PDBsum entry 3glm

Lyase

PDB id: 3glm

Contents

Protein chains

562 a.a.

Ligands

COO ×4

Metals

_CL ×4

Waters ×627

References listed in PDB file

Key reference

Title

An asymmetric model for na+-Translocating glutaconyl-Coa decarboxylases.

Authors

D.Kress, D.Brügel, I.Schall, D.Linder, W.Buckel, L.O.Essen.

Ref.

J Biol Chem, 2009, 284, 28401-28409. [DOI no: 10.1074/jbc.M109.037762]

PubMed id

19654317

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a perfect match.

Abstract

Glutaconyl-CoA decarboxylase (Gcd) couples the biotin-dependent decarboxylation of glutaconyl-CoA with the generation of an electrochemical Na(+) gradient. Sequencing of the genes encoding all subunits of the Clostridium symbiosum decarboxylase membrane complex revealed that it comprises two distinct biotin carrier subunits, GcdC(1) and GcdC(2), which differ in the length of a central alanine- and proline-rich linker domain. Co-crystallization of the decarboxylase subunit GcdA with the substrate glutaconyl-CoA, the product crotonyl-CoA, and the substrate analogue glutaryl-CoA, respectively, resulted in a high resolution model for substrate binding and catalysis revealing remarkable structural changes upon substrate binding. Unlike the GcdA structure from Acidaminococcus fermentans, these data suggest that in intact Gcd complexes, GcdA is associated as a tetramer crisscrossed by a network of solvent-filled tunnels.

Figure 4.
A, overall structure of the C. symbiosum GcdA monomer. α- and 3[10]-helices of the N-terminal domain are colored blue, the respective β-strands are shown in lighter blue. The secondary structure motifs of the C-terminal domain are represented in dark green (helices) and light green (β-strands). The bound crotonyl-CoA is displayed as a magenta stick model and the chloride ion bound to OAH2 is shown as a yellow sphere. Residues missing in the electron density are indicated by broken lines. B, GcdA dimer. N and C terminus of the symmetry-equivalent chain B are colored dark and light gray, respectively. The crotonyl-CoA molecules at the dimer interfaces are represented as CPK models. The second chloride ion is displayed as a green sphere. The positions of the active sites are highlighted by dashed lines. C, two orthogonal orientations of the 222-symmetric GcdA tetramer deduced from the crystal packing. Chains A to D are colored blue, green, red, and yellow, respectively.

Figure 6.
Stereo view of the glutaconyl binding site displayed with amino acid residues within 4 Å of the crotonyl-CoA product. Residues of the N- and C-terminal domains of GcdA are colored blue and gray, respectively. Structurally equivalent residues of A. fermentans GcdA are displayed in orange. Non-conserved residues are marked with orange labels. The dashed lines indicate hydrogen bonds.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 28401-28409) copyright 2009.