PDBsum entry 6cxx

Oxidoreductase

PDB id: 6cxx

Contents

Protein chains

374 a.a.

Ligands

COD ×2

MRD ×4

MRD-MPD

Metals

_ZN ×4

Waters ×553

PDB id:

6cxx

Name:

Oxidoreductase

Title:

Horse liver e267h alcohol dehydrogenase complex with 3'- dephosphocoenzyme a

Structure:

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

Source:

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

Resolution:

1.26Å R-factor: 0.173 R-free: 0.208

Authors:

B.V.Plapp

Key ref:

Y.H.Kim et al. (2018). Substitutions of a buried glutamate residue hinder the conformational change in horse liver alcohol dehydrogenase and yield a surprising complex with endogenous 3'-Dephosphocoenzyme A. Arch Biochem Biophys, 653, 97. PubMed id: 30018019 DOI: 10.1016/j.abb.2018.07.003

Date:

04-Apr-18 Release date: 25-Apr-18

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 = COD) matches with 60.00% similarity) = aldehyde + NADH + H(+)

secondary alcohol + NAD(+) (Bound ligand (Het Group name = COD) matches with 60.00% similarity) = ketone + NADH + H(+)

• Cofactor: Zn(2+) or Fe cation

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

reference

DOI no: 10.1016/j.abb.2018.07.003

Arch Biochem Biophys 653:97 (2018)

PubMed id: 30018019

Substitutions of a buried glutamate residue hinder the conformational change in horse liver alcohol dehydrogenase and yield a surprising complex with endogenous 3'-Dephosphocoenzyme A.

Y.H.Kim, D.S.Gogerty, B.V.Plapp.

ABSTRACT

Glu-267 is highly conserved in alcohol dehydrogenases and buried as a negatively-charged residue in a loop of the NAD coenzyme binding domain. Glu-267 might have a structural role and contribute to a rate-promoting vibration that facilitates catalysis. Substitutions of Glu-267 with histidine or asparagine residues increase the dissociation constants for the coenzymes (NAD⁺ by ∼40-fold, NADH by ∼200-fold) and significantly decrease catalytic efficiencies by 16-1200-fold various substrates and substituted enzymes. The turnover numbers modestly change with the substitutions, but hydride transfer is at least partially rate-limiting for turnover for alcohol oxidation. X-ray structures of the E267H and E267 N enzymes are similar to the apoenzyme (open) conformation of the wild-type enzyme, and the substitutions are accommodated by local changes in the structure. Surprisingly, the E267H and E267 N enzymes have endogenous (from the expression in E. coli) 3'-dephosphocoenzyme A bound in the active site with the ADP moiety in the NAD binding site and the pantethiene sulfhydryl bound to the catalytic zinc. The kinetics and crystallography show that the substitutions of Glu-267 hinder the conformational change, which occurs when wild-type enzyme binds coenzymes, and affect productive binding of substrates.