scholarly journals ω-Oxidation impairs oxidizability of polyenoic fatty acids by 15-lipoxygenases: consequences for substrate orientation at the active site

1998 ◽  
Vol 336 (2) ◽  
pp. 345-352 ◽  
Author(s):  
Igor IVANOV ◽  
Kristin SCHWARZ ◽  
Herman G. HOLZHÜTTER ◽  
Galina MYAGKOVA ◽  
Hartmut KÜHN
Keyword(s):  
Fatty Acids ◽  
Active Site ◽  
Substrate Binding ◽  
Salt Bridge ◽  
Binding Pocket ◽  
Substrate Affinity ◽  
Carboxylate Group ◽  
Fatty Acid Binding ◽  
Substrate Orientation ◽  
Binding Cleft

During oxygenation by 15-lipoxygenases, polyenoic fatty acids are bound at the active site in such a way that the ω-terminus of the fatty acids penetrates into the substrate binding pocket. In contrast, for arachidonic acid 5-lipoxygenation, an inverse head to tail orientation has been suggested. However, an inverse orientation may be hindered by the large energy barrier associated with burying the charged carboxylate group in the hydrophobic environment of the substrate binding cleft. We studied the oxygenation kinetics of ω-modified fatty acids by 15-lipoxygenases and found that ω-hydroxylation strongly impaired substrate affinity (higher Km), but only moderately altered Vmax. In contrast, ω-carboxylation completely prevented the lipoxygenase reaction; however, methylation of the additional carboxylate group restored the activity. Arg403 of the human 15-lipoxygenase has been implicated in fatty acid binding by forming a salt bridge with the carboxylate group, and thus mutation of this amino acid to an uncharged residue was supposed to favour an inverse substrate orientation. The prepared Arg403 → Leu mutant of the rabbit 15-lipoxygenase was found to be a less effective catalyst of linoleic acid oxygenation. However, the oxygenation rate of ω-hydroxyarachidonic acid was similar when the wild-type and mutant enzyme were compared, and the patterns of oxygenation products were identical for both enzyme species. These data suggest that introduction of a polar, or even charged residue, at the ω-terminus of substrate fatty acids in connection with mutation of Arg403 may not alter substrate alignment at the active site of 15-lipoxygenases.

scholarly journals Improving the Substrate Affinity and Catalytic Efficiency of β-Glucosidase Bgl3A from Talaromyces leycettanus JCM12802 by Rational Design

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1882
Author(s):  
Wei Xia ◽  
Yingguo Bai ◽  
Pengjun Shi
Keyword(s):  
Hydrogen Bonding ◽  
Rational Design ◽  
Substrate Binding ◽  
Enzymatic Saccharification ◽  
Catalytic Efficiency ◽  
Binding Pocket ◽  
Glycoside Hydrolases ◽  
Cellulosic Biomass ◽  
Substrate Affinity ◽  
Hydrogen Bonding Networks

Improving the substrate affinity and catalytic efficiency of β-glucosidase is necessary for better performance in the enzymatic saccharification of cellulosic biomass because of its ability to prevent cellobiose inhibition on cellulases. Bgl3A from Talaromyces leycettanus JCM12802, identified in our previous work, was considered a suitable candidate enzyme for efficient cellulose saccharification with higher catalytic efficiency on the natural substrate cellobiose compared with other β-glucosidase but showed insufficient substrate affinity. In this work, hydrophobic stacking interaction and hydrogen-bonding networks in the active center of Bgl3A were analyzed and rationally designed to strengthen substrate binding. Three vital residues, Met36, Phe66, and Glu168, which were supposed to influence substrate binding by stabilizing adjacent binding site, were chosen for mutagenesis. The results indicated that strengthening the hydrophobic interaction between stacking aromatic residue and the substrate, and stabilizing the hydrogen-bonding networks in the binding pocket could contribute to the stabilized substrate combination. Four dominant mutants, M36E, M36N, F66Y, and E168Q with significantly lower Km values and 1.4–2.3-fold catalytic efficiencies, were obtained. These findings may provide a valuable reference for the design of other β-glucosidases and even glycoside hydrolases.

scholarly journals The activation loop and substrate-binding cleft of glutaminase C are allosterically coupled

2019 ◽  
Vol 295 (5) ◽  
pp. 1328-1337
Author(s):  
Yunxing Li ◽  
Sekar Ramachandran ◽  
Thuy-Tien T. Nguyen ◽  
Clint A. Stalnecker ◽  
Richard A. Cerione ◽  
...  
Keyword(s):  
Substrate Binding ◽  
Fluorescence Emission ◽  
Reciprocal Relationship ◽  
Tryptophan Residue ◽  
Substrate Affinity ◽  
Activation Loop ◽  
Conformational Coupling ◽  
Binding Cleft ◽  
Glutaminase Activity

The glutaminase C (GAC) isoform of mitochondrial glutaminase is overexpressed in many cancer cells and therefore represents a potential therapeutic target. Understanding the regulation of GAC activity has been guided by the development of spectroscopic approaches that measure glutaminase activity in real time. Previously, we engineered a GAC protein (GAC(F327W)) in which a tryptophan residue is substituted for phenylalanine in an activation loop to explore the role of this loop in enzyme activity. We showed that the fluorescence emission of Trp-327 is enhanced in response to activator binding, but quenched by inhibitors of the BPTES class that bind to the GAC tetramer and contact the activation loop, thereby constraining it in an inactive conformation. In the present work, we took advantage of a tryptophan substitution at position 471, proximal to the GAC catalytic site, to examine the conformational coupling between the activation loop and the substrate-binding cleft, separated by ∼16 Å. Comparison of glutamine binding in the presence or absence of the BPTES analog CB-839 revealed a reciprocal relationship between the constraints imposed on the activation loop position and the affinity of GAC for substrate. Binding of the inhibitor weakened the affinity of GAC for glutamine, whereas activating anions such as Pi increased this affinity. These results indicate that the conformations of the activation loop and the substrate-binding cleft in GAC are allosterically coupled and that this coupling determines substrate affinity and enzymatic activity and explains the activities of CB-839, which is currently in clinical trials.

scholarly journals Phylogeny and Structure of Fatty Acid Photodecarboxylases and Glucose-Methanol-Choline Oxidoreductases

Catalysts ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1072
Author(s):  
Vladimir A. Aleksenko ◽  
Deepak Anand ◽  
Alina Remeeva ◽  
Vera V. Nazarenko ◽  
Valentin Gordeliy ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Active Site ◽  
Binding Pocket ◽  
Active Site Residues ◽  
Large Dataset ◽  
Fatty Acid Binding ◽  
Fossil Carbon ◽  
Related Family ◽  
Fungal Genes ◽  
Flavin Binding

Glucose-methanol-choline (GMC) oxidoreductases are a large and diverse family of flavin-binding enzymes found in all kingdoms of life. Recently, a new related family of proteins has been discovered in algae named fatty acid photodecarboxylases (FAPs). These enzymes use the energy of light to convert fatty acids to the corresponding Cn-1 alkanes or alkenes, and hold great potential for biotechnological application. In this work, we aimed at uncovering the natural diversity of FAPs and their relations with other GMC oxidoreductases. We reviewed the available GMC structures, assembled a large dataset of GMC sequences, and found that one active site amino acid, a histidine, is extremely well conserved among the GMC proteins but not among FAPs, where it is replaced with alanine. Using this criterion, we found several new potential FAP genes, both in genomic and metagenomic databases, and showed that related bacterial, archaeal and fungal genes are unlikely to be FAPs. We also identified several uncharacterized clusters of GMC-like proteins as well as subfamilies of proteins that lack the conserved histidine but are not FAPs. Finally, the analysis of the collected dataset of potential photodecarboxylase sequences revealed the key active site residues that are strictly conserved, whereas other residues in the vicinity of the flavin adenine dinucleotide (FAD) cofactor and in the fatty acid-binding pocket are more variable. The identified variants may have different FAP activity and selectivity and consequently may prove useful for new biotechnological applications, thereby fostering the transition from a fossil carbon-based economy to a bio-economy by enabling the sustainable production of hydrocarbon fuels.

scholarly journals Purification and characterization of Ak.1 protease, a thermostable subtilisin with a disulphide bond in the substrate-binding cleft

2000 ◽  
Vol 350 (1) ◽  
pp. 321-328 ◽  
Author(s):  
Helen S. TOOGOOD ◽  
Clyde A. SMITH ◽  
Edward N. BAKER ◽  
Roy M. DANIEL
Keyword(s):  
Active Site ◽  
Substrate Binding ◽  
Fold Increase ◽  
Branched Chain Amino Acids ◽  
Disulphide Bond ◽  
Purification And Characterization ◽  
Active Site Cleft ◽  
Binding Cleft ◽  
Branched Chain

Ak.1 protease, a thermostable subtilisin isolated originally from Bacillus st. Ak.1, was purified to homogeneity from the Escherichia coli clone PB5517. It is active against substrates containing neutral or hydrophobic branched-chain amino acids at the P1 site, such as valine, alanine or phenylalanine. The Km and kcat of the enzyme decrease with decreasing temperature, though not to the same degree with all substrates, suggesting that specificity changes with temperature. The protease is markedly stabilized by Ca2+ ions. At 70°C, a 10-fold increase in Ca2+ concentration increases the half-life by three orders of magnitude. Ak.1 protease is stabilized by Ca2+ to a greater extent than is thermitase. This may be due, in part, to the presence of an extra Ca2+-binding site in Ak.1 protease. Other metal ions, such as Sr2+, increase the thermostability of the enzyme, but to a significantly lower degree than does Ca2+. The structure of the protease showed the presence of a disulphide bond located within the active-site cleft. This bond influences both enzyme activity and thermostability. The disulphide bond appears to have a dual role: maintaining the integrity of the substrate-binding cleft and increasing the thermostability of the protease. The protease was originally investigated to determine its usefulness in the clean-up of DNA at high temperatures. However, it was found that this protease has a limited substrate specificity, so this application was not explored further.

scholarly journals Identification of the site of oxidase substrate binding inScytalidium thermophilumcatalase

2018 ◽  
Vol 74 (10) ◽  
pp. 979-985 ◽  
Author(s):  
Yonca Yuzugullu Karakus ◽  
Gunce Goc ◽  
Sinem Balci ◽  
Briony A. Yorke ◽  
Chi H. Trinh ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Kinetic Analysis ◽  
Binding Site ◽  
Active Site ◽  
Oxidase Activity ◽  
Substrate Binding ◽  
Binding Pocket ◽  
Scytalidium Thermophilum ◽  
Lateral Channel

The catalase fromScytalidium thermophilumis a homotetramer containing a hemedin each active site. Although the enzyme has a classical monofunctional catalase fold, it also possesses oxidase activity towards a number of small organics, including catechol and phenol. In order to further investigate this, the crystal structure of the complex of the catalase with the classical catalase inhibitor 3-amino-1,2,4-triazole (3TR) was determined at 1.95 Å resolution. Surprisingly, no binding to the heme site was observed; instead, 3TR occupies a binding site corresponding to the NADPH-binding pocket in mammalian catalases at the entrance to a lateral channel leading to the heme. Kinetic analysis of site-directed mutants supports the assignment of this pocket as the binding site for oxidase substrates.

scholarly journals Effect of replacement of ferriprotoporphyrin IX in the haem domain of cytochrome P-450 BM-3 on substrate binding and catalytic activity

1995 ◽  
Vol 310 (3) ◽  
pp. 939-943 ◽  
Author(s):  
S Modi ◽  
W U Primrose ◽  
L Y Lian ◽  
G C K Roberts
Keyword(s):  
Fatty Acids ◽  
Catalytic Properties ◽  
Substrate Binding ◽  
Dimethyl Ester ◽  
Binding Pocket ◽  
Dodecanoic Acid ◽  
Catalytic Rate ◽  
Cytochrome P 450 ◽  
Haem Iron ◽  
Reductase Domain

Bacillus megaterium cytochrome P-450 BM-3 (coded by gene CYP102) is a catalytically self-sufficient mono-oxygenase, with both cytochrome P-450 and NADPH:cytochrome P-450 reductase domains, that catalyses the hydroxylation of fatty acids. The natural ferriprotoporphyrin IX has been removed from the haem domain of cytochrome P-450 BM-3 by treatment with acidified acetone, and it has been shown that, under carefully controlled conditions, haem can be added back to the resultant apoprotein to obtain a fully reconstituted haem domain with spectroscopic, substrate-binding and catalytic properties indistinguishable from those of the native domain. Replacement of the natural haem with ferriprotoporphyrin IX dimethyl ester yields a protein which has a higher affinity for the substrate dodecanoic acid and (in the presence of the reductase domain) the same catalytic rate as the native haem domain. Replacement with ferrimesoporphyrin IX yields a protein with the same affinity for substrate, but a reduced catalytic turnover. These results suggest that the haem moiety has a role in the creation of the binding pocket for substrate, and that modification of the electron density on the haem iron effects the catalytic rate.

Structural and mechanistic insight into how antibodies inhibit serine proteases

2010 ◽  
Vol 430 (2) ◽  
pp. 179-189 ◽  
Author(s):  
Rajkumar Ganesan ◽  
Charles Eigenbrot ◽  
Daniel Kirchhofer
Keyword(s):  
Active Site ◽  
Serine Proteases ◽  
Structural Changes ◽  
Competitive Inhibition ◽  
Substrate Binding ◽  
Structural Features ◽  
Inhibition Mechanism ◽  
Interaction Sites ◽  
Binding Cleft ◽  
Insight Into

Antibodies display great versatility in protein interactions and have become important therapeutic agents for a variety of human diseases. Their ability to discriminate between highly conserved sequences could be of great use for therapeutic approaches that target proteases, for which structural features are conserved among family members. Recent crystal structures of antibody–protease complexes provide exciting insight into the variety of ways antibodies can interfere with the catalytic machinery of serine proteases. The studies revealed the molecular details of two fundamental mechanisms by which antibodies inhibit catalysis of trypsin-like serine proteases, exemplified by hepatocyte growth factor activator and MT-SP1 (matriptase). Enzyme kinetics defines both mechanisms as competitive inhibition systems, yet, on the molecular level, they involve distinct structural elements of the active-site region. In the steric hindrance mechanism, the antibody binds to protruding surface loops and inserts one or two CDR (complementarity-determining region) loops into the enzyme's substrate-binding cleft, which results in obstruction of substrate access. In the allosteric inhibition mechanism the antibody binds outside the active site at the periphery of the substrate-binding cleft and, mediated through a conformational change of a surface loop, imposes structural changes at important substrate interaction sites resulting in impaired catalysis. At the centre of this allosteric mechanism is the 99-loop, which is sandwiched between the substrate and the antibody-binding sites and serves as a mobile conduit between these sites. These findings provide comprehensive structural and functional insight into the molecular versatility of antibodies for interfering with the catalytic machinery of proteases.

Targeting the Genetic Resistance of JAK2 and BCR/ABL by TG101348

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 3765-3765
Author(s):  
Meenu Kesarwani ◽  
Mohammad Azam
Keyword(s):  
Active Site ◽  
Myeloproliferative Neoplasms ◽  
Substrate Binding ◽  
Genetic Resistance ◽  
Structural Modeling ◽  
Binding Pocket ◽  
Janus Kinase ◽  
Substrate Binding Pocket ◽  
Modeling Studies

Abstract Abstract 3765 The inherent preponderance of genetic resistance against tyrosine kinase inhibitor (TKI) therapy poses significant challenge for effective treatments. Recent approval of Janus kinase 2 (JAK2) inhibitor INCB018424 (Jakafi, ruxolitinib) for the treatment of myeloproliferative neoplasms (MPNs) prompted us to identify resistant mutations that may pose clinical challenge. In vitro drug selection screening against two leading JAK2 inhibitors (INCB018424 and TG101348) were performed. Here we show that like other kinase inhibitors, INCB018424 is prone to genetic resistance while TG101348 is recalcitrant to develop in vitro resistance. Sequencing of INCB018424 resistant clones identified 211 amino acid substitutions spanning across FERM, SH2, JH2 and the kinase domain. Biochemical and structural modeling studies of these mutants demonstrate that mutations within the active site confer resistance either by direct steric hindrance or destabilizing the architecture of the active site. And mutations from the allosteric sites destabilize the intermediary state of the active and inactive conformations of JAK2 to which INCB018424 preferentially binds. Furthermore, these resistant variants are cross resistant to other JAK2 inhbitors (Lestaurtinib, CYT-387 and AZD1480). In contrast, these resistant variants are fully sensitive to TG101348 supporting the lack of resistance against this compound as observed during in vitro screening. Structural modeling studies revealed that TG101348 stabilizes the active conformation of the kinase and binds to the substrate-binding pocket. Mutations affecting the substrate-binding pocket may either alter substrate binding/phosphorylation or encode an incompetent kinase that blocks the emergence of resistance. Because JAK2 and BCR/ABL share a common substrate, STAT5, they might have similar architecture of the substrate-binding pocket, which may allow the inhibition of BCR/ABL by TG101348. Indeed, TG101348 can inhibit both native and gatekeeper variants of BCR/ABL and in vitro drug resistant screening failed to develop emergence of resistant clones. These studies provide evidence that the patients developing resistant variants of JAK2 and BCR/ABL can be treated with TG101348 and support for future drug design geared towards targeting the substrate binding sites in other oncogenic kinases for better and sustained therapeutic response. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Structural Insights for Core Scaffold and Substrate Specificity of B1, B2, and B3 Metallo-β-Lactamases

2022 ◽  
Vol 12 ◽  
Author(s):  
Yeongjin Yun ◽  
Sangjun Han ◽  
Yoon Sik Park ◽  
Hyunjae Park ◽  
Dogyeong Kim ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Active Site ◽  
Chemical Structure ◽  
Substrate Binding ◽  
Binding Pocket ◽  
Structural Features ◽  
Amino Acid Sequences ◽  
Zinc Ions ◽  
Substrate Binding Pocket ◽  
Inhibitory Spectrum

Metallo-β-lactamases (MBLs) hydrolyze almost all β-lactam antibiotics, including penicillins, cephalosporins, and carbapenems; however, no effective inhibitors are currently clinically available. MBLs are classified into three subclasses: B1, B2, and B3. Although the amino acid sequences of MBLs are varied, their overall scaffold is well conserved. In this study, we systematically studied the primary sequences and crystal structures of all subclasses of MBLs, especially the core scaffold, the zinc-coordinating residues in the active site, and the substrate-binding pocket. We presented the conserved structural features of MBLs in the same subclass and the characteristics of MBLs of each subclass. The catalytic zinc ions are bound with four loops from the two central β-sheets in the conserved αβ/βα sandwich fold of MBLs. The three external loops cover the zinc site(s) from the outside and simultaneously form a substrate-binding pocket. In the overall structure, B1 and B2 MBLs are more closely related to each other than they are to B3 MBLs. However, B1 and B3 MBLs have two zinc ions in the active site, while B2 MBLs have one. The substrate-binding pocket is different among all three subclasses, which is especially important for substrate specificity and drug resistance. Thus far, various classes of β-lactam antibiotics have been developed to have modified ring structures and substituted R groups. Currently available structures of β-lactam-bound MBLs show that the binding of β-lactams is well conserved according to the overall chemical structure in the substrate-binding pocket. Besides β-lactam substrates, B1 and cross-class MBL inhibitors also have distinguished differences in the chemical structure, which fit well to the substrate-binding pocket of MBLs within their inhibitory spectrum. The systematic structural comparison among B1, B2, and B3 MBLs provides in-depth insight into their substrate specificity, which will be useful for developing a clinical inhibitor targeting MBLs.

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