PDBsum entry 4nfs

Oxidoreductase

PDB id: 4nfs

Contents

Protein chains

374 a.a.

Ligands

NAJ ×2

ETF ×2

MRD ×4

Metals

_ZN ×4

Waters ×1062

PDB id:

4nfs

Name:

Oxidoreductase

Title:

V203a horse liver alcohol dehydrogenase e complexed with NAD and 2,2, 2-trifluoroethanol

Structure:

Alcohol dehydrogenase e chain. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Equus caballus. Domestic horse,equine. Organism_taxid: 9796. Strain: domestic horse. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.10Å R-factor: 0.138 R-free: 0.175

Authors:

B.V.Plapp

Key ref:

A.Yahashiri et al. (2014). Effects of cavities at the nicotinamide binding site of liver alcohol dehydrogenase on structure, dynamics and catalysis. Biochemistry, 53, 881-894. PubMed id: 24437493 DOI: 10.1021/bi401583f

Date:

31-Oct-13 Release date: 13-Nov-13

Protein chains

P00327  (ADH1E_HORSE) -  Alcohol dehydrogenase E chain from Equus caballus

Seq: 375 a.a.

Struc: 374 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.1.1.1 - alcohol dehydrogenase.
• Reaction:
  1. a primary alcohol + NAD⁺ = an aldehyde + NADH + H⁺
  2. a secondary alcohol + NAD⁺ = a ketone + NADH + H⁺

primary alcohol + NAD(+) (Bound ligand (Het Group name = NAJ) corresponds exactly) = aldehyde + NADH + H(+)

secondary alcohol + NAD(+) (Bound ligand (Het Group name = NAJ) corresponds exactly) = ketone + NADH + H(+)

• Cofactor: Zn(2+) or Fe cation

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/bi401583f

Biochemistry 53:881-894 (2014)

PubMed id: 24437493

Effects of cavities at the nicotinamide binding site of liver alcohol dehydrogenase on structure, dynamics and catalysis.

A.Yahashiri, J.K.Rubach, B.V.Plapp.

ABSTRACT

A role for protein dynamics in enzymatic catalysis of hydrogen transfer has received substantial scientific support, but the connections between protein structure and catalysis remain to be established. Valine residues 203 and 207 are at the binding site for the nicotinamide ring of the coenzyme in liver alcohol dehydrogenase and have been suggested to facilitate catalysis with "protein-promoting vibrations" (PPV). We find that the V207A substitution has small effects on steady-state kinetic constants and the rate of hydrogen transfer; the introduced cavity is empty and is tolerated with minimal effects on structure (determined at 1.2 Å for the complex with NAD(+) and 2,3,4,5,6-pentafluorobenzyl alcohol). Thus, no evidence is found to support a role for Val-207 in the dynamics of catalysis. The protein structures and ligand geometries (including donor-acceptor distances) in the V203A enzyme complexed with NAD(+) and 2,3,4,5,6-pentafluorobenzyl alcohol or 2,2,2-trifluoroethanol (determined at 1.1 Å) are very similar to those for the wild-type enzyme, except that the introduced cavity accommodates a new water molecule that contacts the nicotinamide ring. The structures of the V203A enzyme complexes suggest, in contrast to previous studies, that the diminished tunneling and decreased rate of hydride transfer (16-fold, relative to that of the wild-type enzyme) are not due to differences in ground-state ligand geometries. The V203A substitution may alter the PPV and the reorganization energy for hydrogen transfer, but the protein scaffold and equilibrium thermal motions within the Michaelis complex may be more significant for enzyme catalysis.