Alcohol Dehydrogenases

  1. Introduction to alcohol dehydrogenases
  2. Structure of alcohol dehydrogenases
  3. Conformational changes in alcohol dehydrogenases
  4. References
  5. PDB structure files at Brookhaven National Laboratory

Introduction

Alcohol dehydrogenases oxidises alcohol into aldehydes orketones. The reaction requires conenzyme NAD+ as hydrogen acceptor and has a broad specificity for alcohol substrates. They belong to a family of dehydrogenases that have a nucleotide-binding domain. The strategy of all such NAD-dependent dehydrogenases is to orient the coenzyme and substrate on the enzyme surface, such that the C4 atom on the nicotinamide is directed at the reactive carbon of the substrate. The NAD-binding domains of all these dehydrogenases are highly homologous, but they have markedly different catalytic domains.

Structure of alcohol dehydrogenases

Alcohol dehydrogenase is a homodimer. Each monomer has 374 residues with molecular weight of 74000 dalton. There are two domains. The NAD+-binding domain (residues 176-318) consists of a central beta-sheet of 6 strands flanked by alpha helices. NAD+ binds to the C-terminus of the beta-sheet. The catalytic domain (residues 1-175, 319-374) also has a alpha/beta structure. The inter-domain interface forms a cleft which contains the active catalytic site. The interface is formed by two helices, one from each domain crossing over each other. There are two Zn++ cations per monomer, one at the catalytic site being mandatory for catalysis. The alcohol substrate binds inside the cleft where the Zn++ cation is, whilst the nicotinamide ring of the NAD finds its way pointing into the cleft. The dimer forms with the two NAD-binding domains packing together such that their 2 central beta sheets combine to form a 12-stranded beta sheet. The catalytic domains are situated at opposite ends.

Look at a ribbon view of monomer6ADH- Ribbon view of horse liver alcohol dehydrogenase monomer The NAD+-binding domain is shown with helix in cyan and sheet in blue. The catalytic domain has helix in magenta and sheet in purple. The substrate is dimethylsulphoside (DMSO) in green. The active Zn++ ion is in brown, whilst the other one is in white. NAD+ is in CPK colouring, with its adenine ring bound to the C-terminus of the beta sheet of the NAD+-binding domain. Its nicotinamide ring is brought into close proximity with the substrate and Zn++ ion.

Look at the crossing helices6ADH- Crossing helices shown in van der Waals spaceballs to highlight the crossing of helices between the two domains. NAD+ and DMSO are shown in stick model.

Look at DMSO in the cleft6ADH-_DMSO can be seen buried within the cleft in spacefill model.

Look at NAD pointing its nicotinamide ring into the cleft6ADH- NAD is seen with its nicotinamide ring buried inside the cleft where it interacts with the substrate and Zn++ ion.

Conformational changes between apo- and holo-enzyme

When the apo-enzyme is bound by its substrate and coenzyme, there is a conformational change. This consists of a rotation of about 7.5 around a hinge axis passing through the contact point of the alpha helices connecting the two domains. This domain motion is classified as a shear motion according to Chothia and Lesk's classification of domain motions. This results in a change in the shape of the cleft to accommodate the substrate. The result is closure of the cleft with the substrate and nicotinamide ring surrounding the Zn++ ion. The active Zn++ ion is in tetrahedral coordination. In the apo-enzyme one of its four ligands is a water molecule. In the holo-enzyme the water molecule is replaced by the hydroxyl oxygen of the alcohol substrate, as a result of solvent exclusion upon cleft closure.

Look at the dimer in ribbon6ADH- Dimer ribbon view

Look at dimer in spacefill6ADH- Dimer spacefill view

Look at dimer helices6ADH- Dimer helical shear is highlighted in this view with the helices in spacefill model. The two catalytic domains can be seen with their helices (magenta) wrapping over the central combined alpha/beta structure of 12-stranded beta-sheet and flanking alpha-helices (cyan). With the crossed helices, the catalytic domains can glide over the NAD+-binding domains.

References

  1. EKLUND H. et al Structure of triclinic ternary complex of horse liver alcohol dehydrogenase at 2.9 Angstroms resolution. J.Mol.Biol. 146: 561 1981.
  2. COLONNA F.et al Interdomain motion in liver alcohol dehydrogenase. Structural and energetic analysis of the hinge bending mide. J.Biol.Chem. 261: 15273 1986.
  3. EKLUND H.et al Crystallographic investigations of nicotinamide adenine dinucleotide binding to horse liver alcohol dehydrogenase. Biochemistry 23: 5982 1984.
  4. SCHNEIDER G.et al. Crystal structures of the active site in specifically metal-depleted and cobalt-substituted horse liver alcohol dehydrogenase derivatives. Proc.Nat.Acad.Sci.USA. 80: 5289 1983.
  5. PLAPP B.V. et al. Three-dimensional structure of isonicotinimidylated liver alcohol dehydrogenase. J.Biol.Chem. 258: 5537 1983.
  6. CEDERGREN E. et al. Crystal-structure determination of reduced nicotinamide adenine dinucleotide complex with horse liver alcohol dehydrogenase amintained in its apo conformation by zinc-bound imidazole. Biochemistry 22: 5761 1983.
  7. EKLUND H. et al. Binding of substrate in a ternary complex of horse liver alcohol dehydrogenase. J.Biol.Chem 257: 14349 1982.
  8. CEDERGREN E. et al. Crystal structure determinations of coenzyme analogue and substrate complexes of liver alcohol dehydrogeanse. binding of 1,4,5,6-*tetrahydronicotinamide adenine dinucleotide and trans-4-(N,N-*dimethylamino)cinnamaldehyde to the enzyme. Biochemistry 21: 4895 1982.
  9. EKLUND H. et al. Pyrazole binding in crysralline binary and ternary complexes with liver alcohol dehydrogenase. Biochemistry 21: 4858 1982.
  10. SAMAMA P.et al. Kinetic investigation with major and minor isoenzymes of liver alcohol dehydrogenase and structural determination of its binary cmplex with alcohol dehydrogenase. Eur.J.Biochem. 118: 479 1981.

PDB structure files

  1. 6ADH- Horse liver alcohol dehydrogenase dimeric holoenzyme complexed with NAD+ and DMSO.
  2. 8ADH- Horse liver alcohol dehydrogenase apoenzyme.
  3. 5ADH- Horse liver alcohol dehydrogenase complexed with ADP-ribose and 2-methyl-2-21-pentanediol.
  4. 1CDO- Cod fish liver alcohol dehydrogenase dimer complexed with NAD+.