PDBsum entry 1e3e

Oxidoreductase

PDB id: 1e3e

Contents

Protein chains

376 a.a. *

Ligands

NAI ×2

Metals

_ZN ×4

Waters ×502

* Residue conservation analysis

PDB id:

1e3e

Name:

Oxidoreductase

Title:

Mouse class ii alcohol dehydrogenase complex with nadh

Structure:

Alcohol dehydrogenase, class ii. Chain: a, b. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Organ: liver. Gene: adh-2. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Biol. unit:

Homo-Dimer (from PDB file)

Resolution:

2.12Å R-factor: 0.202 R-free: 0.259

Authors:

S.Svensson,J.O.Hoeoeg,G.Schneider,T.Sandalova

Key ref:

S.Svensson et al. (2000). Crystal structures of mouse class II alcohol dehydrogenase reveal determinants of substrate specificity and catalytic efficiency. J Mol Biol, 302, 441-453. PubMed id: 10970744 DOI: 10.1006/jmbi.2000.4039

Date:

14-Jun-00 Release date: 12-Sep-00

Protein chains

Q9QYY9  (ADH4_MOUSE) -  All-trans-retinol dehydrogenase [NAD(+)] ADH4 from Mus musculus

Seq: 377 a.a.

Struc: 376 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.1.1.105 - all-trans-retinol dehydrogenase (NAD(+)).
• Reaction: all-trans-retinol--[retinol-binding protein] + NAD⁺ = all-trans- retinal--[retinol-binding protein] + NADH + H⁺

all-trans-retinol--[retinol-binding protein] + NAD(+) (Bound ligand (Het Group name = NAI) corresponds exactly) = all-trans- retinal--[retinol-binding protein] + NADH + H(+)

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

Added reference

DOI no: 10.1006/jmbi.2000.4039

J Mol Biol 302:441-453 (2000)

PubMed id: 10970744

Crystal structures of mouse class II alcohol dehydrogenase reveal determinants of substrate specificity and catalytic efficiency.

S.Svensson, J.O.Höög, G.Schneider, T.Sandalova.

ABSTRACT

The structure of mouse class II alcohol dehydrogenase (ADH2) has been determined in a binary complex with the coenzyme NADH and in a ternary complex with both NADH and the inhibitor N-cyclohexylformamide to 2.2 A and 2.1 A resolution, respectively. The ADH2 dimer is asymmetric in the crystal with different orientations of the catalytic domains relative to the coenzyme-binding domains in the two subunits, resulting in a slightly different closure of the active-site cleft. Both conformations are about half way between the open apo structure and the closed holo structure of horse ADH1, thus resembling that of ADH3. The semi-open conformation and structural differences around the active-site cleft contribute to a substantially different substrate-binding pocket architecture as compared to other classes of alcohol dehydrogenase, and provide the structural basis for recognition and selectivity of alcohols and quinones. The active-site cleft is more voluminous than that of ADH1 but not as open and funnel-shaped as that of ADH3. The loop with residues 296-301 from the coenzyme-binding domain is short, thus opening up the pocket towards the coenzyme. On the opposite side, the loop with residues 114-121 stretches out over the inter-domain cleft. A cavity is formed below this loop and adds an appendix to the substrate-binding pocket. Asp301 is positioned at the entrance of the pocket and may control the binding of omega-hydroxy fatty acids, which act as inhibitors rather than substrates. Mouse ADH2 is known as an inefficient ADH with a slow hydrogen-transfer step. By replacing Pro47 with His, the alcohol dehydrogenase activity is restored. Here, the structure of this P47H mutant was determined in complex with NADH to 2.5 A resolution. His47 is suitably positioned to act as a catalytic base in the deprotonation of the substrate. Moreover, in the more closed subunit, the coenzyme is allowed a position closer to the catalytic zinc. This is consistent with hydrogen transfer from an alcoholate intermediate where the Pro/His replacement focuses on the function of the enzyme.

Selected figure(s)

Figure 2.
Figure 2. Comparison of mouse ADH2 subunit A (orange) with horse liver ADH1 apo (green) and holo (blue) subunits. C^a chains of the individual coenzyme-binding domains are superpositioned. Coenzyme-binding domains are to the left and the catalytic domains to the right. Zinc atoms and NADH are depicted in purple and brown, respectively. The three structural segments with insertions, deletions and high rms deviations as compared to other ADH structures are colored red and denoted V1-V3 (V1, residues 55-61; V2, residues 114-121; V3, residues 294-307). The mouse ADH2 A-subunit is semi-open about half way between the open apo and the closed holo form of horse liver ADH1.

Figure 3.
Figure 3. Stereo diagrams of the active site of mouse ADH2 complexed with NADH and N-cyclohexylformamide (CXF). (a), The alternative proton relay via Thr48 and Asn51 is indicated with broken lines and distances are given in Å (red). The 2F[o] -F[c] electron density map (blue) is contoured at 1s and the annealed omit F[o] -F[c] electron density map for CXF is contoured at 2.5s (red). Two of the four zinc ligands are depicted with the coordination to the zinc indicated with dashed lines. (b) Stereo diagram showing all residues lining the substrate pocket.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 302, 441-453) copyright 2000.

Figures were selected by an automated process.