Bovine Kidney Pyruvate Dehydrogenase Complex Research Articles

The remarkable structural and functional organization of the eukaryotic pyruvate dehydrogenase complexes.

The three-dimensional reconstruction of the bovine kidney pyruvate dehydrogenase complex (M(r) approximately 7.8 x 10(6)) comprising about 22 molecules of pyruvate dehydrogenase (E(1)) and about 6 molecules of dihydrolipoamide dehydrogenase (E(3)) with its binding protein associated with the 60-subunit dihydrolipoamide acetyltransferase (E(2)) core provides considerable insight into the structural and functional organization of the largest multienzyme complex known. The structure shows that potentially 60 centers for acetyl-CoA synthesis are organized in sets of three at each of the 20 vertices of the pentagonal dodecahedral core. These centers consist of three E(1) molecules bound to one E(2) trimer adjacent to an E(3) molecule in each of 12 pentagonal openings. The E(1) components are anchored to the E(1)-binding domain of the E(2) subunits through an approximately 50-A-long linker. Three of these linkers emanate from the outside edges of the triangular base of the E(2) trimer and form a cage around its base that may shelter the lipoyl domains and the E(1) and E(2) active sites. The docking of the atomic structures of E(1) and the E(1) binding and lipoyl domains of E(2) in the electron microscopy map gives a good fit and indicates that the E(1) active site is approximately 95 A above the base of the trimer. We propose that the lipoyl domains and its tether (swinging arm) rotate about the E(1)-binding domain of E(2,) which is centrally located 45-50 A from the E(1), E(2), and E(3) active sites, and that the highly flexible breathing core augments the transfer of intermediates between active sites.

Additional binding sites for the pyruvate dehydrogenase kinase but not for protein X in the assembled core of the mammalian pyruvate dehydrogenase complex: Binding region for the kinase

A standard resolution of the bovine kidney pyruvate dehydrogenase complex yields a subcomplex composed of ~60 dihydrolipoyl transacetylase (E2) subunits, ~6 protein X subunits, and ~2 pyruvate dehydrogenase kinase heterodimers (K cK b). Using a preparation of resolved kinase in which K c ⪢ K b, E2-X-K cK b subcomplex additionally bound at least 15 catalytic subunits of the kinase (K c) and a much lower level of K b. The binding of K c to E2 greatly enhanced kinase activity even at high levels of bound kinase. Free protein X, functional in binding the E3 component, did not bind to E2-X-K cK b subcomplex. This pattern of binding K c but not protein X was unchanged either with a preparation of E2 oligomer greatly reduced in protein X or with subcomplex from which the lipoyl domain of protein X was selectively removed. The bound inner domain of protein X associated with the latter subcomplex did not exchange with free protein X. These data support the conclusion that E2 subunits bind the K c subunit of the kinase and suggest that the binding of the inner domain of protein X to the inner domain of the transacetylase occurs during the assembly of the oligomeric core. Selective release of a fragment of E2 subunits that contain the lipoyl domains (E2 l fragment) releases the kinase (M. Rahmatullah et al., 1990, J. Biol. Chem. 265, 14,512–14,517). Sucrose gradient centrifugation yielded an E2 l -kinase fraction with an increased ratio of the kinase to E2 l fragment. A monoclonal antibody specific for E2 l was attached to a gel matrix. Binding of E2 l fragment also led to specific binding of the kinase. Extensive washing did not reduce the level of bound kinase. Thus, the kinase is tightly bound by the lipoyl domain region of E2.

Rat liver mitochondria contain two immunologically distinct dihydrolipoamide dehydrogenases

We have raised antisera against dihydrolipoamide dehydrogenase. One antigen was isolated from purified bovine kidney pyruvate dehydrogenase complex (PDC). The other antigen was a commercial preparation of porcine heart dihydrolipoamide dehydrogenase (E 3) which did not first involve purification of the α-keto acid dehydrogenase complex(es). Both antibody preparations cross-reacted with the E 3 components of PDC, α-ketoglutarate dehydrogenase complex, and branched-chain keto acid dehydrogenase complex. This demonstrates the immunological identity of the E 3 components. These sera totally precipitated E 3 activity from the purified complexes, from purified preparations of E 3, and from extracts of rat heart and kidney mitochondria. The two sera vary in their reaction with rat liver mitochondrial extracts: the anti PDC-E 3 serum left residual E 3 activity (approximately 50% of the original) that was precipitable by the anti-E 3 antiserum. This indicates that liver contains two immunologically distinct forms of E 3. Metabolic assays measuring the differential effects of the two sera on the glycine decarboxylation reaction suggest that the form which is immunologically nonreactive with the anti-PDC-E 3 serum could represent the E 3 involved in the glycine cleavage System.

Properties of a newly characterized protein of the bovine kidney pyruvate dehydrogenase complex.

The dihydrolipoyl transacetylase component, which serves as the structural core of mammalian pyruvate dehydrogenase complexes, is acetylated when treated with either pyruvate or with acetyl-CoA in the presence of NADH. Besides the dihydrolipoyl transacetylase component, we have found that another protein, referred to as protein X, is rapidly acetylated at thiol residues. Protein X remains fully bound to the transacetylase core under conditions that remove the pyruvate dehydrogenase and dihydrolipoyl dehydrogenase components. Mapping of 125I-tryptic peptides indicated that the transacetylase subunits and protein X are structurally distinct; however, under the same mapping conditions, there is considerable similarity in the positions of acetylated peptides derived from these subunits. Affinity-purified rabbit immunoglobulin G prepared against the dihydrolipoyl transacetylase core reacted exclusively with the transacetylase and with both its tryptic-derived inner domain and outer lipolyl-bearing domain. Those results further indicate that protein X is not derived from the transacetylase subunit Affinity-purified mouse antibody to protein X reacted selectively with large tryptic polypeptides derived from protein X and did not react with the inner domain of the transacetylase. However, the anti-protein X antibody did react with the intact transacetylase subunit, the lipoyl-bearing domain of the transacetylase, and weakly with the transsuccinylase component of the alpha-ketoglutarate dehydrogenase complex. This cross-reactivity reflected specificity of a portion of the polyclonal antibodies for a related structural region in the transacetylase and protein X (possibly a similar lipoyl-bearing region). Furthermore, a major portion of that polyclonal antibody was shown to react exclusively with protein X. Thus, protein X subunits differ substantially from transacetylase subunits but the two components have a region of structural similarity. We estimate that there are about 5 mol of protein X per mol of the kidney pyruvate dehydrogenase complex. Under a variety of conditions that result in a wide range of levels of acetylation of sites in the complex, about 1 acetyl group is incorporated into protein X per 10 acetyl groups incorporated into the transacetylase subunits per mol of complex. That ratio is close to the ratio of protein X subunits of transacetylase subunits in the complex, indicating that there are efficient mechanisms for acylation and deacylation of protein X.

Specificity of the pyruvate dehydrogenase kinase for pyruvate dehydrogenase component bound to the surface of the kidney pyruvate dehydrogenase complex and evidence for intracore migration of pyruvate dehydrogenase component.

Using the bovine kidney pyruvate dehydrogenase complex we have investigated the mechanism whereby about three pyruvate dehydrogenase (active form) kinase molecules, tightly bound to the dihydrolipoyl transacetylase core, can rapidly phosphorylate and inactivate about 20 pyruvate dehydrogenase (active form) (PDHa) tetramers which are also bound to the 60-subunit core. Evidence is presented that PDHa kinase activity is not serviced by a process of dissociation and reassociation of PDHa. Rapid inactivation of a full complement of PDHa occurs at a rate exceeding the rate of dissociation of PDHa, indicating that a PDHa must move to the fixed kinase subunits without dissociating from the dihydrolipoyl transacetylase core. Consistent with that concept, at low concentrations of complex where a significant portion of PDHa is free, bound PDHa was inactivated at a rate equivalent to that at higher concentrations of complex, and free PDHa was phosphorylated more slowly at a rate closely approximated by the rate of association of free PDHa with the transacetylase core. Thus, with a low number of PDHa molecules bound, PDHa either is preferentially positioned for phosphorylation and inactivation by PDHa kinase or can rapidly become so positioned without dissociating from the transacetylase core.

Heterogeneity of binding sites for the pyruvate dehydrogenase component on the dihydrolipoyl transacetylase core of bovine kidney pyruvate dehydrogenase complex.

We have characterized the dissociation equilibrium constant (Kd) and the rate constants of association and dissociation for the binding of the pyruvate dehydrogenase component (PDH) to the dihydrolipoyl transacetylase component of kidney pyruvate dehydrogenase complex. We have found about 7 high-affinity sites (Kd = 1.5 X 10(-11) M) and about 13 low-affinity sites (Kd = 2.5 X 10(-8) M) with negative cooperativity for binding of PDH at the weaker sites. The high-affinity sites show a much higher rate constant for association of PDH with the core than do the low-affinity sites. Catalytic turnover strengthens binding of PDH at high-affinity sites when the complex is preincubated in the presence of thiamin pyrophosphate (TPP). In the absence of TPP, appreciably tighter binding occurs at the low-affinity sites (Kd = 5.9 X 10(-10) M). TPP weakens PDH binding at these sites with a half-maximal effect at about 5 microM TPP. In addition to TPP, increased ionic strength or 1-3 mM Mg2+ (with an enhanced effect of Mg2+ at higher ionic strengths) weakens PDH binding at low-affinity sites with a corresponding increase in the rate constant for dissociation. Further studies will be required to determine whether site heterogeneity contributes to dynamic processes in the function and regulation of the pyruvate dehydrogenase complex.

Bovine Kidney Pyruvate Dehydrogenase Complex

1. Bovine kidney pyruvate dehydrogenase multienzyme complex is inactivated by elastase in a similar manner as described earlier for papain. The core component, lipoate acetyltransferase, is cleaved by elastase into an active fragment (Mr 26000) and a fragment with apparent Mr of 45000 as analyzed by dodecylsulfate gel electrophoresis. Due to the fragmentation of the core, the enzyme complex is disassembled into its component enzymes which retain their complete enzymatic activities as assayed separately. 2. A different mechanism was found for the inactivation of pyruvate dehydrogenase complex with trypsin and some other proteases (chymotrypsin, clostripain). In these cases, the pyruvate dehydrogenase component is inactivated rapidly by limited proteolysis. More slowly, the enzyme complex is disassembled simultaneously with fragmentation of the lipoate acetyltransferase which again results in an active fragment of Mr 26000 and another fragment of apparent Mr 45000. Upon prolonged proteolysis, the latter fragment is cleaved further to give products of Mr 36000 or lower. 3. The enzyme-bound lipoyl residues of the pyruvate dehydrogenase complex have been labelled covalently by incubation with [2-14C]pyruvate. After treatment of this [14C]acetyl-enzyme with papain, elastase, or trypsin, radioactivity was associated exclusively with the 45000-Mr and 36000-Mr fragments but not with the active 26000-Mr fragment. 4. It is concluded that the bovine kidney lipoate acetyltransferase core is composed of 60 subunits each consisting of two dissimilar folding domains. One of these contains the intersubunit binding sites as well as the active center for transacylation whereas the other possesses the enzyme-bound lipoyl residues.

Evidence for two-domain subunit structure of kidney lipoate acetyltransferase

1. Introduction Earlier studies on the inactivation of the mamma- lian pyruvate dehydrogenase (EC 1.2.4.1 f complex (PHD complex) by a thiol protease from rat liver [I] had shown that the lipoate acetyltransferase (EC 2.3.1 .12) was cleaved into two smaller fragments detectable on SDS-polyacryla~de gel electrophoresis [ 1,2]. Here we have studied the subunit structure of kidney lipoate acetyitransferase using trypsin (EC 3.4.21.4) which was found to yield also twa fragments with app. mol. wt 36 000 and 28 000. As will be shown here both fragments possess about equal catalytic activity for acetyl transfer, and each appar- ently contains p~ote~-bound lipoamide ~~est~g that the subunit of the mammalian lipoate acetyltransferase consists of two homologous if not identical domains. 2, Mate&Is and methods Bovine kidney pyruvate dehydrogenase complex (spec. act. 16-20 units/mg protein) was prepared by poly(ethylene glycol) precipitation [2] with some mo~~ca~ons to be detailed elsewhere. Lipoaie ace- tyltransferase was resolved according to [Z]. Marker proteins for molecular weight determination (LMW nrotein standards) were from Bio-Rad Labs., CA and poly(ethylene glycol) 6000 from Serva, Heidelberg. Bovine pancreatic trypsin (30 U/m&, other enzymes or eoenzymes came from ~oe~~ger~ Manner. Radiochemicals were purchased from New England Nuclear, Chicago. Laboratory chemicals, analytical grade, were from Merck,

Bovine kidney pyruvate dehydrogenase complex. Isolation of the component enzymes after limited proteolysis with papain.

1. Bovine kidney pyruvate dehydrogenase multienzyme complex is inactivated rapidly by papain. However, none of the component activities of the complex is destroyed during inactivation of the overall reaction. 2. The core component, lipoate acetyltransferase, is cleaved by papain to give principal fragments with Mr 26,500 and 26,000 (as determined by dodecylsulfate gel electrophoresis). Much more slowly, the alpha chain of the pyruvate dehydrogenase component is attacked. 3. Fragmented lipoate acetyltransferase retains its complete enzymatic activity and remains of high molecular weight. It is unable, however, to bind the other component enzymes, pyruvate dehydrogenase and lipoamide dehydrogenase. Therefore, the multienzyme complex is disassembled when treated with papain. 4. A method is described which allows the rapid and convenient isolation of nicked lipoate acetyltransferase as well as unfragmented pyruvate dehydrogenase and lipoamide dehydrogenase from papain-treated complex under very mild conditions. The two uncleaved component enzymes have identical properties and similar specific activities as enzyme preparations obtained by other, more laborious procedures.

Effect of micromolar Ca2+ on NADH inhibition of bovine kidney alpha-ketoglutarate dehydrogenase complex and possible role of Ca2+ in signal amplification.

NADH inhibition of bovine kidney alpha-ketoglutarate dehydrogenase complex was compared at 10 microM free Ca2+ or in the absence of Ca2+ (i.e., less than 1.0 nM free Ca2+). In the presence of Ca2+, NADH inhibition was appreciably decreased for a wide range of NADH:NAD+ ratios. A half-maximal decrease in NADH inhibition occurred at slightly less than 1 microM free Ca/+ (as determined with EGTA-Ca buffers). Of necessity this was observed on top of an effect of Ca2+ on the S0.5 for alpha-ketoglutarate which was decreased by Ca2+ with a half-maximal effect at a similar concentration. The effect of Ca2+ on NADH inhibition was not observed in assays of the dihydrolipoyl dehydrogenase component (using dihydrolipoamide as a substrate) or in assays of bovine kidney pyruvate dehydrogenase complex. This indicates that the overall reaction catalyzed by the alpha-ketoglutarate dehydrogenase complex is required to elicit the effect of Ca2+ on NADH inhibition. At a fixed alpha-ketoglutarate concentration (50 microM), removal of Ca2+ reduced the activity of the alpha-ketoglutarate dehydrogenase complex by 8.5-fold (due to an increase in S0.5 for alpha-ketoglutarate) and, in the presence of different NADH:NAD+ ratios, decreased the activity of the complex by 50 to 100-fold. Effects of the phosphate potential (ATP/ADPxPi) or a combination of the phosphate potential and NADH:NAD+ ratio are also described. The possibility that the level of intramitochondrial free Ca/+ serves as a signal amplifier normally coupled to the energy state of mitochondria is discussed.

An improved procedure for the assay of pyruvate dehydrogenase

A modified procedure for the determination of the decarboxylation of [1- 14C]pyruvate by pyruvate dehydrogenase is described which requires only small amounts of bovine kidney pyruvate dehydrogenase complex. The activity is greatly increased by the addition of high concentrations of ferricyanide.

Binding of thiamin thiazolone pyrophosphate to mammalian pyruvate dehydrogenase and its effects on kinase and phosphatase activities

The pyruvate dehydrogenase component of the bovine kidney pyruvate dehydrogenase complex has two thiamin-PP binding sites per α 2 β 2 tetramer. Titration of these binding sites with the transition state analog, thiamin thiazolone pyrophosphate, strongly inhibits phosphorylation of pyruvate dehydrogenase by pyruvate dehydrogenase kinase and ATP. The analog has little effect, if any, on dephosphorylation of phosphorylated pyruvate dehydrogenase by pyruvate dehydrogenase phosphatase. Phosphorylation of pyruvate dehydrogenase inactivates the enzyme, but does not significantly affect the thiamin-PP binding sites. It appears that phosphorylation produces a conformational change in pyruvate dehydrogenase that displaces a catalytic group (or groups) at the active center.

Function of the nonidentical subunits of mammalian pyruvate dehydrogenase

The pyruvate dehydrogenase (PDH) component of the bovine kidney pyruvate dehydrogenase complex (PDC) contains two nonidentical subunits. PDH catalyzes the decarboxylation of pyruvate to produce α-hydroxyethylthiamine-PP (HETPP) and the reductive acetylation of the lipoyl moieties of dihydrolipoyl transacetylase with HETPP. Phosphorylation of PDH with PDH kinase and ATP markedly inhibits the first reaction but does not inhibit the second reaction. Since the α-subunit but not the β-subunit of PDH undergoes phosphorylation, these results suggest that the α-subunit catalyzes the first reaction and the β-subunit catalyzes the second reaction. Thiamine-PP reduces the rate of phosphorylation of PDC by PDH kinase and ATP. Phosphorylation of PDC increases the K D of the PDC-Mg-thiamine-PP complex about 12-fold. It appears that the thiamine-PP binding site and the phosphorylation site on PDH influence each other and that HETPP is bound to PDH in a different orientation or possibly at a different site than is thiamine-PP.