1ZMD

Crystal Structure of Human dihydrolipoamide dehydrogenase complexed to NADH

Summary for 1ZMD

• Entry DOI: 10.2210/pdb1zmd/pdb
• Related: 1ZMC
• Descriptor: Dihydrolipoyl dehydrogenase, SULFATE ION, FLAVIN-ADENINE DINUCLEOTIDE, ... (5 entities in total)
• Functional Keywords: e3, lipoamide dehydrogenase, pyruvate dehydrogenase, alpha-ketoglutarate dehydrogenase, branched-chain alpha-ketoacid dehydrogenase, glycine decarboxylase, glycine cleavage, oxidoreductase
• Biological source: Homo sapiens (human)
• Cellular location: Mitochondrion matrix: P09622
• Total number of polymer chains: 8
• Total formula weight: 416253.13

Authors

Brautigam, C.A.,Chuang, J.L.,Tomchick, D.R.,Machius, M.,Chuang, D.T. (deposition date: 2005-05-10, release date: 2005-06-28, Last modification date: 2024-11-13)

Primary citation

Brautigam, C.A.,Chuang, J.L.,Tomchick, D.R.,Machius, M.,Chuang, D.T.
Crystal Structure of Human Dihydrolipoamide Dehydrogenase: NAD+/NADH Binding and the Structural Basis of Disease-causing Mutations
J.Mol.Biol., 350:543-552, 2005

PubMed Abstract: Human dihydrolipoamide dehydrogenase (hE3) is an enzymatic component common to the mitochondrial alpha-ketoacid dehydrogenase and glycine decarboxylase complexes. Mutations to this homodimeric flavoprotein cause the often-fatal human disease known as E3 deficiency. To catalyze the oxidation of dihydrolipoamide, hE3 uses two molecules: non-covalently bound FAD and a transiently bound substrate, NAD+. To address the catalytic mechanism of hE3 and the structural basis for E3 deficiency, the crystal structures of hE3 in the presence of NAD+ or NADH have been determined at resolutions of 2.5A and 2.1A, respectively. Although the overall fold of the enzyme is similar to that of yeast E3, these two structures differ at two loops that protrude from the proteins and at their FAD-binding sites. The structure of oxidized hE3 with NAD+ bound demonstrates that the nicotinamide moiety is not proximal to the FAD. When NADH is present, however, the nicotinamide base stacks directly on the isoalloxazine ring system of the FAD. This is the first time that this mechanistically requisite conformation of NAD+ or NADH has been observed in E3 from any species. Because E3 structures were previously available only from unicellular organisms, speculations regarding the molecular mechanisms of E3 deficiency were based on homology models. The current hE3 structures show directly that the disease-causing mutations occur at three locations in the human enzyme: the dimer interface, the active site, and the FAD and NAD(+)-binding sites. The mechanisms by which these mutations impede the function of hE3 are discussed.

PubMed: 15946682
DOI: 10.1016/j.jmb.2005.05.014

Experimental method

X-RAY DIFFRACTION (2.08 Å)