PDBsum entry 2pnr

Transferase

PDB id: 2pnr

Contents

Protein chains

374 a.a.

341 a.a.

79 a.a.

Ligands

RED ×2

Waters ×723

References listed in PDB file

Key reference

Title

Crystal structure of an asymmetric complex of pyruvate dehydrogenase kinase 3 with lipoyl domain 2 and its biological implications.

Authors

Y.Devedjiev, C.N.Steussy, D.G.Vassylyev.

Ref.

J Mol Biol, 2007, 370, 407-416. [DOI no: 10.1016/j.jmb.2007.04.083]

PubMed id

17532006

Abstract

A homodimer of pyruvate dehydrogenase kinase (PDHK) is an integral part of pyruvate dehydrogenase complex (PDC) to which it is anchored primarily through the inner lipoyl-bearing domains (L2) of transacetylase component. The catalytic cycle of PDHK and its translocation over the PDC surface is thought to be mediated by the "symmetric" and "asymmetric" modes, in which the PDHK dimer binds to two and one L2-domain(s), respectively. Whereas the structure of the symmetric PDHK/L2 complex was reported, the structural organization and functional role of the asymmetric complex remain obscure. Here, we report the crystal structure of the asymmetric PDHK3/L2 complex that reveals several functionally important features absent from the previous structures. First, the PDHK3 subunits have distinct conformations: one subunit exhibits "open" and the other "closed" configuration of the putative substrate-binding cleft. Second, access to the closed cleft is additionally restricted by local unwinding of the adjacent alpha-helix. Modeling indicates that the target peptide might gain access to the PDHK active center through the open but not through the closed cleft. Third, the ATP-binding loop in one PDHK3 subunit adopts an open conformation, implying that the nucleotide loading into the active site is mediated by the inactive "pre-insertion" binding mode. Altogether our data suggest that the asymmetric complex represents a physiological state in which binding of a single L2-domain activates one of the PDHK protomers while inactivating another. Thus, the L2-domains likely act not only as the structural anchors but also modulate the catalytic cycle of PDHK.

Figure 2.
Figure 2. The gate helices in the L2-free and L2-bound subunits. (a) and (b) The L2-free open (a) and L2-bound (b) configurations of the SC (marked by yellow hydrophobic residues) correspond to the uniform (magenta (a)) and distorted (orange (b)) conformations of the gate helix. The remainder of the subunits is shown in gray. The PDHK active site is marked by the modeled (PDB ID 1Y8P) ATP molecule. (c) and (d) Superposition of the L2-free (magenta (c)) and L2-bound (orange (d)) PDHK gate helices with the RNA polymerase bridge helix (white) observed in the uniform (c) and locally distorted (d) conformations. (e) Stereo view of the L2-bound subunit showing stabilization of the partially unwound gate helix. The hydrogen bonds are shown by magenta broken lines. The active site is marked by ATP as in (a) and (b). The views in (a), (b), and (e) are the same as in Figure 1(b).

Figure 3.
Figure 3. Modeling of the E1/PDHK complex. (a) The overall stereo view of the E1 α-subunit with the modeled α-helical substrate peptide (yellow) docked into the SC of the L2-free PDHK subunit. The E1 β-chain and PDHK L2-bound subunit are located far from the modeled interface and are omitted from the model for clarity. (b) The close-up stereo view of the interface between the E1 substrate α-helix (yellow) and the SC. Hydrophobic side-chains of the substrate are shown in yellow, the phosphorylation site (Ser264) that is modeled in close proximity ( vert, similar 3.3 Å) to the ATP (green) γ-phosphate is colored in orange. The PDHK backbone and hydrophobic side-chains are shown in the domain-dependent colors corresponding to those in (a). The view is roughly the same as in Figure 1(b). (c) Schematic drawing of the putative van der Waals interactions (broken lines) that may be formed between the E1 substrate α-helix and the PDHK hydrophobic residues in the SC. The color scheme is the same as in (a) and (b).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 370, 407-416) copyright 2007.