Restricted Motion of the Lipoyl-Lysine Swinging Arm in the Pyruvate Dehydrogenase Complex of <i>Escherichia coli</i><sup>,</sup>

Jones, D. Dafydd; Stott, Katherine; Howard, Mark J.; Perham, Richard N.

doi:10.1021/bi992978i

Cited by 60 publications

(86 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The reason for this is not known but multiple cross-peaks have also been observed when the lipoylated domain (E2plip holo ) is reductively acetylated (Jones et al, 2000a). One possible explanation is that the E2plip apo domain undergoes a conformational change on binding to the substrate-loaded E1p and that this``new'' conformation is in slow exchange with one or more other conformations.…”

Section: Discussionmentioning

confidence: 99%

“…An interesting feature of some of these residues, most notably Ile10, Gly12, Glu14, Thr36, Gly62 and Gly68, is that they were not affected by the presence or absence of pyruvate in the interaction of the E2plip apo domain (Figures 1 and 3). What they have in common is that they also undergo a signi®cant change in chemical shift upon lipoylation of the domain (Jones et al, 2000a). Thus, the chemical shift changes observed for these residues in the presence of E1p may simply re¯ect an interaction of the lipoyl group with E1p.…”

Section: Discussionmentioning

confidence: 99%

“…Lipoylation causes signi®-cant changes in chemical shift and the backbone dynamics of residues in the lipoyl-lysine b-turn, implying some potentially important interactions between the domain and the lipoyl-lysine sidechain (Jones et al, 2000a).…”

Section: The Interaction Of E2plip Holo With E1pmentioning

confidence: 99%

“…The nuclear magnetic resonance (NMR) solution structures of the single E. coli E2o (Ricaud et al, 1996) and the innermost of the three E. coli E2p (Jones et al, 2000a) lipoyl domains have been solved, as have those of others from various other organisms (Dardel et al, 1993;Berg et al, 1996Berg et al, , 1997Howard et al, 1998). Their overall backbone structure is virtually identical, comprising a b-barrel formed from two four-stranded b-sheets.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Recognition of the lipoyl domain is the ultimate determinant of substrate channelling in the pyruvate dehydrogenase multienzyme complex

Jones

Stott

Reche

et al. 2001

Journal of Molecular Biology

View full text Add to dashboard Cite

Reductive acetylation of the lipoyl domain (E2plip) of the dihydrolipoyl acetyltransferase component of the pyruvate dehydrogenase multienzyme complex of Escherichia coli is catalysed speci®cally by its partner pyruvate decarboxylase (E1p), and no productive interaction occurs with the analogous 2-oxoglutarate decarboxylase (E1o) of the 2-oxoglutarate dehydrogenase complex. Residues in the lipoyl-lysine b-turn region of the unlipoylated E2plip domain (E2plip apo ) undergo signi®cant changes in both chemical shift and transverse relaxation time (T 2 ) in the presence of E1p but not E1o. Residue Gly11, in a prominent surface loop between b-strands 1 and 2 in the E2plip domain, was also observed to undergo a signi®cant change in chemical shift. Addition of pyruvate to the mixture of E2plip apo and E1p caused larger changes in chemical shift and the appearance of multiple cross-peaks for certain residues, suggesting that the domain was experiencing more than one type of interaction. Residues in both b-strands 4 and 5, together with those in the prominent surface loop and the following b-strand 2, appeared to be interacting with E1p, as did a small patch of residues centred around Glu31. The values of T 2 across the polypeptide chain backbone were also lower than in the presence of E1p alone, suggesting that E2plip apo binds more tightly after the addition of pyruvate. The lipoylated domain (E2plip holo ) also exhibited signi®cant changes in chemical shift and decreases in the overall T 2 relaxation times in the presence of E1p, the residues principally affected being restricted to the half of the domain that contains the lipoyl-lysine (Lys41) residue. In addition, small chemical shift changes and a general drop in T 2 times in the presence of E1o were observed, indicating that E2plip holo can interact, weakly but non-productively, with E1o. It is evident that recognition of the protein domain is the ultimate determinant of whether reductive acetylation of the lipoyl group occurs, and that this is ensured by a mosaic of interactions with the Elp.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: The Interaction Of E2plip Holo With E1pmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Recognition of the lipoyl domain is the ultimate determinant of substrate channelling in the pyruvate dehydrogenase multienzyme complex

Jones

Stott

Reche

et al. 2001

Journal of Molecular Biology

View full text Add to dashboard Cite

show abstract

“…Two of them are biotinyl domains, the C-terminal domain of Escherichia coli biotin carboxyl carrier protein (BCCP) and the biotinyl domain of 1.3 S subunit of transcarboxylase from Propionibacterium shermanii (7)(8)(9)(10). Several structures of lipoyl domains have also been reported (11)(12)(13)(14)(15). All biotinyl domains and lipoyl domains share a very similar overall fold, which is a flattened ␤-barrel formed by two ␤-sheets.…”

mentioning

confidence: 99%

Identification and Solution Structures of a Single Domain Biotin/Lipoyl Attachment Protein from Bacillus subtilis

Cui

Nan

et al. 2006

Journal of Biological Chemistry

View full text Add to dashboard Cite

Protein biotinylation and lipoylation are post-translational modifications, in which biotin or lipoic acid is covalently attached to specific proteins containing biotin/lipoyl attachment domains. All the currently reported natural proteins containing biotin/lipoyl attachment domains are multidomain proteins and can only be modified by either biotin or lipoic acid in vivo. We have identified a single domain protein with 73 amino acid residues from Bacillus subtilis strain 168, and it can be both biotinylated and lipoylated in Escherichia coli. The protein is therefore named as biotin/lipoyl attachment protein (BLAP). This is the first report that a natural single domain protein exists as both a biotin and lipoic acid receptor. The solution structure of apo-BLAP showed that it adopts a typical fold of biotin/lipoyl attachment domain. The structure of biotinylated BLAP revealed that the biotin moiety is covalently attached to the side chain of Lys 35 , and the bicyclic ring of biotin is folded back and immobilized on the protein surface. The biotin moiety immobilization is mainly due to an interaction between the biotin ureido ring and the indole ring of Trp 12 . NMR study also indicated that the lipoyl group of the lipoylated BLAP is also immobilized on the protein surface in a similar fashion as the biotin moiety in the biotinylated protein.The biotin/lipoyl attachment domain (IPR000089) is a signature structural motif, which has a conserved lysine residue that can bind biotin or lipoic acid. This domain can be found in enzymes that require biotin or lipoic acid as cofactor (1). Biotin plays a catalytic role in carboxyl transfer reactions. It is covalently attached to a lysine residue, via an ⑀-amino group, in enzymes such as pyruvate carboxylase, acetyl-CoA carboxylase, and propionyl-CoA carboxylase, etc. (2). This process, called biotinylation, is catalyzed by biotin-protein ligase (BPL) 2 (1, 3).Lipoic acid can serve as cofactor in a variety of proteins, such as E2 acyltransferases (E2p) in the pyruvate dehydrogenase complex and H-protein of the glycine cleavage system (4, 5). It is also covalently bound via an amide linkage to a lysine group. This process, named lipoylation, is catalyzed by lipoate-protein ligase (LPL) (1, 6). It is known that BPLs have broad substrate ranges. Mammalian biotinyl domain can be biotinylated by bacterial BPL and vice versa. The situation for LPLs is also similar (1).The structures of several biotin/lipoyl attachment domains have been determined. Two of them are biotinyl domains, the C-terminal domain of Escherichia coli biotin carboxyl carrier protein (BCCP) and the biotinyl domain of 1.3 S subunit of transcarboxylase from Propionibacterium shermanii (7-10). Several structures of lipoyl domains have also been reported (11-15). All biotinyl domains and lipoyl domains share a very similar overall fold, which is a flattened ␤-barrel formed by two ␤-sheets. The conserved lysine residue is located at the tip of a tight ␤-turn.Although biotinyl and lipoyl domains are quite similar in ...

show abstract

Hydrogen/deuterium exchange for higher specificity of protein identification by peptide mass fingerprinting

Bienvenut¹,

Hoogland²,

Greco³

et al. 2002

Rapid Comm Mass Spectrometry

View full text Add to dashboard Cite

Genome sequencing projects produce large amounts of information that could be translated into potential protein sequences. Such amounts of material continuously increase protein database sizes. At present, 22 times more protein sequences are available in the SWISS-PROT and TrEMBL databases than 8 years ago in SWISS-PROT. One of the methods of choice for protein identification makes use of specific endoproteolytic cleavage followed by matrix-assisted laser desorption/ionisation mass spectrometric (MALDI-MS) analysis of the digested product. Since 1993, when this technique was first demonstrated, the conditions required for a correct identification have changed dramatically. Whilst 4-5 peptides with an uncertainty of 2-3 Da were sufficient for a correct identification in 1993, 10-13 peptides with less than 60 ppm mass error are now required for human and E. coli proteins. This evolution is directly related to the continuous increase in protein database sizes, which causes an increase in the number of false positive matches in identification results. Use of an information complement deduced from the primary protein sequence, in the process of identification by peptide mass fingerprints, can help to increase confidence in the identification results. In this article, we propose the exchange of labile hydrogen atoms with deuterium atoms to provide an alternative information complement. The exchange reaction with optimised techniques has shown an average 95% of hydrogen/deuterium (H/D) exchange on tryptic peptides. This level of exchange was sufficient to single out one or more peptides from a list of potential candidate proteins due to the dependence of H/D exchange on the peptide primary structure. This technique also has clear advantages in the identification of small proteins where direct protein identification is impaired by the limited number of endoproteolytic peptides. Then, information related to primary sequence obtained with this technique could help to identify proteins with high confidence without any expensive tandem mass spectrometry instruments.

show abstract

Restricted Motion of the Lipoyl-Lysine Swinging Arm in the Pyruvate Dehydrogenase Complex of Escherichia coli^,

Cited by 60 publications

References 53 publications

Recognition of the lipoyl domain is the ultimate determinant of substrate channelling in the pyruvate dehydrogenase multienzyme complex

Recognition of the lipoyl domain is the ultimate determinant of substrate channelling in the pyruvate dehydrogenase multienzyme complex

Identification and Solution Structures of a Single Domain Biotin/Lipoyl Attachment Protein from Bacillus subtilis

Hydrogen/deuterium exchange for higher specificity of protein identification by peptide mass fingerprinting

Contact Info

Product

Resources

About

Restricted Motion of the Lipoyl-Lysine Swinging Arm in the Pyruvate Dehydrogenase Complex of Escherichia coli,

Cited by 60 publications

References 53 publications

Recognition of the lipoyl domain is the ultimate determinant of substrate channelling in the pyruvate dehydrogenase multienzyme complex

Recognition of the lipoyl domain is the ultimate determinant of substrate channelling in the pyruvate dehydrogenase multienzyme complex

Identification and Solution Structures of a Single Domain Biotin/Lipoyl Attachment Protein from Bacillus subtilis

Hydrogen/deuterium exchange for higher specificity of protein identification by peptide mass fingerprinting

Contact Info

Product

Resources

About

Restricted Motion of the Lipoyl-Lysine Swinging Arm in the Pyruvate Dehydrogenase Complex of Escherichia coli^,