Pavkov-Keller T

References (8)

Title : Unmasking Crucial Residues in Adipose Triglyceride Lipase (ATGL) for Co-Activation with Comparative Gene Identification-58 (CGI-58) - Kulminskaya_2023_J.Lipid.Res__100491
Author(s) : Kulminskaya N , Rodriguez Gamez CF , Hofer P , Cerk IK , Dubey N , Viertlmayr R , Sagmeister T , Pavkov-Keller T , Zechner R , Oberer M
Ref : J Lipid Res , :100491 , 2023
Abstract : Lipolysis is an essential metabolic process that releases unesterified fatty acids from neutral lipid stores to maintain energy homeostasis in living organisms. Adipose triglyceride lipase (ATGL) plays a key role in intracellular lipolysis and can be co-activated upon interaction with the protein comparative gene identification-58 (CGI-58). The underlying molecular mechanism of ATGL stimulation by CGI-58 is incompletely understood. Based on analysis of evolutionary conservation, we used site directed mutagenesis to study a C-terminally truncated variant and full-length mouse ATGL providing insights in the protein co-activation on a per-residue level. We identified the region from residues N209-N215 in ATGL as essential for co-activation by CGI-58. ATGL variants with amino-acids exchanges in this region were still able to hydrolyze triacylglycerol at the basal level and to interact with CGI-58, yet could not be activated by CGI-58. Our studies also demonstrate that full-length mouse ATGL showed higher tolerance to specific single amino acid exchanges in the N209-N215 region upon CGI-58 co-activation compared to C-terminally truncated ATGL variants. The region is either directly involved in protein-protein interaction or essential for conformational changes required in the co-activation process. Three-dimensional models of the ATGL/CGI-58 complex with the artificial intelligence software AlphaFold demonstrated that a large surface area is involved in the protein-protein interaction. Mapping important amino acids for co-activation of both proteins, ATGL and CGI-58, onto the 3D model of the complex locates these essential amino acids at the predicted ATGL/CGI-58 interface thus strongly corroborating the significance of these residues in CGI-58 mediated co-activation of ATGL.
ESTHER : Kulminskaya_2023_J.Lipid.Res__100491
PubMedSearch : Kulminskaya_2023_J.Lipid.Res__100491
PubMedID: 38135254
Gene_locus related to this paper: human-ABHD5 , mouse-abhd5

Title : Residue-Specific Incorporation of the Non-Canonical Amino Acid Norleucine Improves Lipase Activity on Synthetic Polyesters - Haernvall_2022_Front.Bioeng.Biotechnol_10_769830
Author(s) : Haernvall K , Fladischer P , Schoeffmann H , Zitzenbacher S , Pavkov-Keller T , Gruber K , Schick M , Yamamoto M , Kuenkel A , Ribitsch D , Guebitz GM , Wiltschi B
Ref : Front Bioeng Biotechnol , 10 :769830 , 2022
Abstract : Environmentally friendly functionalization and recycling processes for synthetic polymers have recently gained momentum, and enzymes play a central role in these procedures. However, natural enzymes must be engineered to accept synthetic polymers as substrates. To enhance the activity on synthetic polyesters, the canonical amino acid methionine in Thermoanaerobacter thermohydrosulfuricus lipase (TTL) was exchanged by the residue-specific incorporation method for the more hydrophobic non-canonical norleucine (Nle). Strutural modelling of TTL revealed that residues Met-114 and Met-142 are in close vicinity of the active site and their replacement by the norleucine could modulate the catalytic activity of the enzyme. Indeed, hydrolysis of the polyethylene terephthalate model substrate by the Nle variant resulted in significantly higher amounts of release products than the Met variant. A similar trend was observed for an ionic phthalic polyester containing a short alkyl diol (C5). Interestingly, a 50% increased activity was found for TTL [Nle] towards ionic phthalic polyesters containing different ether diols compared to the parent enzyme TTL [Met]. These findings clearly demonstrate the high potential of non-canonical amino acids for enzyme engineering.
ESTHER : Haernvall_2022_Front.Bioeng.Biotechnol_10_769830
PubMedSearch : Haernvall_2022_Front.Bioeng.Biotechnol_10_769830
PubMedID: 35155387
Gene_locus related to this paper: theet-q3ch51

Title : The Crystal Structure of Mouse Ces2c, a Potential Ortholog of Human CES2, Shows Structural Similarities in Substrate Regulation and Product Release to Human CES1 - Eisner_2022_Int.J.Mol.Sci_23_13101
Author(s) : Eisner H , Riegler-Berket L , Gamez CFR , Sagmeister T , Chalhoub G , Darnhofer B , Jazleena PJ , Birner-Gruenberger R , Pavkov-Keller T , Haemmerle G , Schoiswohl G , Oberer M
Ref : Int J Mol Sci , 23 : , 2022
Abstract : Members of the carboxylesterase 2 (Ces2/CES2) family have been studied intensively with respect to their hydrolytic function on (pro)drugs, whereas their physiological role in lipid and energy metabolism has been realized only within the last few years. Humans have one CES2 gene which is highly expressed in liver, intestine, and kidney. Interestingly, eight homologous Ces2 (Ces2a to Ces2h) genes exist in mice and the individual roles of the corresponding proteins are incompletely understood. Mouse Ces2c (mCes2c) is suggested as potential ortholog of human CES2. Therefore, we aimed at its structural and biophysical characterization. Here, we present the first crystal structure of mCes2c to 2.12 resolution. The overall structure of mCes2c resembles that of the human CES1 (hCES1). The core domain adopts an alpha/beta hydrolase-fold with S230, E347, and H459 forming a catalytic triad. Access to the active site is restricted by the cap, the flexible lid, and the regulatory domain. The conserved gate (M417) and switch (F418) residues might have a function in product release similar as suggested for hCES1. Biophysical characterization confirms that mCes2c is a monomer in solution. Thus, this study broadens our understanding of the mammalian carboxylesterase family and assists in delineating the similarities and differences of the different family members.
ESTHER : Eisner_2022_Int.J.Mol.Sci_23_13101
PubMedSearch : Eisner_2022_Int.J.Mol.Sci_23_13101
PubMedID: 36361897
Gene_locus related to this paper: mouse-Ces2c

Title : Structural Changes in the Cap of Rv0183\/mtbMGL Modulate the Shape of the Binding Pocket - Grininger_2021_Biomolecules_11_1299
Author(s) : Grininger C , Leypold M , Aschauer P , Pavkov-Keller T , Riegler-Berket L , Breinbauer R , Oberer M
Ref : Biomolecules , 11 :1299 , 2021
Abstract : doi:10.3390/biom11091299 Tuberculosis continues to be a major threat to the human population. Global efforts to eradicate the disease are ongoing but are hampered by the increasing occurrence of multidrug-resistant strains of Mycobacterium tuberculosis. Therefore, the development of new treatment, and the exploration of new druggable targets and treatment strategies, are of high importance. Rv0183/mtbMGL, is a monoacylglycerol lipase of M. tuberculosis and it is involved in providing fatty acids and glycerol as building blocks and as an energy source. Since the lipase is expressed during the dormant and active phase of an infection, Rv0183/mtbMGL is an interesting target for inhibition. In this work, we determined the crystal structures of a surface-entropy reduced variant K74A Rv0183/mtbMGL in its free form and in complex with a substrate mimicking inhibitor. The two structures reveal conformational changes in the cap region that forms a major part of the substrate/inhibitor binding region. We present a completely closed conformation in the free form and semi-closed conformation in the ligand-bound form. These conformations differ from the previously published, completely open conformation of Rv0183/mtbMGL. Thus, this work demonstrates the high conformational plasticity of the cap from open to closed conformations and provides useful insights into changes in the substrate-binding pocket, the target of potential small-molecule inhibitors.
ESTHER : Grininger_2021_Biomolecules_11_1299
PubMedSearch : Grininger_2021_Biomolecules_11_1299
PubMedID: 34572512
Gene_locus related to this paper: myctu-rv0183

Title : Accurate prediction of protein structures and interactions using a three-track neural network - Baek_2021_Science_373_871
Author(s) : Baek M , DiMaio F , Anishchenko I , Dauparas J , Ovchinnikov S , Lee GR , Wang J , Cong Q , Kinch LN , Schaeffer RD , Millan C , Park H , Adams C , Glassman CR , DeGiovanni A , Pereira JH , Rodrigues AV , van Dijk AA , Ebrecht AC , Opperman DJ , Sagmeister T , Buhlheller C , Pavkov-Keller T , Rathinaswamy MK , Dalwadi U , Yip CK , Burke JE , Garcia KC , Grishin NV , Adams PD , Read RJ , Baker D
Ref : Science , 373 :871 , 2021
Abstract : DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of Structure Prediction (CASP14) conference. We explored network architectures that incorporate related ideas and obtained the best performance with a three-track network in which information at the one-dimensional (1D) sequence level, the 2D distance map level, and the 3D coordinate level is successively transformed and integrated. The three-track network produces structure predictions with accuracies approaching those of DeepMind in CASP14, enables the rapid solution of challenging x-ray crystallography and cryo-electron microscopy structure modeling problems, and provides insights into the functions of proteins of currently unknown structure. The network also enables rapid generation of accurate protein-protein complex models from sequence information alone, short-circuiting traditional approaches that require modeling of individual subunits followed by docking. We make the method available to the scientific community to speed biological research.
ESTHER : Baek_2021_Science_373_871
PubMedSearch : Baek_2021_Science_373_871
PubMedID: 34282049

Title : The crystal structure of monoacylglycerol lipase from M. tuberculosis reveals the basis for specific inhibition - Aschauer_2018_Sci.Rep_8_8948
Author(s) : Aschauer P , Zimmermann R , Breinbauer R , Pavkov-Keller T , Oberer M
Ref : Sci Rep , 8 :8948 , 2018
Abstract : Monoacylglycerol lipases (MGLs) are enzymes that hydrolyze monoacylglycerol into a free fatty acid and glycerol. Fatty acids can be used for triacylglycerol synthesis, as energy source, as building blocks for energy storage, and as precursor for membrane phospholipids. In Mycobacterium tuberculosis, fatty acids also serve as precursor for polyketide lipids like mycolic acids, major components of the cellular envelope associated to resistance for drug. We present the crystal structure of the MGL Rv0183 from Mycobacterium tuberculosis (mtbMGL) in open conformation. The structure reveals remarkable similarities with MGL from humans (hMGL) in both, the cap region and the alpha/beta core. Nevertheless, mtbMGL could not be inhibited with JZL-184, a known inhibitor of hMGL. Docking studies provide an explanation why the activity of mtbMGL was not affected by the inhibitor. Our findings suggest that specific inhibition of mtbMGL from Mycobacterium tuberculosis, one of the oldest recognized pathogens, is possible without influencing hMGL.
ESTHER : Aschauer_2018_Sci.Rep_8_8948
PubMedSearch : Aschauer_2018_Sci.Rep_8_8948
PubMedID: 29895832
Gene_locus related to this paper: myctu-rv0183

Title : Characterization of a poly(butylene adipate-co-terephthalate)-hydrolyzing lipase from Pelosinus fermentans - Biundo_2016_Appl.Microbiol.Biotechnol_100_1753
Author(s) : Biundo A , Hromic A , Pavkov-Keller T , Gruber K , Quartinello F , Haernvall K , Perz V , Arrell MS , Zinn M , Ribitsch D , Guebitz GM
Ref : Applied Microbiology & Biotechnology , 100 :1753 , 2016
Abstract : Certain alpha/beta hydrolases have the ability to hydrolyze synthetic polyesters. While their partial hydrolysis has a potential for surface functionalization, complete hydrolysis allows recycling of valuable building blocks. Although knowledge about biodegradation of these materials is important regarding their fate in the environment, it is currently limited to aerobic organisms. A lipase from the anaerobic groundwater organism Pelosinus fermentans DSM 17108 (PfL1) was cloned and expressed in Escherichia coli BL21-Gold(DE3) and purified from the cell extract. Biochemical characterization with small substrates showed thermoalkalophilic properties (T opt = 50 degrees C, pHopt = 7.5) and higher activity towards para-nitrophenyl octanoate (12.7 U mg-1) compared to longer and shorter chain lengths (C14 0.7 U mg-1 and C2 4.3 U mg-1, respectively). Crystallization and determination of the 3-D structure displayed the presence of a lid structure and a zinc ion surrounded by an extra domain. These properties classify the enzyme into the I.5 lipase family. PfL1 is able to hydrolyze poly(1,4-butylene adipate-co-terephthalate) (PBAT) polymeric substrates. The hydrolysis of PBAT showed the release of small building blocks as detected by liquid chromatography-mass spectrometry (LC-MS). Protein dynamics seem to be involved with lid opening for the hydrolysis of PBAT by PfL1.
ESTHER : Biundo_2016_Appl.Microbiol.Biotechnol_100_1753
PubMedSearch : Biundo_2016_Appl.Microbiol.Biotechnol_100_1753
PubMedID: 26490551
Gene_locus related to this paper: 9firm-a0a0a0ymq9

Title : An Esterase from Anaerobic Clostridium hathewayi Can Hydrolyze Aliphatic-Aromatic Polyesters - Perz_2016_Environ.Sci.Technol_50_2899
Author(s) : Perz V , Hromic A , Baumschlager A , Steinkellner G , Pavkov-Keller T , Gruber K , Bleymaier K , Zitzenbacher S , Zankel A , Mayrhofer C , Sinkel C , Kueper U , Schlegel K , Ribitsch D , Guebitz GM
Ref : Environ Sci Technol , 50 :2899 , 2016
Abstract : Recently, a variety of biodegradable polymers have been developed as alternatives to recalcitrant materials. Although many studies on polyester biodegradability have focused on aerobic environments, there is much less known on biodegradation of polyesters in natural and artificial anaerobic habitats. Consequently, the potential of anaerobic biogas sludge to hydrolyze the synthetic compostable polyester PBAT (poly(butylene adipate-co-butylene terephthalate) was evaluated in this study. On the basis of reverse-phase high-performance liquid chromatography (RP-HPLC) analysis, accumulation of terephthalic acid (Ta) was observed in all anaerobic batches within the first 14 days. Thereafter, a decline of Ta was observed, which occurred presumably due to consumption by the microbial population. The esterase Chath_Est1 from the anaerobic risk 1 strain Clostridium hathewayi DSM-13479 was found to hydrolyze PBAT. Detailed characterization of this esterase including elucidation of the crystal structure was performed. The crystal structure indicates that Chath_Est1 belongs to the alpha/beta-hydrolases family. This study gives a clear hint that also micro-organisms in anaerobic habitats can degrade manmade PBAT.
ESTHER : Perz_2016_Environ.Sci.Technol_50_2899
PubMedSearch : Perz_2016_Environ.Sci.Technol_50_2899
PubMedID: 26878094
Gene_locus related to this paper: 9clot-r5t6k9