PDBsum entry 1ebd

Complex (oxidoreductase/transferase)

PDB id: 1ebd

Contents

Protein chains

455 a.a. *

41 a.a. *

Ligands

FAD ×2

Waters ×37

* Residue conservation analysis

PDB id:

1ebd

Name:

Complex (oxidoreductase/transferase)

Title:

Dihydrolipoamide dehydrogenase complexed with the binding domain of the dihydrolipoamide acetylase

Structure:

Dihydrolipoamide dehydrogenase. Chain: a, b. Synonym: e3bd. Engineered: yes. Dihydrolipoamide acetyltransferase. Chain: c. Fragment: binding domain, residues 130 - 170. Engineered: yes

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.60Å R-factor: 0.215

Authors:

S.S.Mande,S.Sarfaty,M.D.Allen,R.N.Perham,W.G.J.Hol

Key ref:

S.S.Mande et al. (1996). Protein-protein interactions in the pyruvate dehydrogenase multienzyme complex: dihydrolipoamide dehydrogenase complexed with the binding domain of dihydrolipoamide acetyltransferase. Structure, 4, 277-286. PubMed id: 8805537 DOI: 10.1016/S0969-2126(96)00032-9

Date:

03-Feb-96 Release date: 11-Jul-96

Protein chains

P11959  (DLDH1_GEOSE) -  Dihydrolipoyl dehydrogenase from Geobacillus stearothermophilus

Seq: 470 a.a.

Struc: 455 a.a.

Protein chain

P11961  (ODP2_GEOSE) -  Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex from Geobacillus stearothermophilus

Seq: 428 a.a.

Struc: 41 a.a.

Enzyme reactions

• Enzyme class 1: Chains A, B: 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⁺
• Cofactor: FAD

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

• Enzyme class 2: Chain C: E.C.2.3.1.12 - dihydrolipoyllysine-residue acetyltransferase.

Pathway:

• Reaction: N₆-[(R)-dihydrolipoyl]-L-lysyl-[protein] + acetyl-CoA = N₆-[(R)-S(8)- acetyldihydrolipoyl]-L-lysyl-[protein] + CoA

N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + acetyl-CoA = N(6)-[(R)-S(8)- acetyldihydrolipoyl]-L-lysyl-[protein] (Bound ligand (Het Group name = FAD) matches with 48.53% similarity) + CoA

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1016/S0969-2126(96)00032-9

Structure 4:277-286 (1996)

PubMed id: 8805537

Protein-protein interactions in the pyruvate dehydrogenase multienzyme complex: dihydrolipoamide dehydrogenase complexed with the binding domain of dihydrolipoamide acetyltransferase.

S.S.Mande, S.Sarfaty, M.D.Allen, R.N.Perham, W.G.Hol.

ABSTRACT

BACKGROUND: The ubiquitous pyruvate dehydrogenase multienzyme complex is built around an octahedral or icosahedral core of dihydrolipoamide acetyltransferase (E2) chains, to which multiple copies of pyruvate decarboxylase (E1) and dihydrolipoamide dehydrogenase (E3) bind tightly but non-covalently. E2 is a flexible multidomain protein that mediates interactions with E1 and E3 through a remarkably small binding domain (E2BD). RESULTS: In the Bacillus stearothermophilus complex, the E2 core is an icosahedral assembly of 60 E2 chains. The crystal structure of the E3 dimer (101 kDa) complexed with E2BD (4 kDa) has been solved to 2.6 A resolution. Interactions between E3 and E2BD are dominated by an electrostatic zipper formed by Arg135 and Arg139 in the N-terminal helix of E2BD and Asp344 and Glu431 of one of the monomers of E3. E2BD interacts with both E3 monomers, but the binding site is located close to the twofold axis. Thus, in agreement with earlier biochemical results, it is impossible for two molecules of E2BD to bind simultaneously to one E3 dimer. CONCLUSIONS: Combining this new structure for the E3-E2BD complex with previously determined structures of the E2 catalytic domain and the E2 lipoyl domain creates a model of the E2 core showing how the lipoyl domain can move between the active sites of E2 and E3 in the multienzyme complex.

Selected figure(s)

Figure 3.
Figure 3. Stereo superposition of the B. stearothermophilus E2 binding domain in the complex structure (white) with the uncomplexed NMR structure (grey). The structures are very similar except for the different conformations of loop L2. H1 and H2 indicate the two α-helices which are composed of residues 133–141 and 160–168 respectively. The horizontal 3[10]-helix comprises residues 146–148. Figure 3. Stereo superposition of the B. stearothermophilus E2 binding domain in the complex structure (white) with the uncomplexed NMR structure (grey). The structures are very similar except for the different conformations of loop L2. H1 and H2 indicate the two α-helices which are composed of residues 133–141 and 160–168 respectively. The horizontal 3[10]-helix comprises residues 146–148. (Drawn using MOLSCRIPT [[3]49].)

Figure 5.
Figure 5. Electrostatic zipper between E3 (green, monomer A; pink, monomer B) and E2BD (blue) of B. stearothermophilus. The side chains of Asp344 and Glu431 of monomer B of E3 adopt different conformations in the present complex structure to facilitate the formation of salt bridges with the binding domain. Side chains of Asp344 and Glu431 in the uncomplexed E3 structure are shown with thin bonds. Figure 5. Electrostatic zipper between E3 (green, monomer A; pink, monomer B) and E2BD (blue) of B. stearothermophilus. The side chains of Asp344 and Glu431 of monomer B of E3 adopt different conformations in the present complex structure to facilitate the formation of salt bridges with the binding domain. Side chains of Asp344 and Glu431 in the uncomplexed E3 structure are shown with thin bonds. (Figure drawn using RASTER3D [[3]50 and [4]51].)

The above figures are reprinted by permission from Cell Press: Structure (1996, 4, 277-286) copyright 1996.

Figures were selected by an automated process.