scholarly journals Structural studies on leukotriene A4 hydrolases reveal their catalytic mechanism

2014 ◽  
Vol 70 (a1) ◽  
pp. C413-C413
Author(s):  
Mahmudul Hasan ◽  
Agnes Rinaldo-Matthis ◽  
Marjolein Thunnissen

Vertebrate leukotriene A4 hydrolases are zinc metalloenzymes with an epoxide hydrolase and aminopeptidase activity belonging to the M1 family of aminopeptidases. Bestatin, an amino peptidase inhibitor, can inhibit both the activities. The human enzyme produces LTB4, a powerful mediator of inflammation and is implicated in a wide variety of rheumatoid diseases. The yeast homolog scLTA4H contains only a rudimentary epoxide hydrolase activity. Both the structure of the human enzyme and recently the structure of scLTA4H and have been solved to investigate the molecular architecture of the active site both with and without inhibitor Bestatin. The structure of scLTA4H shows large domain movements creating an open active site. In the human enzyme the LTA4 binding side is a narrow hydrophobic channel. Upon inhibitor a domain shifts occurs and the final binding pocket is formed. The fact that scLTA4H displays this induced fit is an interesting observation. Many members of the M1 family seem to display a certain degree of induced fit, a feature, which however, has never been observed for humLTA4H. Our recent solution SAXS studies show that humLTA4H does not make any conformational changes upon inhibitor binding which is consistent with our previous speculation that it functions by a lock and key mechanism rather than induced fit and is better suited to supply the protective and precise environment for hydrolysis of LTA4 into LTB4. On the other hand Xenopus LTA4H shows conformational change in the higher/wide angular region ( >1 nm-1) and decrease in Porod volume of approximately 20 nm3 but no change in Rg or Dmax was observed. It is also observed that like in crystal structure Xenopus LTA4H forms dimer in solution. Similarly scLTA4H forms dimer in solution, which is unlike the crystal structure, and also make conformational changes upon inhibitor binding. Taken together, Xenopus and scLTA4H makes more compact form, with decrease in flexibility, to perform it's catalytic action.

2015 ◽  
Vol 59 (8) ◽  
pp. 5069-5072 ◽  
Author(s):  
Takuma Oguri ◽  
Yoshikazu Ishii ◽  
Akiko Shimizu-Ibuka

ABSTRACTWe solved the crystal structure of the class C β-lactamase MOX-1 complexed with the inhibitor aztreonam at 1.9Å resolution. The main-chain oxygen of Ser315 interacts with the amide nitrogen of aztreonam. Surprisingly, compared to that in the structure of free MOX-1, this main-chain carboxyl changes its position significantly upon binding to aztreonam. This result indicates that the interaction between MOX-1 and β-lactams can be accompanied by conformational changes in the B3 β-strand main chain.


2011 ◽  
Vol 406 (1) ◽  
pp. 120-134 ◽  
Author(s):  
Charlotte Helgstrand ◽  
Mahmudul Hasan ◽  
Hüseyin Uysal ◽  
Jesper Z. Haeggström ◽  
Marjolein M.G.M. Thunnissen

2014 ◽  
Vol 70 (a1) ◽  
pp. C1636-C1636
Author(s):  
Chun-Liang Chen ◽  
Cynthia Stauffacher

Mevalonate diphosphate decarboxylases (MDD) (EC 4.1.1.33) catalyze the Mg2+-dependent decarboxylation of mevalonate 5-diphosphate (MVAPP) by hydrolyzing adenosine triphosphate (ATP) and producing isopentenyl diphosphate (IPP) in the final step of mevalonate pathway. This enzyme is essential in Enterococcus faecalis and other Gram (+) bacteria; therefore, MDD protein is an ideal drug target for the treatment of bacterial infections. We have studied the enzyme kinetics and structures of MDD from Enterococcus faecalis (MDDEF) which causes clinical enterorococcal infections. In the crystal structure of the MDDEF bound with ATP, the catalytically unfavored orientation of the γ-phosphate of ATP implies that conformational changes of MDDEF might occur in order to accommodate the binding of ATP when the MVAPP binds to the active site in advance. A 10-fold decrease of the dissociation constrant (Kd) value of ATPγS has been observed using isothermal titration calorimetry (ITC) when MDDEF is pre-bound with MVAPP. The increase of binding affinity of ATPγS suggests that cooperative binding of ATP to MDDEF can be achieved by the prerequisite binding of MVAPP. Indeed, the crystal structure of MDDEF soaked with the MVAPP shows that one flexible loop that eventually should bind ATP becomes non-flexible and bends toward the active site of MDDEF. Thus, we hypothesize that the binding of the MVAPP to the active site triggers conformational changes of MDDEF which induces the binding of the other substrate, ATP, in its catalytically favored position. Further experiments will be performed for investigating a substrate-binding mechanism for MDDEF and these will serve as platforms for specific drug development in the near future.


2020 ◽  
Author(s):  
Xiaopeng Tang ◽  
Mingqian Fang ◽  
Juan Zhang ◽  
Zhiyi Liao ◽  
Ruomei Cheng ◽  
...  

Abstract Hypercytokinemia is a critically fatal factor in COVID-19. However, underlying pathogenic mechanisms are unknown. Here we show that fibrinogen and leukotriene-A4 hydrolase (LTA4H), two of the most potent inflammatory contributors, are elevated by 67.7 and astonishing 227.7% in the plasma of patients infected by SARS-CoV-2 and admitted to intensive care unit in comparison with healthy control, respectively. Conversely, transferrin identified as a fibrinogen immobilizer in our recent work and Spink6 are down-regulated by 40.3 and 25.9%, respectively. Furthermore, we identify Spink6 as the first endogenous inhibitor of LTA4H, a pro-inflammatory enzyme catalyzing final and rating limited step in biosynthesis of leukotriene-B4 that is an extremely inflammatory mediator and a target to design superior anti-inflammatory drugs. Additionally, virus Spike protein is found to evoke LTA4H and fibrinogen expression in vivo. Collectively, these findings identify the imbalance between inflammatory drivers and antagonists, which likely contributes to hypercytokinemia in COVID-19. Spink6 may have superior anti-inflammatory function because it specifically targets epoxide hydrolase of LTA4H to inhibit leukotriene-B4 biosynthesis without effecting LTA4H’s aminopeptidase activity.


2020 ◽  
Vol 295 (22) ◽  
pp. 7635-7652
Author(s):  
Christopher D. Radka ◽  
Matthew W. Frank ◽  
Jiangwei Yao ◽  
Jayaraman Seetharaman ◽  
Darcie J. Miller ◽  
...  

Enoyl-acyl carrier protein reductase (FabI) catalyzes a rate-controlling step in bacterial fatty-acid synthesis and is a target for antibacterial drug development. A phylogenetic analysis shows that FabIs fall into four divergent clades. Members of clades 1–3 have been structurally and biochemically characterized, but the fourth clade, found in members of phylum Bacteroidetes, is uncharacterized. Here, we identified the unique structure and conformational changes that distinguish clade 4 FabIs. Alistipes finegoldii is a prototypical Bacteroidetes inhabitant of the gut microbiome. We found that A. finegoldii FabI (AfFabI) displays cooperative kinetics and uses NADH as a cofactor, and its crystal structure at 1.72 Å resolution showed that it adopts a Rossmann fold as do other characterized FabIs. It also disclosed a carboxyl-terminal extension that forms a helix–helix interaction that links the protomers as a unique feature of AfFabI. An AfFabI·NADH crystal structure at 1.86 Å resolution revealed that this feature undergoes a large conformational change to participate in covering the NADH-binding pocket and establishing the water channels that connect the active site to the central water well. Progressive deletion of these interactions led to catalytically compromised proteins that fail to bind NADH. This unique conformational change imparted a distinct shape to the AfFabI active site that renders it refractory to a FabI drug that targets clade 1 and 3 pathogens. We conclude that the clade 4 FabI, found in the Bacteroidetes inhabitants of the gut, have several structural features and conformational transitions that distinguish them from other bacterial FabIs.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 19-19 ◽  
Author(s):  
Wenman Wu ◽  
Heinrich Roder ◽  
Peter N. Walsh

Abstract Abstract 19 Coagulation factor XI (FXI) is a uniquely dimeric coagulation protein, which in its activated form (FXIa) activates FIX to FIXa. We have previously shown that the dimeric structure of FXI is essential for normal autoactivation and activation by thrombin and FXIIa, but not for the expression of enzymatic activity against FIX (Wu W, et al J. Biol. Chem. 283:18655-18664, 2008). A comparison of three separate structures of FXI/XIa from our laboratory (i.e., the crystal structure of the catalytic domain of FXIa in complex with the kunitz protease inhibitor domain of protease nexin-2; the crystal structure of full-length, dimeric FXI; and the NMR structure of the FXI A4 domain) predicts a major conformational change accompanying the conversion of FXI to FXIa. We now show that when FXI binds to the negatively charged polymer, dextran sulfate and is autoactivated to generate FXIa, changes of intrinsic fluorescence are observed, i.e, a decrease in fluorescence intensity and a red shift of emission wavelength, which also suggests that a conformational change accompanies FXI activation. To investigate the mechanism of FXI zymogen activation and the allosteric transition accompanying the conversion of FXI to FXIa, which exposes binding sites for FXIa ligands, we have carried out fluorescence resonance energy transfer (FRET) studies to characterize the conformational changes accompanying zymogen activation. Using a sensitive free thiol quantitation assay, we confirmed the presence of a single free cysteine residue (Cys11) per subunit of recombinant FXI, which was quantitatively labeled with the thiol reactive fluorescence dye IAEDANS (5-({2-[(iodoacetyl)amino]ethyl}amino)naphthalene-1-sulfonic acid). Fluorescence excitation of AEDANS-labeled FXI at 280 nm shows a prominent dansyl emission peak (∼450 nm) in addition to the Trp emission peak (∼325 nm) indicative of efficient FRET from Trp donors to the AEDANS acceptor. Controls using a C11S mutant of FXI showed ∼10-fold lower levels of AEDANS labeling, confirming that Cys11 is the predominant labeling site. Autoactivation of FXI in the presence of dextran sulfate results in a major decrease in donor emission, but has little effect on acceptor emission. This indicates that, for wild-type FXI, FRET is dominated by transfer within the A1 domain originating from Trp55, which is located at a distance of 18 Å from Cys11, far closer than any other tryptophan. The changes in Trp emission, which are similar in the presence and abence of AEDANS, allow us to follow the kinetics of zymogen activation. The S557A active-site mutant of FXI, which cannot undergo autoactivation, showed no fluorescence changes upon addition of dextran sulfate, confirming that the observed decrease in Trp fluorescence is due to formation of active FXIa enzyme. In an effort to observe specific inter-domain FRET, we prepared an AEDANS labeled W55H mutant of FXI, which eliminates the Trp donor in the A1 domain that dominates energy transfer in wild-type FXI. Our data show that autoactivation of the W55H mutant is accompanied by a significant increase in AEDANS emission that can be attributed to the movement of the labeled Cys11 (in A1) relative to Trp228 in the A3 domain of the opposite dimer subunit. In the crystal structure of FXI, the distance for this donor-acceptor pair is 29 Å (compared to a distance of 40 Å for the second closest Trp, Trp407 in the catalytic domain), making it a sensitive and specific FRET probe for monitoring changes in domain arrangement associated with enzyme activation and ligand interactions. A comparison of the FXI crystal structure with our model of FXIa showed that the distance between the active site serines (Ser557) of each catalytic triad is shortened from ∼118 Å in the zymogen to 40–75 Å in the enzyme. Since the distance between the two scissile bonds of each subunit of FXI is also ∼75 Å, we propose that during autoactivation, either the active site of each catalytic domain of FXIa is positioned to cleave the Arg369-Ile370 bond of the opposite subunit (intersubunit transactivation) or a FXIa dimer positions its two active sites adjacent to the two scissile bonds of a separate FXI dimer (intermolecular activation). These studies support a model in which the autoactivating transition from zymogen to enzyme is accompanied by the movement of each catalytic domain of the dimer to facilitate efficient autoactivation of FXI. Disclosures: No relevant conflicts of interest to declare.


2002 ◽  
Vol 2 ◽  
pp. 1734-1749 ◽  
Author(s):  
Jesper Z. Haeggström ◽  
Pär Nordlund ◽  
Marjolein M.G.M. Thunnissen

The leukotrienes are a family of lipid mediators involved in inflammation and allergy. Leukotriene B4is a classical chemoattractant, which triggers adherence and aggregation of leukocytes to the endothelium at only nM concentrations. In addition, leukotriene B4modulates immune responses, participates in the host defense against infections, and is a key mediator of PAF-induced lethal shock. Because of these powerful biological effects, leukotriene B4 is implicated in a variety of acute and chronic inflammatory diseases, e.g., nephritis, arthritis, dermatitis, and chronic obstructive pulmonary disease. The final step in the biosynthesis of leukotriene B4is catalyzed by leukotriene A4hydrolase, a unique bifunctional zinc metalloenzyme with an anion-dependent aminopeptidase activity. Here we describe the most recent developments regarding our understanding of the function and molecular architecture of leukotriene A4hydrolase.


2004 ◽  
Vol 279 (19) ◽  
pp. 20480-20489 ◽  
Author(s):  
Kallol Ray ◽  
Christina S. Hines ◽  
Jerry Coll-Rodriguez ◽  
David W. Rodgers

Thimet oligopeptidase (TOP) is a zinc metallopeptidase that metabolizes a number of bioactive peptides and degrades peptides released by the proteasome, limiting antigenic presentation by MHC class I molecules. We present the crystal structure of human TOP at 2.0-Å resolution. The active site is located at the base of a deep channel that runs the length of the elongated molecule, an overall fold first seen in the closely related metallopeptidase neurolysin. Comparison of the two related structures indicates hinge-like flexibility and identifies elements near one end of the channel that adopt different conformations. Relatively few of the sequence differences between TOP and neurolysin map to the proposed substrate-binding site, and four of these variable residues may account for differences in substrate specificity. In addition, a loop segment (residues 599-611) in TOP differs in conformation and degree of order from the corresponding neurolysin loop, suggesting it may also play a role in activity differences. Cysteines thought to mediate covalent oligomerization of rat TOP, which can inactivate the enzyme, are found to be surface-accessible in the human enzyme, and additional cysteines (residues 321,350, and 644) may also mediate multimerization in the human homolog. Disorder in the N terminus of TOP indicates it may be involved in subcellular localization, but a potential nuclear import element is found to be part of a helix and, therefore, unlikely to be involved in transport. A large acidic patch on the surface could potentially mediate a protein-protein interaction, possibly through formation of a covalent linkage.


2010 ◽  
Vol 66 (2) ◽  
pp. 116-124 ◽  
Author(s):  
Jeyaraman Jeyakanthan ◽  
Shankar Prasad Kanaujia ◽  
Yuya Nishida ◽  
Noriko Nakagawa ◽  
Surendran Praveen ◽  
...  

Asymmetric diadenosine tetraphosphate (Ap4A) hydrolases degrade the metabolite Ap4A back into ATP and AMP. The three-dimensional crystal structure of Ap4A hydrolase (16 kDa) fromAquifex aeolicushas been determined in free and ATP-bound forms at 1.8 and 1.95 Å resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an αβα-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap4A hydrolase fromCaenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule.


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