenzyme structures. The binding of coenzyme to the R475Q enzyme restores its structure and catalytic properties to near wild-type levels. In contrast, the disordered helix within the coenzyme binding pocket of ALDH2(*)2 is reordered, but the active site is only partially reordered. Consistent with the structural data, ALDH2(*)2 showed a concentration-dependent increase in esterase activity and nitroglycerin reductase activity upon addition of coenzyme, but the levels of activity do not approach those of the wild-type enzyme or that of the R475Q enzyme. The data presented shows that Glu-487 maintains a critical function in linking the structure of the coenzyme-binding site to that of the active site through its interactions with Arg-264 and Arg-475, and in doing so, creates the stable structural scaffold conducive to catalysis.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aldehyde dehydrogenase, mitochondrial precursor
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
500Homo sapiensMutation(s): 1 
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
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD
Download Ideal Coordinates CCD File 
CB [auth H],
PA [auth F],
S [auth B],
WA [auth G],
Y [auth C]		NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N		 Ligand Interaction
ADP
Query on ADP
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CA [auth D],
HA [auth E],
IB [auth I],
N [auth A],
NB [auth J],
CA [auth D],
HA [auth E],
IB [auth I],
N [auth A],
NB [auth J],
RB [auth K],
UB [auth L]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AA [auth C],
DA [auth D],
DB [auth H],
EA [auth D],
EB [auth H],
AA [auth C],
DA [auth D],
DB [auth H],
EA [auth D],
EB [auth H],
FB [auth H],
IA [auth E],
JA [auth E],
JB [auth I],
KA [auth E],
KB [auth I],
O [auth A],
QA [auth F],
RA [auth F],
SA [auth F],
SB [auth K],
T [auth B],
TA [auth F],
U [auth B],
V [auth B],
VB [auth L],
WB [auth L],
XA [auth G],
YA [auth G],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
GAI
Query on GAI
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AB [auth G],
FA [auth D],
GB [auth H],
LA [auth E],
LB [auth I],
AB [auth G],
FA [auth D],
GB [auth H],
LA [auth E],
LB [auth I],
MA [auth E],
OB [auth J],
P [auth A],
ZA [auth G]
GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
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BA [auth D],
BB [auth H],
GA [auth E],
HB [auth I],
M [auth A],
BA [auth D],
BB [auth H],
GA [auth E],
HB [auth I],
M [auth A],
MB [auth J],
NA [auth F],
OA [auth F],
PB [auth K],
Q [auth B],
QB [auth K],
R [auth B],
TB [auth L],
UA [auth G],
VA [auth G],
W [auth C],
X [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.201α = 78.99
b = 104.854β = 82.14
c = 162.359γ = 88.55
Software Package:
Software NamePurpose
d*TREKdata processing
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CrystalCleardata reduction
d*TREKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-11-12
    Changes: Structure summary
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations