Crystal structure of D-serine dehydratase from Escherichia coli

Urusova, Darya V.; Isupov, Michail N.; Antonyuk, S.V.; Качалова, Г.С.; Obmolova, Galina; Vagin, A.A.; Лебедев, А. А.; Burenkov, Gleb P.; Dauter, Zbigniew; Bartunik, H.D.; Lamzin, Victor S.; Melik-Adamyan, W.R.; Mueller, Thomas D.; Schnackerz, Klaus D.

doi:10.1016/j.bbapap.2011.10.017

Cited by 20 publications

(18 citation statements)

References 50 publications

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“…The resulting PLP-aminoacrylate intermediate undergoes nucleophilic attack by K41 at C4′, and the resulting tetrahedral gem-diamine intermediate collapses to yield amino acrylate and enzyme-bound PLP; aminoacrylate then undergoes nonenzymatic hydrolysis to yield pyruvate and ammonia. 49 …”

Section: Ppi and Pi In General Acid-general Base Catalysismentioning

confidence: 99%

General base-general acid catalysis by terpenoid cyclases

Pemberton

Christianson

2016

J Antibiot

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Terpenoid cyclases catalyze the most complex reactions in biology, in that more than half of the substrate carbon atoms often undergo changes in bonding during the course of a multistep cyclization cascade that proceeds through multiple carbocation intermediates. Many cyclization mechanisms require stereospecific deprotonation and reprotonation steps, and most cyclization cascades are terminated by deprotonation to yield an olefin product. The first bacterial terpenoid cyclase to yield a crystal structure was pentalenene synthase from Streptomyces exfoliatus UC5319. This cyclase generates the hydrocarbon precursor of the pentalenolactone family of antibiotics. The structures of pentalenene synthase and other terpenoid cyclases reveal predominantly nonpolar active sites typically lacking amino acid side chains capable of serving general base-general acid functions. What chemical species, then, enables the Brønsted acid-base chemistry required in the catalytic mechanisms of these enzymes? The most likely candidate for such general base-general acid chemistry is the co-product inorganic pyrophosphate. Here, we briefly review biological and nonbiological systems in which phosphate and its derivatives serve general base and general acid functions in catalysis. These examples highlight the fact that the Brønsted acid-base activities of phosphate derivatives are comparable to the Brønsted acid-base activities of amino acid side chains.

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Section: Ppi and Pi In General Acid-general Base Catalysismentioning

confidence: 99%

General base-general acid catalysis by terpenoid cyclases

Pemberton

Christianson

2016

J Antibiot

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“…However, an alignment of DsdA [19080] with all DsdA sequences from the studied P. pentosaceus strains and DsdA from E. coli showed that at position 67 a threonine residue is replaced with an alanine residue and at position 278 a proline residue is replaced with a leucine residue. The latter amino acid substitution lies next to the so-called tetraglycine loop (residues G279, G281, G282, and G283 in DsdA from E. coli), which is conserved in PLP-dependent enzymes and is involved in the binding of PLP (30). Therefore, we think that the binding of PLP is impaired in DsdA from P. pentosaceus FAM19080.…”

Section: Discussionmentioning

confidence: 99%

Catabolism of Serine by Pediococcus acidilactici and Pediococcus pentosaceus

Irmler

Bavan

Oberli

et al. 2013

Appl Environ Microbiol

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The ability to produce diacetyl from pyruvate and L-serine was studied in various strains of Pediococcus pentosaceus and Pediococcus acidilactici isolated from cheese. After being incubated on both substrates, only P. pentosaceus produced significant amounts of diacetyl. This property correlated with measurable serine dehydratase activity in cell extracts. A gene encoding the serine dehydratase (dsdA) was identified in P. pentosaceus, and strains that showed no serine dehydratase activity carried mutations that rendered the gene product inactive. A functional dsdA was cloned from P. pentosaceus FAM19132 and expressed in Escherichia coli. The purified recombinant enzyme catalyzed the formation of pyruvate from L-and D-serine and was active at low pH and elevated NaCl concentrations, environmental conditions usually present in cheese. Analysis of the amino acid profiles of culture supernatants from dsdA wild-type and dsdA mutant strains of P. pentosaceus did not show differences in serine levels. In contrast, P. acidilactici degraded serine. Moreover, this species also catabolized threonine and produced alanine and ␣-aminobutyrate. Pediococcus pentosaceus and Pediococcus acidilactici are homofermentative Gram-positive cocci that produce D-and L-lactate from carbohydrates. These bacteria are regularly found in the nonstarter population of raw milk cheeses at the end of the ripening process. Thus, Pediococcus spp. were isolated from cheddar, ewes' milk cheeses, Comté, AOC Salers, Puzzone di Moena, and various raw milk cheeses traditionally produced in Switzerland, such as Gruyère, Emmentaler, Appenzeller, and Tilsit (1-8).Although several reports have indicated that pediococci alone or combined with lactobacilli can accelerate cheese ripening and enhance flavor development, respectively (9-13), knowledge about metabolic activities affecting the maturation of cheese is limited. Studies on the physiological and biochemical activities of Pediococcus spp. have mainly focused on carbohydrate metabolism and proteolytic and lipolytic activities (14-16). Researchers have also reported that pediococci racemize L-lactate to D-lactate under anaerobic conditions and that pediococci can oxidize lactate to acetate and carbon dioxide under aerobic conditions (17). However, information on the enzymatic degradation of amino acids, important precursors for flavor compounds, is sparse.Diacetyl contributes to desirable flavor in fermented dairy products. A pathway well-known for producing diacetyl is through degradation of citrate (18). In this pathway, pyruvate is formed as an intermediary compound that is then converted via ␣-acetolactate to diacetyl. Although pediococci do not appear to utilize citrate, these species have been reported to form diacetyl (19,20). Pyruvate, which is derived from the metabolism of carbohydrates or amino acids, is likely used for synthesizing diacetyl.In this study, the ability of various strains of P. acidilactici and of P. pentosaceus isolated from cheese to produce diacetyl from pyruvate and serine wa...

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“…Figure S1(A) shows the sequence alignment of DAPAL with DSD and SR carried out using CLUSTAL W. All three enzymes catalyze single substrate reactions and can use serine as a substrate. The N1 of PLP is hydrogen bonded to a serine residue in DSD and SR [6,23]. However, in DAPAL, the equivalent residue is a threonine.…”

Section: Mutation Of Thr385: Residue Interacting With N1 Of Plpmentioning

confidence: 99%

“…Enzymes of the fold‐type II family carry out β‐elimination and β‐replacement reactions and share a low level of amino acid sequence identity (< 20%). Well‐characterized enzymes from this family are tryptophan synthase‐β subunit (TrpS; http://www.chem.qmul.ac.uk/iubmb/enzyme/EC4/2/1/20.html) , d ‐serine dehydratase (DSD; http://www.chem.qmul.ac.uk/iubmb/enzyme/EC4/3/1/17.html) , cystathionine‐βsynthase (CBS; http://www.chem.qmul.ac.uk/iubmb/enzyme/EC4/2/1/22.html) , O ‐acetylserine sulfhydrylase (OASS; http://www.chem.qmul.ac.uk/iubmb/enzyme/EC4/2/99/8.html) , threonine deaminase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC4/3/1/19.html) , d ‐cysteine desulfhydrase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC4/4/1/15.html), etc.…”

Section: Introductionmentioning

confidence: 99%

“…Enzymes of the fold-type II family carry out b-elimination and b-replacement reactions and share a low level of amino acid sequence identity (< 20%). Well-characterized enzymes from this family are tryptophan synthaseb subunit (TrpS; EC 4.2.1.20) [2,3], D-serine dehydratase (DSD; EC 4.3.1.17) [4][5][6], cystathionine-b synthase (CBS; EC 4.2.1.22) [7,8], O-acetylserine sulfhydrylase (OASS; EC 4.2.99.8) [9][10][11], threonine deaminase (EC 4.3.1.19) [12,13], D-cysteine desulfhydrase (EC 4.4.1.15), etc. Diaminopropionate ammonialyase (DAPAL; EC 4.3.1.15) belongs to the fold-type II family of PLP-dependent enzymes.…”

Section: Introductionmentioning

confidence: 99%

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Identification of key amino acid residues in the catalytic mechanism of diaminopropionate ammonialyase from Salmonella typhimurium

et al. 2013

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Diaminopropionate ammonialyase (DAPAL), a fold-type II pyridoxal 5′-phosphate-dependent enzyme, catalyzes the a,b-elimination of diaminopropionate (DAP) to pyruvate and ammonia. DAPAL was able to utilize both D-and L-DAP as substrates with almost equal efficiency. Mutational analysis of functionally important residues such as Thr385, Asp125 and Asp194 was carried out to understand the mechanism by which the isomers are hydrolyzed. Further, the putative residues involved in the formation of disulfide bond Cys271 and Cys299 were also mutated. T385S, T385D sDA-PAL were as active with DL-DAP as substrate as sDAPAL, whereas the later exhibited a threefold increase in catalytic efficiency with D-Ser as substrate. Further analysis of these mutants suggested that DAPAL might follow an anti-E 2 mechanism of catalysis that does not involve the formation of a quinonoid intermediate. Of the two mutants of Asp125, D125E showed complete loss of activity with D-DAP as substrate, whereas the reaction with L-DAP was not affected significantly, demonstrating that Asp125 was essential for abstraction of protons from the D-isomer. By contrast, mutational analysis of Asp194 showed that the residue may not be directly involved in proton abstraction from L-DAP. sDAPAL does not form a disulfide bond in solution, although the position of Cys299 and Cys271 in the modeled structure of sDAPAL favored the formation of a disulfide bond. Further, unlike eDAPAL, sDAPAL could be activated by monovalent cations. Mutation of the cysteine residues showed that Cys271 may be involved in coordinating the monovalent cation, as observed in the case of other fold-type II enzymes.

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Crystal structure of D-serine dehydratase from Escherichia coli

Cited by 20 publications

References 50 publications

General base-general acid catalysis by terpenoid cyclases

General base-general acid catalysis by terpenoid cyclases

Catabolism of Serine by Pediococcus acidilactici and Pediococcus pentosaceus

Identification of key amino acid residues in the catalytic mechanism of diaminopropionate ammonialyase from Salmonella typhimurium

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