1eae
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ATOMIC STRUCTURE OF THE CUBIC CORE OF THE PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX
OverviewOverview
The catalytic domain of dihydrolipoyl transacetylase (E2pCD) forms the, core of the pyruvate dehydrogenase multienzyme complex and catalyzes the, acetyltransferase reaction using acetylCoA as acetyl donor and, dihydrolipoamide (Lip(SH)2) as acceptor. The crystal structures of six, complexes and derivatives of Azotobacter vinelandii E2pCD were solved. The, binary complexes of the enzyme with CoA and Lip(SH)2 were determined at, 2.6- and 3.0-A resolutions, respectively. The two substrates are found in, an extended conformation at the two opposite entrances of the 30 A long, channel which runs at the interface between two 3-fold-related subunits, and forms the catalytic center. The reactive thiol groups of both, substrates are within hydrogen-bond distance from the side chain of His, 610. This fact supports the indication, derived from the similarity with, chloramphenicol acetyl transferase, that the histidine side chain acts as, general-base catalyst in the deprotonation of the reactive thiol of CoA., The conformation of Asn 614 appears to be dependent on the protonation, state of the active site histidine, whose function as base catalyst is, modulated in this way. Studies on E2pCD soaked in a high concentration of, dithionite lead to the structure of the binary complex between E2pCD and, hydrogen sulfite solved at 2.3-A resolution. It appears that the anion is, bound in the middle of the catalytic center and is therefore capable of, hosting and stabilizing a negative charge, which is of special interest, since the reaction catalyzed by E2pCD is thought to proceed via a, negatively charged tetrahedral intermediate. The structure of the binary, complex between E2pCD and hydrogen sulfite suggests that transition-state, stabilization can be provided by a direct hydrogen bond between the side, chain of Ser 558 and the oxy anion of the putative intermediate. In the, binary complex with CoA, the hydroxyl group of Ser 558 is hydrogen bonded, to the nitrogen atom of one of the two peptide-like units of the, substrate. Thus, CoA itself is involved in keeping the Ser hydroxyl group, in the proper position for transition-state stabilization. Quite, unexpectedly, the structure at 2.6-A resolution of a ternary complex in, which CoA and Lip(SH)2 are simultaneously bound to E2pCD reveals that CoA, has an alternative, nonproductive binding mode. In this abortive ternary, complex, CoA adopts a helical conformation with two intramolecular, hydrogen bonds and the reactive sulfur of the pantetheine arm positioned, 12 A away from the active site residues involved in the transferase, reaction.(ABSTRACT TRUNCATED AT 400 WORDS)
About this StructureAbout this Structure
1EAE is a Single protein structure of sequence from Azotobacter vinelandii with LPM as ligand. Active as Dihydrolipoyllysine-residue acetyltransferase, with EC number 2.3.1.12 Full crystallographic information is available from OCA.
ReferenceReference
Crystallographic analysis of substrate binding and catalysis in dihydrolipoyl transacetylase (E2p)., Mattevi A, Obmolova G, Kalk KH, Teplyakov A, Hol WG, Biochemistry. 1993 Apr 20;32(15):3887-901. PMID:8471601
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