- Atomic-Resolution 1.3 ? Crystal Structure, Inhibition by Sulfate, and Molecular Dynamics of the Bacterial Enzyme DapE
-
We report the atomic-resolution (1.3 ?) X-ray crystal structure of an open conformation of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE, EC 3.5.1.18) from Neisseria meningitidis. This structure [Protein Data Bank (PDB) entry 5UEJ] contains two bound sulfate ions in the active site that mimic the binding of the terminal carboxylates of the N-succinyl-l,l-diaminopimelic acid (l,l-SDAP) substrate. We demonstrated inhibition of DapE by sulfate (IC50 = 13.8 ± 2.8 mM). Comparison with other DapE structures in the PDB demonstrates the flexibility of the interdomain connections of this protein. This high-resolution structure was then utilized as the starting point for targeted molecular dynamics experiments revealing the conformational change from the open form to the closed form that occurs when DapE binds l,l-SDAP and cleaves the amide bond. These simulations demonstrated closure from the open to the closed conformation, the change in RMS throughout the closure, and the independence in the movement of the two DapE subunits. This conformational change occurred in two phases with the catalytic domains moving toward the dimerization domains first, followed by a rotation of catalytic domains relative to the dimerization domains. Although there were no targeting forces, the substrate moved closer to the active site and bound more tightly during the closure event.
- Kochert, Matthew,Nocek, Boguslaw P.,Habeeb Mohammad, Thahani S.,Gild, Elliot,Lovato, Kaitlyn,Heath, Tahirah K.,Holz, Richard C.,Olsen, Kenneth W.,Becker, Daniel P.
-
p. 908 - 917
(2021/04/07)
-
- Synthesis of characteristic Mycobacterium peptidoglycan (PGN) fragments utilizing with chemoenzymatic preparation of meso-diaminopimelic acid (DAP), and their modulation of innate immune responses
-
Peptidoglycan (PGN) is a major component of bacterial cell wall and is recognized as a potent immunostimulant. The PGN in the cell envelope of Mycobacterium Tuberculosis has been shown to possess several unique characteristics including the presence of N-glycolyl groups (in addition to N-acetyl groups) in the muramic acid residues, and amidation of the free carboxylic acid of d-Glu or of meso-DAP in the peptide chains. Using a newly developed, highly stereoselective, chemoenzymatic approach for the synthesis of meso-DAP in peptide stems, we successfully synthesized for the first time, a series of Mycobacterium PGN fragments that include both mono- and disaccharides of MurNGlyc or 1,6-anhydro-MurNGlyc, as well as peptide-amidated variants. The ability of these PGN fragments to stimulate the immune system through activation of human Nod1 and Nod2 was examined. The PGN fragments were found to modulate immune stimulation, specifically, amidation at the d-Glu and meso-DAP in the peptide stem strongly reduced hNod1 activation. This effect was dependent on modification position. Additionally, N-glycolyl (instead of acetyl) of muramic acid was associated with slightly reduced human Nod1 and Nod2 stimulatory capabilities.
- Wang, Qianqian,Matsuo, Yusuke,Pradipta, Ambara R.,Inohara, Naohiro,Fujimoto, Yukari,Fukase, Koichi
-
supporting information
p. 1013 - 1023
(2016/01/15)
-
- Synthesis of bis-α,α′-amino acids through diastereoselective bis-alkylations of chiral Ni(ii)-complexes of glycine
-
The Ni(ii) complex derived from glycine Schiff base with (S)-N-(benzylprolyl)-2-aminobenzophenone can be effectively alkylated with α,ω-dibromide reagents to furnish the corresponding bis-alkylated products. This method presents a direct approach for the preparation of the corresponding bis-α,α′-amino acids with high biological importance. Heterogeneous (phase-transfer) as well as homogeneous conditions for the alkylation reactions have been investigated and the latter proved to be more efficient in terms of stereochemical outcome. In particular, alkylation of the glycine Schiff base Ni(ii) complex with 1,3-dibromopropane followed by acid-catalysed hydrolysis of the resulting bis-alkylation product, allowed for the preparation of naturally occurring (2S,6S)-diaminopimelic acid in high overall yield. The Royal Society of Chemistry 2013.
- Wang, Jiang,Liu, Hong,Ace?a, José Luis,Houck, Daniel,Takeda, Ryosuke,Moriwaki, Hiroki,Sato, Tatsunori,Soloshonok, Vadim A.
-
p. 4508 - 4515
(2013/08/23)
-
- A simple chromatographic route for the isolation of meso diaminopimelic acid
-
Meso diaminopimelic acid is an important noncoded amino acid found in Gram-negative bacterial peptidoglycan. In spite of its importance, this stereoisomer is not available commercially. A simple, economical procedure was developed for the isolation of pur
- Toth, Gabor K.,Hetenyi, Anasztazia,Ilisz, Istvan,Peter, Antal
-
experimental part
p. 133 - 137
(2011/11/05)
-
- Structural Basis for Catalysis by the Mono- and Dimetalated Forms of the dapE-Encoded N-succinyl-l,l-Diaminopimelic Acid Desuccinylase
-
Biosynthesis of lysine and meso-diaminopimelic acid in bacteria provides essential components for protein synthesis and construction of the bacterial peptidoglycan cell wall. The dapE operon enzymes synthesize both meso-diaminopimelic acid and lysine and, therefore, represent potential targets for novel antibacterials. The dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase functions in a late step of the pathway and converts N-succinyl-l,l-diaminopimelic acid to l,l-diaminopimelic acid and succinate. Deletion of the dapE gene is lethal to Helicobacter pylori and Mycobacterium smegmatis, indicating that DapE's are essential for cell growth and proliferation. Since there are no similar pathways in humans, inhibitors that target DapE may have selective toxicity against only bacteria. A major limitation in developing antimicrobial agents that target DapE has been the lack of structural information. Herein, we report the high-resolution X-ray crystal structures of the DapE from Haemophilus influenzae with one and two zinc ions bound in the active site, respectively. These two forms show different activity. Based on these newly determined structures, we propose a revised catalytic mechanism of peptide bond cleavage by DapE enzymes. These structures provide important insight into catalytic mechanism of DapE enzymes as well as a structural foundation that is critical for the rational design of DapE inhibitors.
- Nocek, Boguslaw P.,Gillner, Danuta M.,Fan, Yao,Holz, Richard C.,Joachimiak, Andrzej
-
experimental part
p. 617 - 626
(2011/04/26)
-
- An efficient synthesis of (2S, 6S)- and meso-diaminopimelic acids via asymmetric hydrogenation
-
An efficient synthesis of the title compounds 1 and 2 has been successfully developed. The key step is the asymmetric hydrogenation of dehydroamino acid 7 using [Rh(I)(COD)-(S,S) or - (R,R)-Et-DuPHOS)]+OTf- to produce the optically active, protected amino acid derivatives in high ee (>95%). The approach also can be used for the synthesis of other isomers and analogues.
- Wang,Xiong,Yang,Hruby
-
-
- Enantiomerically pure α-amino acid synthesis via hydroboration - Suzuki cross-coupling
-
The Garner aldehyde-derived methylene alkene 5 and the corresponding benzyloxycarbonyl compound 25 undergo hydroboration with 9-BBN-H followed by palladium-catalyzed Suzuki coupling reactions with aryl and vinyl halides. After one-pot hydrolysis -oxidation, a range of known and novel nonproteinogenic amino acids were isolated as their N-protected derivatives. These novel organoborane homoalanine anion equivalents are generated and transformed under mild conditions and with wide functional group tolerance: electron-rich and -poor aromatic iodides and bromides (and a vinyl bromide) all undergo efficient Suzuki coupling. The extension of this methodology to prepare meso-DAP, R,R-DAP, and R,R-DAS is also described.
- Collier, Philip N.,Campbell, Andrew D.,Patel, Ian,Raynham, Tony M.,Taylor, Richard J. K.
-
p. 1802 - 1815
(2007/10/03)
-
- Asymmetric synthesis of differentially protected meso-2,6-diaminopimelic acid
-
meso-2,6-Diaminopimelic acid, an important linking component of bacterial cell walls and a biosynthetic precursor of L-lysine has been prepared differentially protected in a stereospecific manner from both L-aspartic and L-glutamic acid. The key step to establish the second chiral center involves the asymmetric reduction of a pyruvate moiety with Alpine-Borane. S-2-Amino-6-oxopimelic acid, the hydrolyzed open chain form of tetrahydrodipicolinic acid, a biosynthetic precursor of meso-2,6-diaminopimelic acid, was also prepared via deprotection of the key pyruvate intermediate.
- Roberts, John L.,Chan, Cecil
-
p. 7679 - 7682
(2007/10/03)
-
- A concise, stereoselective synthesis of meso-2,6-diaminopimelic acid (DAP)
-
The preparation of meso-2,6-diaminopimelic acid 1 is described. The key step in the synthesis is Suzuki coupling of the novel organoboron homoalanine equivalent 3 with methyl (2Z)-3-bromo-2-[(tert-butoxycarbonyl)amino]-2-propenoate 5.
- Collier, Philip N.,Patel, Ian,Taylor, Richard J.K.
-
p. 5953 - 5954
(2007/10/03)
-
- A simple asymmetric synthesis of (+)- and (-)-2,6-diaminopimelic acids
-
The asymmetric synthesis of both the enantiomers of 2,6-diaminopimelic acid (2,6-DAP) has been accomplished starting from the chiral synthon 1. (C) 2000 Elsevier Science Ltd.
- Paradisi,Porzi,Rinaldi,Sandri
-
p. 1259 - 1262
(2007/10/03)
-
- Stereoselective synthesis of meso-2,6-diaminopimelic acid and its selectively protected derivatives
-
Four synthetic routes to selectively protected derivatives and isomers of meso-diaminopimelic acid (DAP) (1a), a key constituent of bacterial peptidoglycan, were investigated. N-(tert-butyloxycarbonyl)-D-allylglycine (2) and N-(benzyloxycarbonyl)-L-allylglycine (4) were esterified to ethylene glycol and cyclized via olefin metathesis to a protected derivative 7 of 2,7- diaminosuberic acid. Analogous linking of propane-1,3-diol with 2 and potential precursors of N-(benzyloxycarbonyl)-L-vinylglycine moieties, such as N-(benzyloxycarbonyl)-L-glutamate or N-(benzyloxycarbonyl)-L-methionine sulfoxide, gave 12 or 15, both of which produced the α,β-unsaturated ester 14 upon attempted generation of the vinylglycine precursor for olefin metathesis to DAP derivatives. An alternative route, based on SnCl4- catalyzed ene reaction of methyl N-(benzyloxycarbonyl)-L-allylglycinate (18) with glyoxylate esters of phenylcyclohexanol isomers as chiral auxiliaries, gave ca. 85:15 ratios of diastereomeric alcohols (19 or 20). These could be transformed to DAP derivatives in a series of steps employing azide displacement of corresponding mesylates to introduce the second nitrogen. A third method, involving reduction of pure dimethyl (6S)-2-keto-6-[N- (benzyloxycarbonyl)amino]pimelate (32) to the corresponding alcohol 33 with (S)-binaphthol-ruthenium catalyst as the key step, gives a 79:21 isomeric ratio. The fourth route employs the bis(oxazoline)-copper complex 41 as a chiral catalyst for the ene reaction of methyl (S)-4- (phenylthio)allylglycinate (39) and methyl glyoxylate to afford 42 and 94:6 isometric ratio. Nickel boride removal of sulfur and the double bond in the presence of the Cbz group gives the desired alcohol, dimethyl (2S,6S)-6-[N- (benzyloxycarbonyl)amino]-2-hydroxyheptane-1,7-dioate (33). The required selectively protected second nitrogen is introduced using Mitsunobu inversion with N-tert-butyl [[2-(trimethylsilyl)-ethyl]sulfonyl]carbomate (34) as a key step.
- Gao, Yong,Lane-Bell, Patricia,Vederas, John C.
-
p. 2133 - 2143
(2007/10/03)
-
- Stereospecific synthesis of meso-diaminodicarboxylic acids
-
The hetero Diels-Alder adducts 1 derived from azodibenzoyl and cyclic dienes were transformed to the meso-diaminodicarboxylic acids 6 via the new cyclic hydrazoacetic acids 3.
- Arakawa,Goto,Kawase,Yoshifuji
-
p. 535 - 536
(2007/10/02)
-
- Asymmetric Synthesis of 2,6-Diaminopimelic Acids
-
The preparations of (R,R)-2,6-diaminopimelic acid, (S,S)-2,6-diaminopimelic acid, (S,R)-2,6-diaminopimelic acid, and (S,S)-2,7-diaminosuberic acid are described.The synthesis of mono-N-protected (S,R)-2,6-diaminopimelic acid is also described.
- Williams, Robert M.,Yuan, Chenguang
-
p. 6519 - 6527
(2007/10/02)
-
- 68. Stereoselective Synthesis of (2S,6S)-2,6-Diaminoheptanedioic Acid and of Unsymmetrical Derivatives of meso-2,6-Diaminoheptanedioic Acid
-
Specific inhibition of enzymes of the diaminopimelate pathway (L-lysine biosynthesis) should, in principle, lead to selective antibacterial agents or herbicides.For this purpose, enantioselective syntheses were devised for (2S,6S)-2,6-diaminoheptanedioic acid (L,L-diaminopimelate, 1), (2R,6S)-2,6-diamino-2-methylhept-3-enedioic acid (10), (2R,6S)-2,6-diaminohept-3-enedioic acid (9),(2R,6S)-2,6-diamino-4-fluorohept-3-enedioic (42),and (2S,6S)-2,6-diamino-3-chloroheptanedioic acid (5).The Schoellkopf bislactim-ether methodology was applied to control the configuration of C(2) and C(6) of 1, C(2) of 10, as well as C(6) of 9 and 42.Semialdehyde derivatives of L-glutamate afforded C(6) of 10 and 5, while the (R)-configurated C(2) of 9 and 42 were derived from L-serine.For this purpose, the synthesis of the Garner aldehyde 32 has been improved.As chromatographic purifications and the low temperatures for the reduction of the carboxylic acid are eliminated, this valuable intermediate can now be prepared in bulk quantities.An enantio- and diastereoselective aldol addition of a glycine titanium-enolate was applied for the construction of 5(C(2) and C(3)).As all chiral building blocks and reagents used are available in both enantiomeric forms, these routes should also be suitable for the selective synthesis of the other stereoisomers of these bis(α-amino acids).
- Bold, Guido,Allmendinger, Thomas,Herold, Peter,Moesch, Luzia,Schaer, Hans-Peter,et al.
-
p. 865 - 882
(2007/10/02)
-
- Synthesis of RP 56142: a New Immunoactive Peptide
-
RP 56142, a new immunoactive peptide was synthesized on large scale (ca. 500 g) via L-2,6-diaminopimelic acid which was prepared by chemical or biochemical synthesis.The key derivative, N6-benzyloxycarbonyl-L-2,6-diaminopimelamic acid was synthesized by two methods.In the first, we used a copper chelate procedure.In the second, we selectively deblocked the amine at the α-position to the free carboxylic group by the N-carboxyanhydride method.Condensation of N6-benzyloxycarbonyl-L-2,6-diaminopimelamic acid and the appropriately protected lauroyl dipeptide and removal of the protecting groups afforded RP 56142.
- Bouchaudon, Jean,Dutruc-Rosset, Gilles,Farge, Daniel,James, Claude
-
p. 695 - 701
(2007/10/02)
-
- Characterization of meso-Diaminopimelate Dehydrogenase from Corynebacterium glutamicum and Its Distribution in Bacteria
-
meso-Diaminopimelate dehydrogenase (EC 1.4.1.16) was purified to homogeneity from Corynebacterium glutamicum ATCC 13032.The enzyme had a molecular weight of about 70,000 and consisted of two subunits identical in molecular weight.The enzyme was highly specific for meso-2,6-diaminopimelate.The pH optima for deamination and amination were about 9.8 and 7.9, respectively.The Michaelis contants were 3.1 mM for meso-2,6-diaminopimelate, 0.12 mM for NADP+, 0.28mM for L-2-amino-6-ketopimelate, 36 mM for ammonia, and 0.13 mM for NADPH.D and L isomers of 2,6-diaminopimelate competitively inhibited the oxidative deamination of meso-2,6-diaminopimelate.The enzyme was distributed in a wider range of bacterial species than reported previously when assayed by a sensitive formazan formation method.
- Misono, Haruo,Ogasawara, Masanobu,Nagasaki, Susumu
-
p. 2729 - 2734
(2007/10/02)
-
- STNTHESIS OF EDEINE ANTIBIOTICS AND THEIR ANALOGS. PART V. ABSOLUTE CONFIGURATION OF 2,6-DIAMINO-7-HYDROXYAZELAIC ACID ISOLATED FROM EDEINES
-
Absolute configuration of amino acid component of edeine antibiotics: 2,6-diamino-7-hydroxyazelaic acid was assigned as: (2R,6S,7R) by chemical correlation with (R)-2-aminoadipic and meso-2,6-diaminopimelic acids and 1H NMR and ORD data.
- Gumieniak, Jerzy,Wojciechowska, Hanna,Borowski, Edward
-
p. 1519 - 1526
(2007/10/02)
-
