scholarly journals Crystal Structure of Mouse Thymidylate Synthase in Tertiary Complex with dUMP and Raltitrexed Reveals N-Terminus Architecture and Two Different Active Site Conformations

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Anna Dowierciał ◽  
Piotr Wilk ◽  
Wojciech Rypniewski ◽  
Wojciech Rode ◽  
Adam Jarmuła

The crystal structure of mouse thymidylate synthase (mTS) in complex with substrate dUMP and antifolate inhibitor Raltitrexed is reported. The structure reveals, for the first time in the group of mammalian TS structures, a well-ordered segment of 13 N-terminal amino acids, whose ordered conformation is stabilized due to specific crystal packing. The structure consists of two homodimers, differing in conformation, one being more closed (dimer AB) and thus supporting tighter binding of ligands, and the other being more open (dimer CD) and thus allowing weaker binding of ligands. This difference indicates an asymmetrical effect of the binding of Raltitrexed to two independent mTS molecules. Conformational changes leading to a ligand-induced closing of the active site cleft are observed by comparing the crystal structures of mTS in three different states along the catalytic pathway: ligand-free, dUMP-bound, and dUMP- and Raltitrexed-bound. Possible interaction routes between hydrophobic residues of the mTS protein N-terminal segment and the active site are also discussed.

Antioxidants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 946
Author(s):  
Tom E. Forshaw ◽  
Julie A. Reisz ◽  
Kimberly J. Nelson ◽  
Rajesh Gumpena ◽  
J. Reed Lawson ◽  
...  

Human peroxiredoxins (Prx) are a family of antioxidant enzymes involved in a myriad of cellular functions and diseases. During the reaction with peroxides (e.g., H2O2), the typical 2-Cys Prxs change oligomeric structure between higher order (do)decamers and disulfide-linked dimers, with the hyperoxidized inactive state (-SO2H) favoring the multimeric structure of the reduced enzyme. Here, we present a study on the structural requirements for the repair of hyperoxidized 2-Cys Prxs by human sulfiredoxin (Srx) and the relative efficacy of physiological reductants hydrogen sulfide (H2S) and glutathione (GSH) in this reaction. The crystal structure of the toroidal Prx1-Srx complex shows an extended active site interface. The loss of this interface within engineered Prx2 and Prx3 dimers yielded variants more resistant to hyperoxidation and repair by Srx. Finally, we reveal for the first time Prx isoform-dependent use of and potential cooperation between GSH and H2S in supporting Srx activity.


Author(s):  
Kohei Sasamoto ◽  
Tomoki Himiyama ◽  
Kunihiko Moriyoshi ◽  
Takashi Ohmoto ◽  
Koichi Uegaki ◽  
...  

The acetylxylan esterases (AXEs) classified into carbohydrate esterase family 4 (CE4) are metalloenzymes that catalyze the deacetylation of acetylated carbohydrates. AXE from Caldanaerobacter subterraneus subsp. tengcongensis (TTE0866), which belongs to CE4, is composed of three parts: a signal sequence (residues 1–22), an N-terminal region (NTR; residues 23–135) and a catalytic domain (residues 136–324). TTE0866 catalyzes the deacetylation of highly substituted cellulose acetate and is expected to be useful for industrial applications in the reuse of resources. In this study, the crystal structure of TTE0866 (residues 23–324) was successfully determined. The crystal diffracted to 1.9 Å resolution and belonged to space group I212121. The catalytic domain (residues 136–321) exhibited a (β/α)7-barrel topology. However, electron density was not observed for the NTR (residues 23–135). The crystal packing revealed the presence of an intermolecular space without observable electron density, indicating that the NTR occupies this space without a defined conformation or was truncated during the crystallization process. Although the active-site conformation of TTE0866 was found to be highly similar to those of other CE4 enzymes, the orientation of its Trp264 side chain near the active site was clearly distinct. The unique orientation of the Trp264 side chain formed a different-shaped cavity within TTE0866, which may contribute to its reactivity towards highly substituted cellulose acetate.


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.


2020 ◽  
Vol 76 (12) ◽  
pp. 1211-1221
Author(s):  
Manon Mirgaux ◽  
Laurence Leherte ◽  
Johan Wouters

Indoleamine 2,3-dioxygenase 1 has sparked interest as an immunotherapeutic target in cancer research. Its structure includes a loop, named the JK-loop, that controls the orientation of the substrate or inhibitor within the active site. However, little has been reported about the crystal structure of this loop. In the present work, the conformation of the JK-loop is determined for the first time in the presence of the heme cofactor in the active site through X-ray diffraction experiments (2.44 Å resolution). Molecular-dynamics trajectories were also obtained to provide dynamic information about the loop according to the presence of cofactor. This new structural and dynamic information highlights the importance of the JK-loop in confining the labile heme cofactor to the active site.


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 ◽  
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.


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.


2004 ◽  
Vol 279 (16) ◽  
pp. 16638-16645 ◽  
Author(s):  
Kenneth K.-S. Ng ◽  
Natalia Pendás-Franco ◽  
Jorge Rojo ◽  
José A. Boga ◽  
Àngeles Machín ◽  
...  

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.


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