Crystal structure of aspartate decarboxylase at 2.2 Å resolution provides evidence for an ester in protein self–processing

Albert, Armando; Dhanaraj, V.; Genschel, Ulrich; Khan, Gulraiz; Ramjee, Manoj K.; Pulido, Rafael; Sibanda, B. L.; Delft, Frank von; Witty, Michael; Blundell, Tom L.; Smith, Alison G.; Abell, Chris

doi:10.1038/nsb0498-289

Cited by 97 publications

(134 citation statements)

References 23 publications

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“…Although no intermediates have been isolated for AdoMetDC, site-directed mutagenesis experiments showing that replacement of Ser-68 with either Cys or Thr still allow cleavage to generate an ␣ subunit with an amino-terminal ␣-keto acid suggest that it also applies to AdoMetDC (13). Recently, the crystal structure of aspartate 1-decarboxylase has provided further support for this model since, in this case, one of the four active sites was identified not as the finished pyruvoyl enzyme but as the ester intermediate (20).…”

Section: S-adenosylmethionine Decarboxylase (Adometdc)mentioning

confidence: 73%

“…Aspartate 1-decarboxylase from Escherichia coli has an (␣␤) 4 structure in which each ␣␤ unit comprises a six-stranded ␤-barrel capped by small helices at each end. The pyruvates are each placed in a loop connecting two nonadjacent strands within the same ␤-sheet (20). Human AdoMetDC is an (␣␤) 2 tetramer with each ␣␤ unit having a novel four-layer ␣/␤ sandwich fold made up of two antiparallel eight-stranded sheets flanked by several ␣ and 3 10 helices.…”

Section: S-adenosylmethionine Decarboxylase (Adometdc)mentioning

confidence: 99%

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Mechanistic Studies of the Processing of Human S-Adenosylmethionine Decarboxylase Proenzyme

Xiong

Pegg

1999

Journal of Biological Chemistry

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Human S-adenosylmethionine decarboxylase is synthesized as a proenzyme that undergoes an autocatalytic cleavage reaction generating the ␣ and ␤ subunits and forming the pyruvate prosthetic group, which is derived from an internal Ser residue (Ser-68). The mechanism of this processing reaction was studied using sitedirected mutagenesis of conserved residues (His-243 and Ser-229) located close to the cleavage site. Mutant S229A failed to process, and mutant S229C cleaved very slowly, whereas mutant S229T processed normally, suggesting that the hydroxyl group of residue 229 is required for the processing reaction where Ser-229 may act as a proton acceptor. Mutant His-243A cleaved very slowly, forming a small amount of the correctly processed pyruvoyl enzyme but a much larger proportion of the ␣ subunit with an amino-terminal Ser. The cleavage to form the latter was greatly enhanced by hydroxylamine. This result suggests that the N-O acyl shift needed for ester formation occurs normally in this mutant but that the next step, which is a ␤-elimination reaction leading to the two subunits, does not occur. His-243 may therefore act as the basic residue that extracts the hydrogen of the ␣-carbon of Ser-68 in the ester in order to facilitate this reaction. The availability of the recombinant H243A S-adenosylmethionine decarboxylase proenzyme provides a useful model system to examine the processing reaction in vitro and test the design of specific inactivators aimed at blocking the production of the pyruvoyl prosthetic group. S-Adenosylmethionine decarboxylase (AdoMetDC)1 is an essential enzyme for the biosynthesis of polyamines (1-4) and is one of a small class of enzymes that use a covalently bound pyruvate as a prosthetic group (5, 6). Four of these enzymes, histidine decarboxylase (HisDC), phosphatidylserine decarboxylase, aspartate-1-decarboxylase (AspDC), and AdoMetDC are decarboxylases forming important biological amines. All of these enzymes are known to have the pyruvoyl prosthetic group attached via an amide linkage to the amino terminus of the ␣ subunit. Two other enzymes that contain a similar bound pyruvate prosthetic group are D-proline reductase and glycine reductase. Although these enzymes were originally reported to contain the pyruvate in an ester linkage, recent studies have also demonstrated its presence bound to the amino terminus of one of the subunits by an amide bond (7,8).All of the known pyruvoyl enzymes are synthesized in a proenzyme form. In the case of the four decarboxylases described above, it is clear that the source of the pyruvate is an internal Ser residue and that an autocatalytic cleavage reaction occurs to generate the pyruvate and the ␣ and ␤ subunits. Site-directed mutagenesis of this Ser residue in the proenzyme has shown that changing it to Ala completely prevents the processing and the formation of active enzyme (9 -11). Replacement with Cys allows processing and pyruvate formation to occur although at a slower rate (11-13). Although it has been studied in less detail, it appears ...

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Section: S-adenosylmethionine Decarboxylase (Adometdc)mentioning

confidence: 73%

Section: S-adenosylmethionine Decarboxylase (Adometdc)mentioning

confidence: 99%

Mechanistic Studies of the Processing of Human S-Adenosylmethionine Decarboxylase Proenzyme

Xiong

Pegg

1999

Journal of Biological Chemistry

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“…In most cases, the cofactor pyridoxal 5Ј-phosphate has been shown to catalyze the same decarboxylations, either in the context of an analogous enzyme or in solution, paired with a metal cation (34,36). Crystallographic studies show unrelated topologies for the pyruvoyl group containing histidine decarboxylase, aspartate-1-decarboxylase, and human AdoMetDCs (2,10,20). Although eucaryal AdoMetDCs are highly similar to one another and previously identified bacterial AdoMetDCs are quite similar among themselves, these two groups are dissimilar to each other and may not be homologous.…”

mentioning

confidence: 84%

S -Adenosylmethionine Decarboxylase from the Archaeon Methanococcus jannaschii : Identification of a Novel Family of Pyruvoyl Enzymes

et al. 2000

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Polyamines are present in high concentrations in archaea, yet little is known about their synthesis, except by extrapolation from bacterial and eucaryal systems. S-Adenosylmethionine (AdoMet) decarboxylase, a pyruvoyl group-containing enzyme that is required for spermidine biosynthesis, has been previously identified in eucarya and Escherichia coli. Despite spermidine concentrations in the Methanococcales that are several times higher than in E. coli, no AdoMet decarboxylase gene was recognized in the complete genome sequence of Methanococcus jannaschii. The gene encoding AdoMet decarboxylase in this archaeon is identified herein as a highly diverged homolog of the E. coli speD gene (less than 11% identity). The M. jannaschii enzyme has been expressed in E. coli and purified to homogeneity. Mass spectrometry showed that the enzyme is composed of two subunits of 61 and 63 residues that are derived from a common proenzyme; these proteins associate in an (␣␤) 2 complex. The pyruvoyl-containing subunit is less than one-half the size of that in previously reported AdoMet decarboxylases, but the holoenzyme has enzymatic activity comparable to that of other AdoMet decarboxylases. The sequence of the M. jannaschii enzyme is a prototype of a class of AdoMet decarboxylases that includes homologs in other archaea and diverse bacteria. The broad phylogenetic distribution of this group suggests that the canonical SpeD-type decarboxylase was derived from an archaeal enzyme within the gamma proteobacterial lineage. Both SpeD-type and archaeal-type enzymes have diverged widely in sequence and size from analogous eucaryal enzymes.Polyamines are ubiquitous small molecules that are found at high concentrations in most organisms (7,16,30). They appear to stabilize molecular complexes, such as ribosomes, and to facilitate protein-nucleic acid interactions. Deregulation or inhibition of polyamine synthesis broadly affects the eucaryal cell cycle, making these enzymes attractive targets for drug therapy against cancer and parasitic infections (15).Mesophilic species of the Methanococcales group of methanogenic euryarchaea contain substantial concentrations of three common polyamines: putrescine (0.5 to 3.4 mol/g), 1,3-diaminopropane (0.3 mol/g), and spermidine (29 to 40 mol/g) (27). Putrescine, the diamine precursor to spermidine, is produced either by the single enzyme ornithine decarboxylase or by the consecutive actions of arginine decarboxylase and agmatine ureohydrolase. Spermidine synthase catalyzes the transfer of a propylamine moiety to putrescine, producing spermidine, a triamine.The most unusual feature of spermidine biosynthesis is the nature of the propylamine donor, decarboxylated S-adenosylmethionine (AdoMet) (35). AdoMet plays a central role in the metabolism of all known organisms (31). AdoMet is best known as an activated methyl donor used by cells to modify DNA, RNA, proteins, cofactors, lipids, etc. In addition, eucaryotes, some bacteria, and the crenarchaeon Sulfolobus solfataricus have been shown to contain AdoMet...

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“…The decarboxylase is translated as an inactive pro-protein (π-protein) of 13.8 kDa which subsequently undergoes an intramolecular rearrangement and is self-cleaved at the Gly24-Ser25 bond (103) to a mature form which has a β-chain (2.8 kDa) with a hydroxyl group at its C-terminus and an α-chain (11 kDa) which becomes activated by formation of the pyruvoyl group at its N-terminus. The α-and β-chains associate together and constitute a subunit of the tetramer (3,71). A crystal structure of the tetramer shows three cleaved subunits containing pyruvoyl moieties and one subunit with the ester intermediate.…”

Section: β-Alanine Biosynthesismentioning

confidence: 99%

Biosynthesis of Pantothenic Acid and Coenzyme A

Leonardi¹,

Jackowski²

2007

EcoSal

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Crystal structure of aspartate decarboxylase at 2.2 Å resolution provides evidence for an ester in protein self–processing

Cited by 97 publications

References 23 publications

Mechanistic Studies of the Processing of Human S-Adenosylmethionine Decarboxylase Proenzyme

Mechanistic Studies of the Processing of Human S-Adenosylmethionine Decarboxylase Proenzyme

S -Adenosylmethionine Decarboxylase from the Archaeon Methanococcus jannaschii : Identification of a Novel Family of Pyruvoyl Enzymes

Biosynthesis of Pantothenic Acid and Coenzyme A

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