PDBsum entry 5kjc

Oxidoreductase

PDB id: 5kjc

Contents

Protein chains

374 a.a.

Ligands

NAJ ×2

PFB ×2

MRD ×5

Metals

_ZN ×4

Waters ×930

PDB id:

5kjc

Name:

Oxidoreductase

Title:

V222i horse liver alcohol dehydrogenase complexed with NAD+ and pentafluorobenzyl alcohol

Structure:

Alcohol dehydrogenase e chain. Chain: a, b. Engineered: yes. Mutation: yes. Other_details: v222i substitution in wild-type

Source:

Equus caballus. Horse. Organism_taxid: 9796. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.20Å R-factor: 0.129 R-free: 0.168

Authors:

B.V.Plapp

Key ref:

K.K.Shanmuganatham et al. (2018). Contribution of buried distal amino acid residues in horse liver alcohol dehydrogenase to structure and catalysis. Protein Sci, 27, 750-768. PubMed id: 29271062

Date:

18-Jun-16 Release date: 29-Jun-16

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

Protein Sci 27:750-768 (2018)

PubMed id: 29271062

Contribution of buried distal amino acid residues in horse liver alcohol dehydrogenase to structure and catalysis.

K.K.Shanmuganatham, R.S.Wallace, A.Ting-I Lee, B.V.Plapp.

ABSTRACT

The dynamics of enzyme catalysis range from the slow time scale (∼ms) for substrate binding and conformational changes to the fast time (∼ps) scale for reorganization of substrates in the chemical step. The contribution of global dynamics to catalysis by alcohol dehydrogenase was tested by substituting five different, conserved amino acid residues that are distal from the active site and located in the hinge region for the conformational change or in hydrophobic clusters. X-ray crystallography shows that the structures for the G173A, V197I, I220 (V, L, or F), V222I, and F322L enzymes complexed with NAD⁺and an analogue of benzyl alcohol are almost identical, except for small perturbations at the sites of substitution. The enzymes have very similar kinetic constants for the oxidation of benzyl alcohol and reduction of benzaldehyde as compared to the wild-type enzyme, and the rates of conformational changes are not altered. Less conservative substitutions of these amino acid residues, such as G173(V, E, K, or R), V197(G, S, or T), I220(G, S, T, or N), and V222(G, S, or T) produced unstable or poorly expressed proteins, indicating that the residues are critical for global stability. The enzyme scaffold accommodates conservative substitutions of distal residues, and there is no evidence that fast, global dynamics significantly affect the rate constants for hydride transfers. In contrast, other studies show that proximal residues significantly participate in catalysis.