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PDBsum entry 2onm

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
2onm
Jmol
Contents
Protein chain
(+ 6 more) 494 a.a. *
Ligands
ADP ×7
EDO ×25
GAI ×9
NAD ×5
Metals
_NA ×17
Waters ×1932
* Residue conservation analysis
PDB id:
2onm
Name: Oxidoreductase
Title: Human mitochondrial aldehyde dehydrogenase asian variant, aldh2 2, Complexed with NAD+
Structure: Aldehyde dehydrogenase, mitochondrial precursor. Chain: a, b, c, d, e, f, g, h, i, j, k, l. Synonym: aldh class 2, aldhi, aldh-e2. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: aldh2, aldm. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.50Å     R-factor:   0.230     R-free:   0.271
Authors: H.N.Larson,T.D.Hurley
Key ref:
H.N.Larson et al. (2007). Structural and functional consequences of coenzyme binding to the inactive asian variant of mitochondrial aldehyde dehydrogenase: roles of residues 475 and 487. J Biol Chem, 282, 12940-12950. PubMed id: 17327228 DOI: 10.1074/jbc.M607959200
Date:
24-Jan-07     Release date:   06-Mar-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P05091  (ALDH2_HUMAN) -  Aldehyde dehydrogenase, mitochondrial
Seq:
Struc:
517 a.a.
494 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.2.1.3  - Aldehyde dehydrogenase (NAD(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: An aldehyde + NAD+ + H2O = a carboxylate + NADH
aldehyde
Bound ligand (Het Group name = EDO)
matches with 40.00% similarity
+
NAD(+)
Bound ligand (Het Group name = NAD)
corresponds exactly
+ H(2)O
= carboxylate
+ NADH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular vesicular exosome   3 terms 
  Biological process     metabolic process   10 terms 
  Biochemical function     electron carrier activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M607959200 J Biol Chem 282:12940-12950 (2007)
PubMed id: 17327228  
 
 
Structural and functional consequences of coenzyme binding to the inactive asian variant of mitochondrial aldehyde dehydrogenase: roles of residues 475 and 487.
H.N.Larson, J.Zhou, Z.Chen, J.S.Stamler, H.Weiner, T.D.Hurley.
 
  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.
 
  Selected figure(s)  
 
Figure 1.
FIGURE 1. Structures of ALDH2^*2. a, subunits C (dark gray) and D (blue) of the apoenzyme ALDH2^*2 structure (PDB ID 1ZUM) which lack ordered G helices. b, subunits A and B of the coenzyme-bound ALDH2^*2 structure with the G helices colored red. The bound coenzyme molecules are represented using space-filling atoms. The ordered portion of the NAD^+ molecule in subunit A, modeled as ADP, is shown in yellow, and the bound NAD^+ molecule in subunit B is shown in gold. All figures for publication were created using either the PyMol Molecular Graphics program (34) or Deep View Swiss PDB Viewer (35) and Pov-Ray (36).
Figure 9.
FIGURE 9. The interactions across the dimer interface contributed by residues 463-478. The structure of the wild-type ALDH2 enzyme with coenzyme-bound (PDB code 1O02) is used for this representation. Subunits A (blue) and B (violet) are shown. a, the loop comprised of residues 463-478 is shown in red for both subunits with the side chain for residue 475 colored according to its subunit. Hydrogen bonds are represented by green dashed lines. b, contacts among residues 463-478, the G helices, and -strands at the interface. The view in this panel is rotated 90° about a horizontal axis with respect to a. The elements of secondary structure are labeled. Residues 246 and 261, which mark the beginning and end of G, are labeled as is residue 470 within the loop that contacts these regions. The bound coenzyme molecules are shown using space-filling atoms and are colored gold.
 
  The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2007, 282, 12940-12950) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19906643 M.Beretta, A.C.Gorren, M.V.Wenzl, R.Weis, M.Russwurm, D.Koesling, K.Schmidt, and B.Mayer (2010).
Characterization of the East Asian variant of aldehyde dehydrogenase-2: bioactivation of nitroglycerin and effects of Alda-1.
  J Biol Chem, 285, 943-952.  
20062057 S.Perez-Miller, H.Younus, R.Vanam, C.H.Chen, D.Mochly-Rosen, and T.D.Hurley (2010).
Alda-1 is an agonist and chemical chaperone for the common human aldehyde dehydrogenase 2 variant.
  Nat Struct Mol Biol, 17, 159-164.
PDB codes: 3inj 3inl
19456322 H.Li, S.Borinskaya, K.Yoshimura, N.Kal'ina, A.Marusin, V.A.Stepanov, Z.Qin, S.Khaliq, M.Y.Lee, Y.Yang, A.Mohyuddin, D.Gurwitz, S.Q.Mehdi, E.Rogaev, L.Jin, N.K.Yankovsky, J.R.Kidd, and K.K.Kidd (2009).
Refined geographic distribution of the oriental ALDH2*504Lys (nee 487Lys) variant.
  Ann Hum Genet, 73, 335-345.  
19506075 M.V.Wenzl, M.Beretta, A.C.Gorren, A.Zeller, P.K.Baral, K.Gruber, M.Russwurm, D.Koesling, K.Schmidt, and B.Mayer (2009).
Role of the general base Glu-268 in nitroglycerin bioactivation and superoxide formation by aldehyde dehydrogenase-2.
  J Biol Chem, 284, 19878-19886.  
18574453 B.Mayer, and M.Beretta (2008).
The enigma of nitroglycerin bioactivation and nitrate tolerance: news, views and troubles.
  Br J Pharmacol, 155, 170-184.  
18611112 S.A.Marchitti, C.Brocker, D.Stagos, and V.Vasiliou (2008).
Non-P450 aldehyde oxidizing enzymes: the aldehyde dehydrogenase superfamily.
  Expert Opin Drug Metab Toxicol, 4, 697-720.  
17885622 G.S.Peng, Y.C.Chen, T.P.Tsao, M.F.Wang, and S.J.Yin (2007).
Pharmacokinetic and pharmacodynamic basis for partial protection against alcoholism in Asians, heterozygous for the variant ALDH2*2 gene allele.
  Pharmacogenet Genomics, 17, 845-855.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.