The role of loop and β-turn residues as structural and functional determinants for the lipoyl domain from the Escherichia coli 2-oxoglutarate dehydrogenase complex

The 2-oxoglutarate dehydrogenase multienzyme complex of Escherichia coli was treated with trypsin at pH 7.0 at 0 degrees C. Loss of the overall catalytic activity was accompanied by rapid cleavage of the lipoate succinyltransferase polypeptide chains, this apparent Mr falling from 50 000 to 36 000 as judged by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis. A slower shortening of the 2-oxoglutarate decarboxylase chains was also observed, whereas the lipoamide dehydrogenase chains were unaffected. The inactive trypsin-treated enzyme had lost the lipoic acid-containing regions of the lipoate succinyltransferase polypeptide chains, yet remained a highly assembled structure, as judged by gel filtration and electron microscopy. The lipoic acid-containing regions are therefore likely to be physically exposed in the complex, protruding from the structural core formed by the lipoate succinyltransferase component between the subunits of the other component enzymes. Proton nuclear magnetic resonance spectroscopy of the 2-oxoglutarate dehydrogenase complex revealed the existence of substantial regions of polypeptide chain with remarkable intramolecular mobility, most of which were retained after removal of the lipoic acid-containing regions by treatment of the complex with trypsin. By analogy with the comparably mobile regions of the pyruvate dehydrogenase complex of E. coli, it is likely that the highly mobile regions of polypeptide chain in the 2-oxoglutarate complex are in the lipoate succinyltransferase component and encompass the lipoyl-lysine residues. It is clear, however, that the mobility of this polypeptide chain is not restricted to the immediate vicinity of these residues.

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Expression and lipoylation in Escherichia coli of the inner lipoyl domain of the E2 component of the human pyruvate dehydrogenase complex

Biochemical Journal ◽

10.1042/bj2890081 ◽

1993 ◽

Vol 289 (1) ◽

pp. 81-85 ◽

Cited By ~ 35

Author(s):

J Quinn ◽

A G Diamond ◽

A K Masters ◽

D E Brookfield ◽

N G Wallis ◽

...

Keyword(s):

Escherichia Coli ◽

Pyruvate Dehydrogenase ◽

Pyruvate Dehydrogenase Complex ◽

Structural Studies ◽

Gene Encoding ◽

E Coli ◽

Inner Lipoyl Domain ◽

Dehydrogenase Complex ◽

Lipoyl Domain

The dihydrolipoamide acetyltransferase subunit (E2p) of mammalian pyruvate dehydrogenase complex has two highly conserved lipoyl domains each modified with a lipoyl cofactor bound in amide linkage to a specific lysine residue. A sub-gene encoding the inner lipoyl domain of human E2p has been over-expressed in Escherichia coli. Two forms of the domain have been purified, corresponding to lipoylated and non-lipoylated species. The apo-domain can be lipoylated in vitro with partially purified E. coli lipoate protein ligase, and the lipoylated domain can be reductively acetylated by human E1p (pyruvate dehydrogenase). Availability of the two forms will now allow detailed biochemical and structural studies of the human lipoyl domains.

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Cross-linking and 1H n.m.r. spectroscopy of the pyruvate dehydrogenase complex of Escherichia coli

Biochemical Journal ◽

10.1042/bj2050389 ◽

1982 ◽

Vol 205 (2) ◽

pp. 389-396 ◽

Cited By ~ 9

Author(s):

Leonard C. Packman ◽

Richard N. Perham ◽

Gordon C. K. Roberts

Keyword(s):

Escherichia Coli ◽

Pyruvate Dehydrogenase ◽

Pyruvate Dehydrogenase Complex ◽

The Other ◽

Random Coil ◽

Cross Linking ◽

Enzyme Complex ◽

Cross Links ◽

Dehydrogenase Complex ◽

Lipoyl Domain

The pyruvate dehydrogenase complex of Escherichia coli was treated with o-phenylene bismaleimide in the presence of the substrate pyruvate, producing almost complete cross-linking of the lipoate acetyltransferase polypeptide chains as judged by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis. This took place without effect on the catalytic activities of the other two component enzymes and with little evidence of cross-links being formed with other types of protein subunit. Limited proteolysis with trypsin indicated that the cross-links were largely confined to the lipoyl domains of the lipoate acetyltransferase component of the same enzyme particle. This intramolecular cross-linking had no effect on the very sharp resonances observed in the 1H n.m.r. spectrum of the enzyme complex, which derive from regions of highly mobile polypeptide chain in the lipoyl domains. Comparison of the spin–spin relaxation times, T2, with the measured linewidths supported the idea that the highly mobile region is best characterized as a random coil. Intensity measurements in spin-echo spectra showed that it comprises a significant proportion (probably not less than one-third) of a lipoyl domain and is thus much more than a small hinge region, but there was insufficient intensity in the resonances to account for the whole lipoyl domain. On the other hand, no evidence was found in the 1H n.m.r. spectrum for a substantial structured region around the lipoyl-lysine residues that was free to move on the end of this highly flexible connection. If such a structured region were bound to other parts of the enzyme complex for a major part of its time, its resonances might be broadened sufficiently to evade detection by 1H n.m.r. spectroscopy.

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The role of loop and β-turn residues as structural and functional determinants for the lipoyl domain from the Escherichia coli 2-oxoglutarate dehydrogenase complex

Biochemical Journal ◽

10.1042/bj20071119 ◽

2007 ◽

Vol 409 (2) ◽

pp. 357-366 ◽

Cited By ~ 12

Author(s):

D. Dafydd Jones ◽

Richard N. Perham

Keyword(s):

Escherichia Coli ◽

Structural Integrity ◽

Pyruvate Decarboxylase ◽

Covalent Attachment ◽

E Coli ◽

Loop Sequence ◽

Equivalent Residue ◽

Oxoglutarate Dehydrogenase ◽

And Function ◽

Lipoyl Domain

The lipoyl domain of the dihydrolipoyl succinyltransferase (E2o) component of the 2OGDH (2-oxoglutarate dehydrogenase) multienzyme complex houses the lipoic acid cofactor through covalent attachment to a specific lysine side chain residing at the tip of a β-turn. Residues within the lipoyl-lysine β-turn and a nearby prominent loop have been implicated as determinants of lipoyl domain structure and function. Protein engineering of the Escherichia coli E2o lipoyl domain (E2olip) revealed that removal of residues from the loop caused a major structural change in the protein, which rendered the domain incapable of reductive succinylation by 2-oxoglutarate decarboxylase (E1o) and reduced the lipoylation efficiency. Insertion of a new loop corresponding to that of the E. coli pyruvate dehydrogenase lipoyl domain (E2plip) restored lipoylation efficiency and the capacity to undergo reductive succinylation returned, albeit at a lower rate. Exchange of the E2olip loop sequence significantly improved the ability of the domain to be reductively acetylated by pyruvate decarboxylase (E1p), retaining approx. 10-fold more acetyl groups after 25 min than wild-type E2olip. Exchange of the β-turn residue on the N-terminal side of the E2o lipoyl-lysine DKA/V motif to the equivalent residue in E2plip (T42G), both singly and in conjunction with the loop exchange, reduced the ability of the domain to be reductively succinylated, but led to an increased capacity to be reductively acetylated by the non-cognate E1p. The T42G mutation also slightly enhanced the lipoylation rate of the domain. The surface loop is important to the structural integrity of the protein and together with Thr42 plays an important role in specifying the interaction of the lipoyl domain with its partner E1o in the E. coli 2OGDH complex.

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A comparative study of the regulation of Ca2+ of the activities of the 2-oxoglutarate dehydrogenase complex and NAD+-isocitrate dehydrogenase from a variety of sources

Biochemical Journal ◽

10.1042/bj1960619 ◽

1981 ◽

Vol 196 (2) ◽

pp. 619-624 ◽

Cited By ~ 65

Author(s):

J G McCormack ◽

R M Denton

Keyword(s):

Escherichia Coli ◽

Comparative Study ◽

Isocitrate Dehydrogenase ◽

Human Heart ◽

Flight Muscle ◽

Rat Tissues ◽

Similar Extent ◽

E Coli ◽

Oxoglutarate Dehydrogenase ◽

Dehydrogenase Complex

Ca2+ was shown to activate oxoglutarate dehydrogenase and NAD+-isocitrate dehydrogenase from heart and other rat tissues by markedly decreasing the Km values of the enzymes for their respective substrates [see Denton & McCormack (1980) FEBS Lett. 119, 1-8]. Similar effects of Ca2+ were observed in the present study with both enzymes from other vertebrate sources (pigeon, trout, frog and human heart), but not with the enzymes from blowfly or locust flight muscle, or potato or Escherichia coli. In contrast, the Km values of the oxoglutarate dehydrogenases were affected by ADP, ATP and H+ to a similar extent in every case, except for the enzyme from E. coli, which was not sensitive to regulation by these agents.

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Lipoylation of the E2 components of the 2-oxo acid dehydrogenase multienzyme complexes of Escherichia coli

Biochemical Journal ◽

10.1042/bj2770153 ◽

1991 ◽

Vol 277 (1) ◽

pp. 153-158 ◽

Cited By ~ 8

Author(s):

L C Packman ◽

B Green ◽

R N Perham

Keyword(s):

Escherichia Coli ◽

Pyruvate Dehydrogenase ◽

Catalytic Mechanism ◽

Chemical Reduction ◽

Pyruvate Dehydrogenase Complex ◽

Exchange Chromatography ◽

Lysine Residue ◽

Multienzyme Complex ◽

Dehydrogenase Complex ◽

Lipoyl Domain

The number of functional lipoyl groups in the dihydrolipoyl acetyltransferase (E2) chain of the pyruvate dehydrogenase multienzyme complex from Escherichia coli has been re-assessed by means of a combination of protein-chemical and mass-spectrometric techniques. (1) After the complex had been treated with N-ethyl[2,3-14C]maleimide in the presence of pyruvate, the lipoyl domains were excised from the complex, treated with NaBH4 and re-exposed to N-ethyl[2,3-14C]maleimide. All the chemically reactive lipoyl groups in the native complex were found to be catalytically active. (2) Proteolytic digests of the separated lipoyl domains were examined for the presence of the lipoylation-site peptide, GDKASME, with and without the lipoyl group in N6-linkage to the lysine residue. Only the lipoylated form of the peptide was detected, suggesting that all three lipoyl domains are fully substituted at this site. (3) The behaviour of each lipoyl domain was examined on ion-exchange chromatography in response to alkylation with 4-vinylpyridine after either chemical reduction of the lipoyl group with dithiothreitol or reductive acetylation by the pyruvate dehydrogenase complex in the presence of pyruvate. All three domains exhibited a quantitative shift in retention time, confirming that each domain was fully substituted by an enzymically reactive lipoyl group. (4) When subjected to electrospray mass spectrometry, each domain gave a mass consistent with a fully lipoylated domain, and no aberrant substitution of the target lysine residue was detected. The same result was obtained for the lipoyl domain from the E. coli 2-oxoglutarate dehydrogenase complex. (5) Previous widespread attempts to assess the number of functional lipoyl groups in the pyruvate dehydrogenase multienzyme complex, which have led to the view that a maximum of two lipoyl groups per E2 chain may be involved in the catalytic mechanism, are in error.

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