Dreveny I

References (7)

Title : Identification of lipases with activity towards monoacylglycerol by criterion of conserved cap architectures - Riegler-Berket_2018_Biochim.Biophys.Acta_1863_679
Author(s) : Riegler-Berket L , Leitmeier A , Aschauer P , Dreveny I , Oberer M
Ref : Biochimica & Biophysica Acta , 1863 :679 , 2018
Abstract : Monoacylglycerol lipases (MGL) are a subclass of lipases that predominantly hydrolyze monoacylglycerol (MG) into glycerol and fatty acid. MGLs are ubiquitous enzymes across species and play a role in lipid metabolism, affecting energy homeostasis and signaling processes. Structurally, MGLs belong to the alpha/beta hydrolase fold family with a cap covering the substrate binding pocket. Analysis of the known 3D structures of human, yeast and bacterial MGLs revealed striking similarity of the cap architecture. Since MGLs from different organisms share very low sequence similarity, it is difficult to identify MGLs based on the amino acid sequence alone. Here, we investigated whether the cap architecture could be a characteristic feature of this subclass of lipases with activity towards MG and whether it is possible to identify MGLs based on the cap shape. Through database searches, we identified the structures of five different candidate alpha/beta hydrolase fold proteins with unknown or reported esterase activity. These proteins exhibit cap architecture similarities to known human, yeast and bacterial MGL structures. Out of these candidates we confirmed MGL activity for the protein LipS, which displayed the highest structural similarity to known MGLs. Two further enzymes, Avi_0199 and VC1974, displayed low level MGL activities. These findings corroborate our hypothesis that this conserved cap architecture can be used as criterion to identify lipases with activity towards MGs.
ESTHER : Riegler-Berket_2018_Biochim.Biophys.Acta_1863_679
PubMedSearch : Riegler-Berket_2018_Biochim.Biophys.Acta_1863_679
PubMedID: 29627382
Gene_locus related to this paper: 9bact-TtEst , agrvs-b9jym4 , bac25-mglp , bacsu-cbxnp , human-MGLL , symth-q67mr3 , vibch-VC1974 , yeast-mgll

Title : Conformational plasticity and ligand binding of bacterial monoacylglycerol lipase - Rengachari_2013_J.Biol.Chem_288_31093
Author(s) : Rengachari S , Aschauer P , Schittmayer M , Mayer N , Gruber K , Breinbauer R , Birner-Gruenberger R , Dreveny I , Oberer M
Ref : Journal of Biological Chemistry , 288 :31093 , 2013
Abstract : Monoacylglycerol lipases (MGLs) play an important role in lipid catabolism across all kingdoms of life by catalyzing the release of free fatty acids from monoacylglycerols. The three-dimensional structures of human and a bacterial MGL were determined only recently as the first members of this lipase family. In addition to the alpha/beta-hydrolase core, they showed unexpected structural similarities even in the cap region. Nevertheless, the structural basis for substrate binding and conformational changes of MGLs is poorly understood. Here, we present a comprehensive study of five crystal structures of MGL from Bacillus sp. H257 in its free form and in complex with different substrate analogs and the natural substrate 1-lauroylglycerol. The occurrence of different conformations reveals a high degree of conformational plasticity of the cap region. We identify a specific residue, Ile-145, that might act as a gatekeeper restricting access to the binding site. Site-directed mutagenesis of Ile-145 leads to significantly reduced hydrolase activity. Bacterial MGLs in complex with 1-lauroylglycerol, myristoyl, palmitoyl, and stearoyl substrate analogs enable identification of the binding sites for the alkyl chain and the glycerol moiety of the natural ligand. They also provide snapshots of the hydrolytic reaction of a bacterial MGL at different stages. The alkyl chains are buried in a hydrophobic tunnel in an extended conformation. Binding of the glycerol moiety is mediated via Glu-156 and water molecules. Analysis of the structural features responsible for cap plasticity and the binding modes of the ligands suggests conservation of these features also in human MGL.
ESTHER : Rengachari_2013_J.Biol.Chem_288_31093
PubMedSearch : Rengachari_2013_J.Biol.Chem_288_31093
PubMedID: 24014019
Gene_locus related to this paper: bac25-mglp

Title : The structure of monoacylglycerol lipase from Bacillus sp. H257 reveals unexpected conservation of the cap architecture between bacterial and human enzymes - Rengachari_2012_Biochim.Biophys.Acta_1821_1012
Author(s) : Rengachari S , Bezerra GA , Riegler-Berket L , Gruber CC , Sturm C , Taschler U , Boeszoermenyi A , Dreveny I , Zimmermann R , Gruber K , Oberer M
Ref : Biochimica & Biophysica Acta , 1821 :1012 , 2012
Abstract : Monoacylglycerol lipases (MGLs) catalyse the hydrolysis of monoacylglycerol into free fatty acid and glycerol. MGLs have been identified throughout all genera of life and have adopted different substrate specificities depending on their physiological role. In humans, MGL plays an integral part in lipid metabolism affecting energy homeostasis, signalling processes and cancer cell progression. In bacteria, MGLs degrade short-chain monoacylglycerols which are otherwise toxic to the organism. We report the crystal structures of MGL from the bacterium Bacillus sp. H257 (bMGL) in its free form at 1.2 and in complex with phenylmethylsulfonyl fluoride at 1.8 resolution. In both structures, bMGL adopts an alpha/beta hydrolase fold with a cap in an open conformation. Access to the active site residues, which were unambiguously identified from the protein structure, is facilitated by two different channels. The larger channel constitutes the highly hydrophobic substrate binding pocket with enough room to accommodate monoacylglycerol. The other channel is rather small and resembles the proposed glycerol exit hole in human MGL. Molecular dynamics simulation of bMGL yielded open and closed states of the entrance channel and the glycerol exit hole. Despite differences in the number of residues, secondary structure elements, and low sequence identity in the cap region, this first structure of a bacterial MGL reveals striking structural conservation of the overall cap architecture in comparison with human MGL. Thus it provides insight into the structural conservation of the cap amongst MGLs throughout evolution and provides a framework for rationalising substrate specificities in each organism.
ESTHER : Rengachari_2012_Biochim.Biophys.Acta_1821_1012
PubMedSearch : Rengachari_2012_Biochim.Biophys.Acta_1821_1012
PubMedID: 22561231
Gene_locus related to this paper: bac25-mglp

Title : Substrate binding in the FAD-dependent hydroxynitrile lyase from almond provides insight into the mechanism of cyanohydrin formation and explains the absence of dehydrogenation activity - Dreveny_2009_Biochemistry_48_3370
Author(s) : Dreveny I , Andryushkova AS , Glieder A , Gruber K , Kratky C
Ref : Biochemistry , 48 :3370 , 2009
Abstract : In a large number of plant species hydroxynitrile lyases catalyze the decomposition of cyanohydrins in order to generate hydrogen cyanide upon tissue damage. Hydrogen cyanide serves as a deterrent against herbivores and fungi. In vitro hydroxynitrile lyases are proficient biocatalysts for the stereospecific synthesis of cyanohydrins. Curiously, hydroxynitrile lyases from different species are completely unrelated in structure and substrate specificity despite catalyzing the same reaction. The hydroxynitrile lyase from almond shows close resemblance to flavoproteins of the glucose-methanol-choline oxidoreductase family. We report here 3D structural data of this lyase with the reaction product benzaldehyde bound within the active site, which allow unambiguous assignment of the location of substrate binding. Based on the binding geometry, a reaction mechanism is proposed that involves one of the two conserved active site histidine residues acting as a general base abstracting the proton from the cyanohydrin hydroxyl group. Site-directed mutagenesis shows that both active site histidines are required for the reaction to occur. There is no evidence that the flavin cofactor directly participates in the reaction. Comparison with other hydroxynitrile lyases reveals a large diversity of active site architectures, which, however, share the common features of a general active site base and a nearby patch with positive electrostatic potential. On the basis of the difference in substrate binding geometry between the FAD-dependent HNL from almond and the related oxidases, we can rationalize why the HNL does not act as an oxidase.
ESTHER : Dreveny_2009_Biochemistry_48_3370
PubMedSearch : Dreveny_2009_Biochemistry_48_3370
PubMedID: 19256550

Title : Comprehensive step-by-step engineering of an (R)-hydroxynitrile lyase for large-scale asymmetric synthesis -
Author(s) : Glieder A , Weis R , Skranc W , Poechlauer P , Dreveny I , Majer S , Wubbolts M , Schwab H , Gruber K
Ref : Angew Chem Int Ed Engl , 42 :4815 , 2003
PubMedID: 14562357

Title : The active site of hydroxynitrile lyase from Prunus amygdalus: modeling studies provide new insights into the mechanism of cyanogenesis - Dreveny_2002_Protein.Sci_11_292
Author(s) : Dreveny I , Kratky C , Gruber K
Ref : Protein Science , 11 :292 , 2002
Abstract : The FAD-dependent hydroxynitrile lyase from almond (Prunus amygdalus, PaHNL) catalyzes the cleavage of R-mandelonitrile into benzaldehyde and hydrocyanic acid. Catalysis of the reverse reaction-the enantiospecific formation of alpha-hydroxynitriles--is now widely utilized in organic syntheses as one of the few industrially relevant examples of enzyme-mediated C-C bond formation. Starting from the recently determined X-ray crystal structure, systematic docking calculations with the natural substrate were used to locate the active site of the enzyme and to identify amino acid residues involved in substrate binding and catalysis. Analysis of the modeled substrate complexes supports an enzymatic mechanism that includes the flavin cofactor as a mere "spectator" of the reaction and relies on general acid/base catalysis by the conserved His-497. Stabilization of the negative charge of the cyanide ion is accomplished by a pronounced positive electrostatic potential at the binding site. PaHNL activity requires the FAD cofactor to be bound in its oxidized form, and calculations of the pKa of enzyme-bound HCN showed that the observed inactivation upon cofactor reduction is largely caused by the reversal of the electrostatic potential within the active site. The suggested mechanism closely resembles the one proposed for the FAD-independent, and structurally unrelated HNL from Hevea brasiliensis. Although the actual amino acid residues involved in the catalytic cycle are completely different in the two enzymes, a common motif for the mechanism of cyanogenesis (general acid/base catalysis plus electrostatic stabilization of the cyanide ion) becomes evident.
ESTHER : Dreveny_2002_Protein.Sci_11_292
PubMedSearch : Dreveny_2002_Protein.Sci_11_292
PubMedID: 11790839

Title : The hydroxynitrile lyase from almond: a lyase that looks like an oxidoreductase - Dreveny_2001_Structure_9_803
Author(s) : Dreveny I , Gruber K , Glieder A , Thompson A , Kratky C
Ref : Structure , 9 :803 , 2001
Abstract : BACKGROUND: Cyanogenesis is a defense process of several thousand plant species. Hydroxynitrile lyase, a key enzyme of this process, cleaves a cyanohydrin into hydrocyanic acid and the corresponding aldehyde or ketone. The reverse reaction constitutes an important tool in biocatalysis. Different classes of hydroxynitrile lyases have convergently evolved from FAD-dependent oxidoreductases, alpha/beta hydrolases, and alcohol dehydrogenases. The FAD-dependent hydroxynitrile lyases (FAD-HNLs) carry a flavin cofactor whose redox properties appear to be unimportant for catalysis.
RESULTS: We have determined the crystal structure of a 61 kDa hydroxynitrile lyase isoenzyme from Prunus amygdalus (PaHNL1) to 1.5 A resolution. Clear electron density originating from four glycosylation sites could be observed. As concerns the overall protein fold including the FAD cofactor, PaHNL1 belongs to the family of GMC oxidoreductases. The active site for the HNL reaction is probably at a very similar position as the active sites in homologous oxidases.
CONCLUSIONS: There is strong evidence from the structure and the reaction product that FAD-dependent hydroxynitrile lyases have evolved from an aryl alcohol oxidizing precursor. Since key residues implicated in oxidoreductase activity are also present in PaHNL1, it is not obvious why this enzyme shows no oxidase activity. Similarly, features proposed to be relevant for hydroxy-nitrile lyase activity in other hydroxynitrile lyases, i.e., a general base and a positive charge to stabilize the cyanide, are not obviously present in the putative active site of PaHNL1. Therefore, the reason for its HNL activity is far from being well understood at this point.
ESTHER : Dreveny_2001_Structure_9_803
PubMedSearch : Dreveny_2001_Structure_9_803
PubMedID: 11566130