PDBsum entry 1zmd

Oxidoreductase

PDB id: 1zmd

Contents

Protein chain

(+ 2 more) 472 a.a. *

Ligands

SO4 ×31

FAD ×8

NAI ×8

Waters ×1899

* Residue conservation analysis

PDB id:

1zmd

Name:

Oxidoreductase

Title:

Crystal structure of human dihydrolipoamide dehydrogenase complexed to nadh

Structure:

Dihydrolipoyl dehydrogenase. Chain: a, b, c, d, e, f, g, h. Synonym: dihydrolipoamide dehydrogenase, glycine cleavage system l protein. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: dld, gcsl, lad, phe3. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.08Å R-factor: 0.221 R-free: 0.249

Authors:

C.A.Brautigam,J.L.Chuang,D.R.Tomchick,M.Machius,D.T.Chuang

Key ref:

C.A.Brautigam et al. (2005). Crystal structure of human dihydrolipoamide dehydrogenase: NAD+/NADH binding and the structural basis of disease-causing mutations. J Mol Biol, 350, 543-552. PubMed id: 15946682 DOI: 10.1016/j.jmb.2005.05.014

Date:

10-May-05 Release date: 28-Jun-05

Protein chains

P09622  (DLDH_HUMAN) -  Dihydrolipoyl dehydrogenase, mitochondrial from Homo sapiens

Seq: 509 a.a.

Struc: 472 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.8.1.4 - dihydrolipoyl dehydrogenase.
• Pathway: Glycine Cleavage System
• Reaction: N₆-[(R)-dihydrolipoyl]-L-lysyl-[protein] + NAD⁺ = N₆-[(R)-lipoyl]- L-lysyl-[protein] + NADH + H⁺

N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + NAD(+) (Bound ligand (Het Group name = NAI) corresponds exactly) = N(6)-[(R)-lipoyl]- L-lysyl-[protein] + NADH + H(+)

• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAD) corresponds exactly)

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

reference

DOI no: 10.1016/j.jmb.2005.05.014

J Mol Biol 350:543-552 (2005)

PubMed id: 15946682

Crystal structure of human dihydrolipoamide dehydrogenase: NAD+/NADH binding and the structural basis of disease-causing mutations.

C.A.Brautigam, J.L.Chuang, D.R.Tomchick, M.Machius, D.T.Chuang.

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.

Selected figure(s)

Figure 1.
Figure 1. The crystal structure of the hE3 homodimer. Shown is a stereo ribbon diagram of the dimer. The atoms from the FAD and NADH are shown as spheres. In the left monomer, the domains are differently colored: the FAD-binding domain is green; the NAD^+-binding domain, purple; the central domain, blue; the interface domain, orange. The other monomer is colored tan. Bound molecules of FAD and NADH are colored brown and cyan, respectively, for the left monomer, and tan in the right monomer.

Figure 6.
Figure 6. Residues whose mutation causes E3 deficiency. Stereo representations of disease-causing mutations that occur (a) at the homodimer interface, (b) near to the disulfide-exchange site, or (c) near to the bound FAD or NADH molecules. The coordinates represented here come from the G (blue) and H (tan) monomers of hE3-Lip-NADH. Mutation to V188 is not known to cause disease; it is included to show its proximity to I358. The section of electron density in (b) is a 2F[o] -F[c] map contoured at the 1s level. In (b), the N3 atom of FAD is labeled. Secondary structure is shown semi-transparently to allow all atoms to be viewed. Atoms and secondary structural features are colored as in Figure 2 and Figure 3.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 350, 543-552) copyright 2005.

Figures were selected by an automated process.