scholarly journals Substrate-specifying determinants of the nucleotide pyrophosphatases/phosphodiesterases NPP1 and NPP2

2004 ◽  
Vol 381 (1) ◽  
pp. 71-77 ◽  
Author(s):  
Anisoara CIMPEAN ◽  
Cristiana STEFAN ◽  
Rik GIJSBERS ◽  
Willy STALMANS ◽  
Mathieu BOLLEN

The nucleotide pyrophosphatases/phosphodiesterases NPP1 and NPP2/autotaxin are structurally related eukaryotic ecto-enzymes, but display a very different substrate specificity. NPP1 releases nucleoside 5′-monophosphates from various nucleotides, whereas NPP2 mainly functions as a lysophospholipase D. We have used a domain-swapping approach to map substrate-specifying determinants of NPP1 and NPP2. The catalytic domain of NPP1 fused to the N- and C-terminal domains of NPP2 was hyperactive as a nucleotide phosphodiesterase, but did not show any lysophospholipase D activity. In contrast, chimaeras of the catalytic domain of NPP2 and the N- and/or C-terminal domains of NPP1 were completely inactive. These data indicate that the catalytic domain as well as both extremities of NPP2 contain lysophospholipid-specifying sequences. Within the catalytic domain of NPP1 and NPP2, we have mapped residues close to the catalytic site that determine the activities towards nucleotides and lysophospholipids. We also show that the conserved Gly/Phe-Xaa-Gly-Xaa-Xaa-Gly (G/FXGXXG) motif near the catalytic site is required for metal binding, but is not involved in substrate-specification. Our data suggest that the distinct activities of NPP1 and NPP2 stem from multiple differences throughout the polypeptide chain.

2010 ◽  
Vol 54 (9) ◽  
pp. 3738-3745 ◽  
Author(s):  
Sharon King-Keller ◽  
Minyong Li ◽  
Alyssa Smith ◽  
Shilong Zheng ◽  
Gurpreet Kaur ◽  
...  

ABSTRACT Trypanosoma cruzi phosphodiesterase (PDE) C (TcrPDEC), a novel and rather unusual PDE in which, unlike all other class I PDEs, the catalytic domain is localized in the middle of the polypeptide chain, is able to hydrolyze cyclic GMP (cGMP), although it prefers cyclic AMP (cAMP), and has a FYVE-type domain in its N-terminal region (S. Kunz et al., FEBS J. 272:6412-6422, 2005). TcrPDEC shows homology to the mammalian PDE4 family members. PDE4 inhibitors are currently under development for the treatment of inflammatory diseases, such as asthma, chronic pulmonary diseases, and psoriasis, and for treating depression and serving as cognitive enhancers. We therefore tested a number of compounds originally synthesized as potential PDE4 inhibitors on T. cruzi amastigote growth, and we obtained several useful hits. We then conducted homology modeling of T. cruzi PDEC and identified other compounds as potential inhibitors through virtual screening. Testing of these compounds against amastigote growth and recombinant TcrPDEC activity resulted in several potent inhibitors. The most-potent inhibitors were found to increase the cellular concentration of cAMP. Preincubation of cells in the presence of one of these compounds stimulated volume recovery after hyposmotic stress, in agreement with their TcrPDEC inhibitory activity in vitro, providing chemical validation of this target. The compounds found could be useful tools in the study of osmoregulation in T. cruzi. In addition, their further optimization could result in the development of new drugs against Chagas' disease and other trypanosomiases.


2022 ◽  
Author(s):  
Jai Krishna Mahto ◽  
Neetu Neetu ◽  
Monica Sharma ◽  
Monika Dubey ◽  
Bhanu Prakash Vellanki ◽  
...  

Biodegradation of terephthalate (TPA) is a highly desired catabolic process for the bacterial utilization of this Polyethylene terephthalate (PET) depolymerization product, but to date, the structure of terephthalate dioxygenase (TPDO), a Rieske oxygenase (RO) that catalyzes the dihydroxylation of TPA to a cis -diol is unavailable. In this study, we characterized the steady-state kinetics and first crystal structure of TPDO from Comamonas testosteroni KF1 (TPDO KF1 ). The TPDO KF1 exhibited the substrate specificity for TPA ( k cat / K m = 57 ± 9 mM −1 s −1 ). The TPDO KF1 structure harbors characteristics RO features as well as a unique catalytic domain that rationalizes the enzyme’s function. The docking and mutagenesis studies reveal that its substrate specificity to TPA is mediated by Arg309 and Arg390 residues, two residues positioned on opposite faces of the active site. Additionally, residue Gln300 is also proven to be crucial for the activity, its substitution to alanine decreases the activity ( k cat ) by 80%. Together, this study delineates the structural features that dictate the substrate recognition and specificity of TPDO. Importance The global plastic pollution has become the most pressing environmental issue. Recent studies on enzymes depolymerizing polyethylene terephthalate plastic into terephthalate (TPA) show some potential in tackling this. Microbial utilization of this released product, TPA is an emerging and promising strategy for waste-to-value creation. Research from the last decade has discovered terephthalate dioxygenase (TPDO), as being responsible for initiating the enzymatic degradation of TPA in a few Gram-negative and Gram-positive bacteria. Here, we have determined the crystal structure of TPDO from Comamonas testosteroni KF1 and revealed that it possesses a unique catalytic domain featuring two basic residues in the active site to recognize TPA. Biochemical and mutagenesis studies demonstrated the crucial residues responsible for the substrate specificity of this enzyme.


2004 ◽  
Vol 78 (16) ◽  
pp. 8673-8686 ◽  
Author(s):  
Xiaoli Wang ◽  
Lonnie Lybarger ◽  
Rose Connors ◽  
Michael R. Harris ◽  
Ted H. Hansen

ABSTRACT The mK3 protein of gammaherpesvirus 68 and the kK5 protein of Kaposi's sarcoma-associated herpesvirus are members of a family of structurally related viral immune evasion molecules that all possess a RING-CH domain with ubiquitin ligase activity. These proteins modulate the expression of major histocompatibility complex class I molecules (mK3 and kK5) as well as other molecules like ICAM-1 and B7.2 (kK5). Previously, mK3 was shown to ubiquitinate nascent class I molecules, resulting in their rapid degradation, and this process was found to be dependent on TAP and tapasin, endoplasmic reticulum molecules involved in class I assembly. Here, we demonstrate that in murine cells, kK5 does not affect class I expression but does downregulate human B7.2 molecules in a TAP/tapasin-independent manner. These differences in substrate specificity and TAP/tapasin dependence between mK3 and kK5 permitted us, using chimeric molecules, to map the sites of mK3 interaction with TAP/tapasin and to determine the requirements for substrate recognition by mK3. Our findings indicate that mK3 interacts with TAP1 and -2 via their C-terminal domains and with class I molecules via their N-terminal domains. Furthermore, by orienting the RING-CH domain of mK3 appropriately with respect to class I, mK3 binding to TAP/tapasin, rather than the presence of unique sequences in class I, appears to be the primary determinant of substrate specificity.


2018 ◽  
Vol 293 (21) ◽  
pp. 7993-8008 ◽  
Author(s):  
Subrata Debnath ◽  
Dalibor Kosek ◽  
Harichandra D. Tagad ◽  
Stewart R. Durell ◽  
Daniel H. Appella ◽  
...  

Metal-dependent protein phosphatases (PPM) are evolutionarily unrelated to other serine/threonine protein phosphatases and are characterized by their requirement for supplementation with millimolar concentrations of Mg2+ or Mn2+ ions for activity in vitro. The crystal structure of human PPM1A (also known as PP2Cα), the first PPM structure determined, displays two tightly bound Mn2+ ions in the active site and a small subdomain, termed the Flap, located adjacent to the active site. Some recent crystal structures of bacterial or plant PPM phosphatases have disclosed two tightly bound metal ions and an additional third metal ion in the active site. Here, the crystal structure of the catalytic domain of human PPM1A, PPM1Acat, complexed with a cyclic phosphopeptide, c(MpSIpYVA), a cyclized variant of the activation loop of p38 MAPK (a physiological substrate of PPM1A), revealed three metal ions in the active site. The PPM1Acat D146E–c(MpSIpYVA) complex confirmed the presence of the anticipated third metal ion in the active site of metazoan PPM phosphatases. Biophysical and computational methods suggested that complex formation results in a slightly more compact solution conformation through reduced conformational flexibility of the Flap subdomain. We also observed that the position of the substrate in the active site allows solvent access to the labile third metal-binding site. Enzyme kinetics of PPM1Acat toward a phosphopeptide substrate supported a random-order, bi-substrate mechanism, with substantial interaction between the bound substrate and the labile metal ion. This work illuminates the structural and thermodynamic basis of an innate mechanism regulating the activity of PPM phosphatases.


2005 ◽  
Vol 391 (2) ◽  
pp. 285-289 ◽  
Author(s):  
Nandita S. Raikwar ◽  
Rosario F. Bowen ◽  
Mark A. Deeg

Glycosylphosphatidylinositol (GPI)-specific phospholipase D (GPI-PLD) specifically cleaves GPIs. This phospholipase D is a secreted protein consisting of two domains: an N-terminal catalytic domain and a predicted C-terminal β-propeller. Although the biochemical properties of GPI-PLD have been extensively studied, its catalytic site has not been identified. We hypothesized that a histidine residue(s) may play a critical role in the catalytic activity of GPI-PLD, based on the observations that (i) Zn2+, which utilizes histidine residues for binding, is required for GPI-PLD catalytic activity, (ii) a phosphohistidine intermediate is involved in phospholipase D hydrolysis of phosphatidylcholine, (iii) computer modelling suggests a catalytic site containing histidine residues, and (iv) our observation that diethyl pyrocarbonate, which modifies histidine residues, inhibits GPI-PLD catalytic activity. Individual mutation of the ten histidine residues to asparagine in the catalytic domain of murine GPI-PLD resulted in three general phenotypes: not secreted or retained (His56 or His88), secreted with catalytic activity (His34, His81, His98 or His219) and secreted without catalytic activity (His29, His125, His133 or His158). Changing His133 but not His29, His125 or His158 to Cys resulted in a mutant that retained catalytic activity, suggesting that at least His133 is involved in Zn2+ binding. His133 and His158 also retained the biochemical properties of wild-type GPI-PLD including trypsin cleavage pattern and phosphorylation by protein kinase A. Hence, His29, His125, His133 and His158 are required for GPI-PLD catalytic activity.


2005 ◽  
Vol 388 (2) ◽  
pp. 515-525 ◽  
Author(s):  
Peter BENCÚR ◽  
Herta STEINKELLNER ◽  
Barbara SVOBODA ◽  
Jan MUCHA ◽  
Richard STRASSER ◽  
...  

XylT (β1,2-xylosyltransferase) is a unique Golgi-bound glycosyltransferase that is involved in the biosynthesis of glycoprotein-bound N-glycans in plants. To delineate the catalytic domain of XylT, a series of N-terminal deletion mutants was heterologously expressed in insect cells. Whereas the first 54 residues could be deleted without affecting the catalytic activity of the enzyme, removal of an additional five amino acids led to the formation of an inactive protein. Characterization of the N-glycosylation status of recombinant XylT revealed that all three potential N-glycosylation sites of the protein are occupied by N-linked oligosaccharides. However, an unglycosylated version of the enzyme displayed substantial catalytic activity, demonstrating that N-glycosylation is not essential for proper folding of XylT. In contrast with most other glycosyltransferases, XylT is enzymatically active in the absence of added metal ions. This feature is not due to any metal ion directly associated with the enzyme. The precise acceptor substrate specificity of XylT was assessed with several physiologically relevant compounds and the xylosylated reaction products were subsequently tested as substrates of other Golgi-resident glycosyltransferases. These experiments revealed that the substrate specificity of XylT permits the enzyme to act at multiple stages of the plant N-glycosylation pathway.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 1383-1383 ◽  
Author(s):  
Wenjing Cao ◽  
Catherine B. Zander ◽  
X. Long Zheng

Abstract Background: ADAMTS13, a plasma metalloprotease, cleaves von Willebrand factor (VWF), thereby regulating normal hemostasis. While VWF is the only substrate identified to date, more evidence is emerging to indicate that ADAMTS13 may exert direct thrombolytic activity that cannot be fully explained by its known VWF-cleaving activity. We hypothesize that ADAMTS13 may directly interact with the fibrinolytic system to accelerate fibrinolysis; the distal carboxyl-terminal domains of ADAMTS13 may be important in determining its substrate specificity. Objective: To determine the effect of full-length ADAMTS13 (FL-A13) and various carboxyl-terminally truncated ADAMTS13 variants in plasminogen activation and ultimate fibrinolysis. Methods: Using biochemical and biophysical approaches to assess the proteolytic cleavage of plasminogen and fibrinogen/fibrin by ADAMTS13 and variants and binding interactions between plasminogen/fibrinogen and ADAMTS13 and variants. Results: Coomassie blue staining and Western Blot assays demonstrated that a carboxyl terminally truncated ADAMTS13 variant (MT7) that was truncated after the 7th TSP1 repeat cleaved both Glu-plasminogen (Glu-Plg) and Lys-plasminogen (Lys-Plg) to form plasmin in a concentration and time-dependent manner (Fig. 1). MT8 (truncated after the 8th TSP1) and MS (truncated after the spacer domain) also cleaved both types of plasminogen but with much lower efficiency. Interestingly, full-length ADAMTS13 (FL-A13) did not show proteolytic activity towards plasminogen. The plasmin formed by MT7 is biologically active in proteolysis of fibrinogen in a time- and dose-dependent manner. The fibrinogen degradation product pattern, generated by MT7 and other carboxyl terminally truncated ADAMTS13 variants in the presence of plasminogen, was similar to those by tissue-plasminogen activation (t-PA). In addition, the plasmin formed by MT7 cleaved the peptidyl substrate S-2251 in a dose dependent manner. The MT7 and other carboxyl terminally truncated variants exhibited no direct proteolytic activity towards fibrinogen. When added to the preformed clot, MT7 was able to accelerate the lysis of the fibrin clot, initially slowly, but then rapidly as time progressed. The kinetics of fibrinolysis by MT7 was different from that of the t-PA control. Direct binding interactions between the carboxyl terminally truncated ADAMTS13 variants and plasminogen were then determined by surface plasmon resonance. MT7 bound to both types of plasminogen with similar affinities (KD of ~7 nM). However, FL-A13 did not bind to either Glu-Plg or Lys-Plg immobilized on a CM5 chip. Interestingly, when FL-A13 was immobilized on a CM5 chip, it bound to Lys- Plg but not Glu- Plg, but with 20-fold lower affinity compared to MT7. These results suggest that conformational change induced by ligand binding, proteolysis, or truncation may be necessary to expose ADAMTS13 binding site for plasminogen and alter its substrate recognition and specificity. Conclusion: We are able to identify a novel substrate for ADAMTS13 ˗ plasminogen. The carboxyl terminal domains of ADAMTS13 appear to regulate the substrate specificity. These findings not only shed new light on the allosteric regulation of ADAMTS13 function but also provide rationale for the use of ADAMTS13 variants for a broader spectrum of thrombotic disorders including thrombotic thrombocytopenic purpura, ischemic cerebral stroke, myocardial infarction, as well as pulmonary embolism and deep vein thrombosis. Disclosures Zheng: Ablynx: Consultancy; Alexion: Research Funding.


2000 ◽  
Vol 9 (11) ◽  
pp. 2285-2291 ◽  
Author(s):  
Tirso Pons ◽  
Lázaro Hernández ◽  
Frank R. Batista ◽  
Glay Chinea

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