1MC5: Ternary complex of Human glutathione-dependent formaldehyde dehydrogenase with S-(hydroxymethyl)glutathione and NADH

Citation:
Abstract
Human glutathione-dependent formaldehyde dehydrogenase plays an important role in the metabolism of glutathione adducts such as S-(hydroxymethyl)glutathione and S-nitrosoglutathione. The role of specific active site residues in binding these physiologically important substrates and the structural changes during the catalytic cycle of glutathione-dependent formaldehyde dehydrogenase was examined by determining the crystal structure of a ternary complex with S-(hydroxymethyl)glutathione and the reduced coenzyme to 2.6 A resolution. The formation of the ternary complex caused the movement of the catalytic domain toward the coenzyme-binding domain. This represents the first observation of domain closure in glutathione-dependent formaldehyde dehydrogenase in response to substrate binding. A water molecule adjacent to the 2'-ribose hydroxyl of NADH suggests that the alcohol proton is relayed to solvent directly from the coenzyme, rather than through the action of the terminal histidine residue as observed in the proton relay system for class I alcohol dehydrogenases. S-(Hydroxymethyl)glutathione is directly coordinated to the active site zinc and forms interactions with the highly conserved residues Arg114, Asp55, Glu57, and Thr46. The active site zinc has a tetrahedral coordination environment with Cys44, His66, and Cys173 as the three protein ligands in addition to S-(hydroxymethyl)glutathione. This is in contrast to zinc coordination in the binary coenzyme complex where all of the ligands were contributed by the enzyme and included Glu67 as the fourth protein ligand. This change in zinc coordination is accomplished by an approximately 2.3 A movement of the catalytic zinc.
PDB ID: 1MC5Download
MMDB ID: 22036
PDB Deposition Date: 2002/8/5
Updated in MMDB: 2012/12
Experimental Method:
x-ray diffraction
Resolution: 2.6  Å
Source Organism:
Similar Structures:
Biological Unit for 1MC5: dimeric; determined by author and by software (PISA)
Molecular Components in 1MC5
Label Count Molecule
Proteins (2 molecules)
2
Alcohol Dehydrogenase Class III CHI Chain(Gene symbol: ADH5)
Molecule annotation
Chemicals (11 molecules)
1
4
2
1
3
3
4
2
5
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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