2ONP | pdb_00002onp

Arg475Gln Mutant of Human Mitochondrial Aldehyde Dehydrogenase, complexed with NAD+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.240 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2ONP

Ligand Structure Quality Assessment 


This is version 1.6 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 Biological Chem 282: 12940-12950

  • DOI: https://doi.org/10.1074/jbc.M607959200
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 445.52 kDa 
  • Atom Count: 33,651 
  • Modeled Residue Count: 3,952 
  • Deposited Residue Count: 4,000 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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): 1 
Gene Names: ALDH2ALDM
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
GTEx:  ENSG00000111275 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05091
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD

Query on NAD



Download:Ideal Coordinates CCD File
DC [auth G]
EB [auth E]
HA [auth C]
K [auth A]
NC [auth H]
DC [auth G],
EB [auth E],
HA [auth C],
K [auth A],
NC [auth H],
RB [auth F],
UA [auth D],
W [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
EC [auth G]
FB [auth E]
FC [auth G]
AA [auth B],
BA [auth B],
EC [auth G],
FB [auth E],
FC [auth G],
GB [auth E],
GC [auth G],
HB [auth E],
HC [auth G],
IA [auth C],
IB [auth E],
JA [auth C],
JB [auth E],
KA [auth C],
KB [auth E],
L [auth A],
LA [auth C],
M [auth A],
MA [auth C],
N [auth A],
NA [auth C],
O [auth A],
OC [auth H],
P [auth A],
PC [auth H],
QC [auth H],
RC [auth H],
SB [auth F],
TB [auth F],
UB [auth F],
VA [auth D],
VB [auth F],
WA [auth D],
WB [auth F],
X [auth B],
XA [auth D],
XB [auth F],
Y [auth B],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
GAI

Query on GAI



Download:Ideal Coordinates CCD File
AB [auth D]
AC [auth F]
BB [auth D]
CA [auth B]
DA [auth B]
AB [auth D],
AC [auth F],
BB [auth D],
CA [auth B],
DA [auth B],
EA [auth B],
IC [auth G],
JC [auth G],
KC [auth G],
LB [auth E],
MB [auth E],
NB [auth E],
OA [auth C],
OB [auth E],
PA [auth C],
Q [auth A],
QA [auth C],
R [auth A],
RA [auth C],
S [auth A],
SC [auth H],
T [auth A],
TC [auth H],
UC [auth H],
YA [auth D],
YB [auth F],
ZA [auth D],
ZB [auth F]
GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
BC [auth G]
CB [auth E]
FA [auth C]
I [auth A]
LC [auth H]
BC [auth G],
CB [auth E],
FA [auth C],
I [auth A],
LC [auth H],
PB [auth F],
SA [auth D],
U [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
CC [auth G]
DB [auth E]
GA [auth C]
J [auth A]
MC [auth H]
CC [auth G],
DB [auth E],
GA [auth C],
J [auth A],
MC [auth H],
QB [auth F],
TA [auth D],
V [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.240 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.854α = 90
b = 150.837β = 90
c = 177.482γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: 2017-10-18
    Changes: Refinement description
  • Version 1.5: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.6: 2023-08-30
    Changes: Data collection, Refinement description