Journal articles: 'Enzyme structure/function'

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Poulos, Thomas L. "Heme Enzyme Structure and Function." Chemical Reviews 114, no. 7 (January 8, 2014): 3919–62. http://dx.doi.org/10.1021/cr400415k.

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Latip, Wahhida, Victor Feizal Knight, Norhana Abdul Halim, Keat Khim Ong, Noor Azilah Mohd Kassim, Wan Md Zin Wan Yunus, Siti Aminah Mohd Noor, and Mohd Shukuri Mohamad Ali. "Microbial Phosphotriesterase: Structure, Function, and Biotechnological Applications." Catalysts 9, no. 8 (August 7, 2019): 671. http://dx.doi.org/10.3390/catal9080671.

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The role of phosphotriesterase as an enzyme which is able to hydrolyze organophosphate compounds cannot be disputed. Contamination by organophosphate (OP) compounds in the environment is alarming, and even more worrying is the toxicity of this compound, which affects the nervous system. Thus, it is important to find a safer way to detoxify, detect and recuperate from the toxicity effects of this compound. Phosphotriesterases (PTEs) are mostly isolated from soil bacteria and are classified as metalloenzymes or metal-dependent enzymes that contain bimetals at the active site. There are three separate pockets to accommodate the substrate into the active site of each PTE. This enzyme generally shows a high catalytic activity towards phosphotriesters. These microbial enzymes are robust and easy to manipulate. Currently, PTEs are widely studied for the detection, detoxification, and enzyme therapies for OP compound poisoning incidents. The discovery and understanding of PTEs would pave ways for greener approaches in biotechnological applications and to solve environmental issues relating to OP contamination.

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Sakiyama, Fumio. "Modification of enzyme structure and function." Kobunshi 35, no. 10 (1986): 950–53. http://dx.doi.org/10.1295/kobunshi.35.950.

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Hatzimanikatis, Vassily, Chunhui Li, Justin A. Ionita, and Linda J. Broadbelt. "Metabolic networks: enzyme function and metabolite structure." Current Opinion in Structural Biology 14, no. 3 (June 2004): 300–306. http://dx.doi.org/10.1016/j.sbi.2004.04.004.

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Thornton, Janet. "THE EVOLUTION OF ENZYME STRUCTURE AND FUNCTION." Biochemical Society Transactions 28, no. 3 (June 1, 2000): A53. http://dx.doi.org/10.1042/bst028a053.

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Kuriki, Takashi, Han-Ping Guan, and Jack Preiss. "Structure and Function of Starch Branching Enzyme." Journal of the agricultural chemical society of Japan 68, no. 11 (1994): 1581–84. http://dx.doi.org/10.1271/nogeikagaku1924.68.1581.

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von Grotthuss, M., D. Plewczynski, G. Vriend, and L. Rychlewski. "3D-Fun: predicting enzyme function from structure." Nucleic Acids Research 36, Web Server (May 19, 2008): W303—W307. http://dx.doi.org/10.1093/nar/gkn308.

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Carroll, Joanne M., Kwang Soo Kim, M. Elizabeth Ross, Marian J. Evinger, Soonjung L. Hahn, and Tong H. Joh. "Structure and function of catecholamine enzyme genes." Journal of the Autonomic Nervous System 33, no. 2 (May 1991): 129–30. http://dx.doi.org/10.1016/0165-1838(91)90160-5.

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ALDERTON, Wendy K., Chris E. COOPER, and Richard G. KNOWLES. "Nitric oxide synthases: structure, function and inhibition." Biochemical Journal 357, no. 3 (July 25, 2001): 593–615. http://dx.doi.org/10.1042/bj3570593.

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This review concentrates on advances in nitric oxide synthase (NOS) structure, function and inhibition made in the last seven years, during which time substantial advances have been made in our understanding of this enzyme family. There is now information on the enzyme structure at all levels from primary (amino acid sequence) to quaternary (dimerization, association with other proteins) structure. The crystal structures of the oxygenase domains of inducible NOS (iNOS) and vascular endothelial NOS (eNOS) allow us to interpret other information in the context of this important part of the enzyme, with its binding sites for iron protoporphyrin IX (haem), biopterin, l-arginine, and the many inhibitors which interact with them. The exact nature of the NOS reaction, its mechanism and its products continue to be sources of controversy. The role of the biopterin cofactor is now becoming clearer, with emerging data implicating one-electron redox cycling as well as the multiple allosteric effects on enzyme activity. Regulation of the NOSs has been described at all levels from gene transcription to covalent modification and allosteric regulation of the enzyme itself. A wide range of NOS inhibitors have been discussed, interacting with the enzyme in diverse ways in terms of site and mechanism of inhibition, time-dependence and selectivity for individual isoforms, although there are many pitfalls and misunderstandings of these aspects. Highly selective inhibitors of iNOS versus eNOS and neuronal NOS have been identified and some of these have potential in the treatment of a range of inflammatory and other conditions in which iNOS has been implicated.

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Watschinger, Katrin, Julian E. Fuchs, Vladimir Yarov-Yarovoy, Markus A. Keller, Georg Golderer, Albin Hermetter, Gabriele Werner-Felmayer, Nicolas Hulo, and Ernst R. Werner. "First insights into structure-function relationships of alkylglycerol monooxygenase." Pteridines 24, no. 1 (June 1, 2013): 99–103. http://dx.doi.org/10.1515/pterid-2013-0007.

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AbstractAlkylglycerol monooxygenase is a tetrahydrobiopterin-dependent enzyme that cleaves the O-alkyl-bond of alkylglycerols. It is an exceptionally unstable, hydrophobic membrane protein which has never been purified in active form. Recently, we were able to identify the sequence of alkylglycerol monooxygenase. TMEM195, the gene coding for alkylglycerol monooxygenase, belongs to the fatty acid hydroxylases, a family of integral membrane enzymes which have an 8-histidine motif crucial for catalysis. Mutation of each of these residues resulted in a complete loss of activity. We now extended the mutational analysis to another 25 residues and identified three further residues conserved throughout all members of the fatty acid hydroxylases which are essential for alkylglycerol monooxygenase activity. Furthermore, mutation of a specific glutamate resulted in an 18-fold decreased affinity of the protein to tetrahydrobiopterin, strongly indicating a potential important role in cofactor interaction. A glutamate residue in a comparable amino acid surrounding had already been shown to be responsible for tetrahydrobiopterin binding in the aromatic amino acid hydroxylases. Ab initio modelling of the enzyme yielded a structural model for the central part of alkylglycerol monooxygenase where all essential residues identified by mutational analysis are in close spatial vicinity, thereby defining the potential catalytic site of this enzyme.

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Schilling, Klaus, Alexandra Körner, Saskia Sehmisch, Annett Kreusch, Ramona Kleint, Yvonne Benedix, Anne Schlabrakowski, and Bernd Wiederanders. "Selectivity of propeptide-enzyme interaction in cathepsin L-like cysteine proteases." Biological Chemistry 390, no. 2 (February 1, 2009): 167–74. http://dx.doi.org/10.1515/bc.2009.023.

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Abstract Cathepsin L-like endopeptidases of the papain family are synthesized as proenzymes. N-terminal proregions are essential for folding and latency of the enzyme unit. While selectivity has been reported for the inhibitory function of papain-family propeptides, there is no systematic investigation of the selectivity of their chaperone-like function to date. The chaperone-like cross-reactivity between the cathepsins S, K, and L were thoroughly quantified in trans-experiments, i.e., with isolated propeptides and mature enzymes, and compared to the inhibitory cross-reactivity. The three endopeptidases have been chosen due to only minimal evolutionary distance and nearly identical X-ray structures of their zymogenes. The intramolecular chaperone function of the proregion was found to be more selective than the inhibitory activity and significant differences were found between the selectivity profiles, underlining the assumption that the inhibitory and the chaperone-like propeptide functions are autonomous. Considering the data published on the intramolecular chaperone-like propeptide function within other protease classes as well, our data suggest that intrinsically structured propeptides are more selective than intrinsically unstructured propeptides, i.e., those adopting tertiary structure elements only in complex with their maternal enzyme.

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Supuran, Claudiu T. "Structure and function of carbonic anhydrases." Biochemical Journal 473, no. 14 (July 12, 2016): 2023–32. http://dx.doi.org/10.1042/bcj20160115.

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Carbonic anhydrases (CAs, EC 4.2.1.1) catalyse the interconversion between CO2 and bicarbonate as well as other hydrolytic reactions. Among the six genetic families known to date, the α-, β-, γ-, δ-, ζ- and η-CAs, detailed kinetic and X-ray crystallographic studies have allowed a deep understanding of the structure–function relationship in this superfamily of proteins. A metal hydroxide nucleophilic species of the enzyme, and a unique active site architecture, with half of it hydrophilic and the opposing part hydrophobic, allow these enzymes to act as some of the most effective catalysts known in Nature. The CA activation and inhibition mechanisms are also known in detail, with a large number of new inhibitor classes being described in the last years. Apart from the zinc binders, some classes of inhibitors anchor to the metal ion coordinated nucleophile, others occlude the entrance of the active site cavity and more recently, compounds binding outside the active site were described. CA inhibition has therapeutic applications for drugs acting as diuretics, antiepileptics, antiglaucoma, antiobesity and antitumour agents. Targeting such enzymes from pathogens may lead to novel anti-infectives. Successful structure-based drug design campaigns allowed the discovery of highly isoform selective CA inhibitors (CAIs), which may lead to a new generation of drugs targeting these widespread enzymes. The use of CAs in CO2 capture processes for mitigating the global temperature rise has also been investigated more recently.

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Page, Michael J., and Enrico Di Cera. "Role of Na+and K+in Enzyme Function." Physiological Reviews 86, no. 4 (October 2006): 1049–92. http://dx.doi.org/10.1152/physrev.00008.2006.

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Metal complexation is a key mediator or modifier of enzyme structure and function. In addition to divalent and polyvalent metals, group IA metals Na+and K+play important and specific roles that assist function of biological macromolecules. We examine the diversity of monovalent cation (M+)-activated enzymes by first comparing coordination in small molecules followed by a discussion of theoretical and practical aspects. Select examples of enzymes that utilize M+as a cofactor (type I) or allosteric effector (type II) illustrate the structural basis of activation by Na+and K+, along with unexpected connections with ion transporters. Kinetic expressions are derived for the analysis of type I and type II activation. In conclusion, we address evolutionary implications of Na+binding in the trypsin-like proteases of vertebrate blood coagulation. From this analysis, M+complexation has the potential to be an efficient regulator of enzyme catalysis and stability and offers novel strategies for protein engineering to improve enzyme function.

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Mano, Erica Candido Costa, Ana Ligia Scott, and Kathia M. Honorio. "UDP-glucuronosyltransferases: Structure, Function and Drug Design Studies." Current Medicinal Chemistry 25, no. 27 (September 4, 2018): 3247–55. http://dx.doi.org/10.2174/0929867325666180226111311.

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UDP-glucuronosyltransferases (UGTs) are important phase II metabolic enzymes responsible for approximately 40-70% of endo and xenobiotic reactions. It catalyzes the transfer of glucuronic acid to lipophilic substrates, converting them into hydrophilic compounds that are excreted. There are 22 active human UGTs that belong to 4 families. This review focuses on human UGTs, highlighting the most current issues in order to connect all information available and allowing a discussion on the challenges already solved and those in which we need to move forward. Although, several UGTs studies have been conducted, the most recent ones addressing drug-drug interactions and polymorphism issues, there are still bottlenecks to overcome. Tridimensional structure is difficult to obtain due to overexpression, purification, and crystallization problems as well as the action mechanism - since overlapping of substrate specificities renders impasses on the identification of which isoform is responsible for a particular drug metabolic pathway. For this reason, bioinformatic tools are gaining more space, since it is a faster and less expensive reliable methodology that complements in vitro and in vivo researches. Combinations of quantum and molecular methods have become increasingly common, leading to the incorporation of enzyme features comprising their structure, dynamics and chemical reactions. Breakthroughs related to the enzyme, not only enable the discovery of new drugs essential for the treatment of various diseases, but also provide an improved action of the existing drugs.

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Eklund, Hans, Ulla Uhlin, Mathias Färnegårdh, Derek T. Logan, and Pär Nordlund. "Structure and function of the radical enzyme ribonucleotide reductase." Progress in Biophysics and Molecular Biology 77, no. 3 (November 2001): 177–268. http://dx.doi.org/10.1016/s0079-6107(01)00014-1.

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Mikami, Bunzo, Hirotaka Bitoh, Yurie Anzai, Kimihiko Mizutani, Nobuyuki Takahashi, Masamichi Okada, and Shotaro Yamaguchi. "Structure and Function Analysis of Geobacillus Starch Antistaling Enzyme." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C469. http://dx.doi.org/10.1107/s2053273314095308.

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Glycosyltransferase from Geobacillus sp. (SAS) is expected to see wide use as a starch antistaling enzyme in food including bread and rice products. The enzyme is thought to transfer maltotriose (G3) unit into non-reducing ends of sarch with unknown likage except for usual alpha-1,4 linkage. SAS was crystallized by sitting drop vapar diffusion method in 14~28% PEG4000 (w/v), 10mM CaCl2, 0.1M NaAC at pH 4.6 and 20°C for 1 month. The obtained crystals belong to a space group of P6522 with cell dimensions of a = b = 112 and c = 320 Å. The crystals were soaked in various oligomaltosaccharides (G1, G2, G3, G4, G5 and G6) for 15 min before flash cooling. The diffraction data of each complex were collected at beam-lines of BL26B1, BL38B1 and BL44XU in SPring-8. The crystal data were collected with 97-99 % completeness and Rmerge of 0.07-0.09 up to 1.6-2.3 Å resolution. The structures were determined by molecular replacement with cyclodextrin glucanotransferase (CGTase, PDB 1CYG) as a search model and were refined with PHENIX. The refined models of SAS/sugars contain one molecule of SAS comprising 733 amino acid residues, 5-8 calcium ions, 543-1141 water molecules and several sugars with R = 0.15-0.19 and Rfree = 0.16-0.23 for the data up to 1.6-2.3 Å resolution. SAS has almost the same overall structure with the CGTase except for several loops in the catalytic domain A. They share a similar active site except for subsite +3 where the non-reducing ends of the oligosaccharides bind. G1 bound to subsite +3, indicating +3 site has the highest affinity to G1. Only G3 was found to bind at subsites +3 ~ +1 when G3, G5 and G6 were soaked, whereas G4 bound at subsites +3 ~ -1 when G4 was soaked. From the clear density map of the bound G4, the bound glucose residue at subsute -1 is found to have alpha-1,6 linkage, indicating the product of this transglucosidase.

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Höfer, Katharina, Sisi Li, Florian Abele, Jens Frindert, Jasmin Schlotthauer, Julia Grawenhoff, Jiamu Du, Dinshaw J. Patel, and Andres Jäschke. "Structure and function of the bacterial decapping enzyme NudC." Nature Chemical Biology 12, no. 9 (July 18, 2016): 730–34. http://dx.doi.org/10.1038/nchembio.2132.

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Corazza, A., M. Scarpa, A. Corazza, F. Vianello, L. Zennaro, N. Gourova, M. L. Di Paolo, L. Signor, O. Marin, and A. Rigo. "Enzyme mimics complexing Cu(II) ion: structure-function relationships." Journal of Peptide Research 54, no. 6 (December 1999): 491–504. http://dx.doi.org/10.1034/j.1399-3011.1999.00139.x.

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Kenyon, George L., John A. Gerlt, Gregory A. Petsko, and John W. Kozarich. "Mandelate Racemase: Structure-Function Studies of a Pseudosymmetric Enzyme." Accounts of Chemical Research 28, no. 4 (April 1995): 178–86. http://dx.doi.org/10.1021/ar00052a003.

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Carlson, Brian L., Edward R. Ballister, Emmanuel Skordalakes, David S. King, Mark A. Breidenbach, Sarah A. Gilmore, James M. Berger, and Carolyn R. Bertozzi. "Function and Structure of a Prokaryotic Formylglycine-generating Enzyme." Journal of Biological Chemistry 283, no. 29 (April 4, 2008): 20117–25. http://dx.doi.org/10.1074/jbc.m800217200.

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Lloyd, Emma, and Beatrice Tam. "Structure/function studies on the haem enzyme ascorbate peroxidase." Journal of Inorganic Biochemistry 59, no. 2-3 (August 1995): 459. http://dx.doi.org/10.1016/0162-0134(95)97555-5.

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Brown, Shoshana D., and Patricia C. Babbitt. "New Insights about Enzyme Evolution from Large Scale Studies of Sequence and Structure Relationships." Journal of Biological Chemistry 289, no. 44 (September 10, 2014): 30221–28. http://dx.doi.org/10.1074/jbc.r114.569350.

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Understanding how enzymes have evolved offers clues about their structure-function relationships and mechanisms. Here, we describe evolution of functionally diverse enzyme superfamilies, each representing a large set of sequences that evolved from a common ancestor and that retain conserved features of their structures and active sites. Using several examples, we describe the different structural strategies nature has used to evolve new reaction and substrate specificities in each unique superfamily. The results provide insight about enzyme evolution that is not easily obtained from studies of one or only a few enzymes.

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Heider, Johann, Maciej Szaleniec, Berta M. Martins, Deniz Seyhan, Wolfgang Buckel, and Bernard T. Golding. "Structure and Function of Benzylsuccinate Synthase and Related Fumarate-Adding Glycyl Radical Enzymes." Journal of Molecular Microbiology and Biotechnology 26, no. 1-3 (2016): 29–44. http://dx.doi.org/10.1159/000441656.

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The pathway of anaerobic toluene degradation is initiated by a remarkable radical-type enantiospecific addition of the chemically inert methyl group to the double bond of a fumarate cosubstrate to yield (R)-benzylsuccinate as the first intermediate, as catalyzed by the glycyl radical enzyme benzylsuccinate synthase. In recent years, it has become clear that benzylsuccinate synthase is the prototype enzyme of a much larger family of fumarate-adding enzymes, which play important roles in the anaerobic metabolism of further aromatic and even aliphatic hydrocarbons. We present an overview on the biochemical properties of benzylsuccinate synthase, as well as its recently solved structure, and present the results of an initial structure-based modeling study on the reaction mechanism. Moreover, we compare the structure of benzylsuccinate synthase with those predicted for different clades of fumarate-adding enzymes, in particular the paralogous enzymes converting p-cresol, 2-methylnaphthalene or n-alkanes.

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Pangburn, M. K., and N. Rawal. "Structure and function of complement C5 convertase enzymes." Biochemical Society Transactions 30, no. 6 (November 1, 2002): 1006–10. http://dx.doi.org/10.1042/bst0301006.

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The multisubunit enzymes of the complement system that cleave C5 have many unusual properties, the most striking of which is that they acquire their specificity for C5 following cleavage of another substrate C3. C5 convertases are assemblies of two proteins C4b and C2a (classical or lectin pathways) or C3b and Bb (alternative pathway) and additional C3b molecules. The catalytic complexes (C4b, C2a or C3b, Bb) are intrinsically unstable (t1,2 = 1–3 min) and the enzymes are controlled by numerous regulatory proteins that accelerate this natural decay rate. Immediately after assembly, the bi-molecular enzymes preferentially cleave the protein C3 and exhibit poor activity toward C5 (a Km of approx. 25 μM and a C5 cleavage rate of 0.3-1 C5/min at Vmax). Efficient C3 activation results in the covalent attachment of C3b to the cell surface and to the enzyme itself, resulting in formation of C3b-C3b and C4b-C3b complexes. Our studies have shown that deposition of C3b alters the specificity of the enzymes of both pathways by changing the Km for C5 more than 1000-fold from far above the physiological C5 concentration to far below it. Thus, after processing sufficient C3 at the surface of a microorganism, the enzymes switch to processing C5, which initiates the formation of the cytolytic membrane attack complex of complement.

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Noree, Chalongrat, Elena Monfort, Andrew K. Shiau, and James E. Wilhelm. "Common regulatory control of CTP synthase enzyme activity and filament formation." Molecular Biology of the Cell 25, no. 15 (August 2014): 2282–90. http://dx.doi.org/10.1091/mbc.e14-04-0912.

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The ability of enzymes to assemble into visible supramolecular complexes is a widespread phenomenon. Such complexes have been hypothesized to play a number of roles; however, little is known about how the regulation of enzyme activity is coupled to the assembly/disassembly of these cellular structures. CTP synthase is an ideal model system for addressing this question because its activity is regulated via multiple mechanisms and its filament-forming ability is evolutionarily conserved. Our structure–function studies of CTP synthase in Saccharomyces cerevisiae reveal that destabilization of the active tetrameric form of the enzyme increases filament formation, suggesting that the filaments comprise inactive CTP synthase dimers. Furthermore, the sites responsible for feedback inhibition and allosteric activation control filament length, implying that multiple regions of the enzyme can influence filament structure. In contrast, blocking catalysis without disrupting the regulatory sites of the enzyme does not affect filament formation or length. Together our results argue that the regulatory sites that control CTP synthase function, but not enzymatic activity per se, are critical for controlling filament assembly. We predict that the ability of enzymes to form supramolecular structures in general is closely coupled to the mechanisms that regulate their activity.

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Karplus, P. A., K. M. Fox, and V. Massey. "Flavoprotein structure and mechanism. 8. Structure-function relations for old yellow enzyme." FASEB Journal 9, no. 15 (December 1995): 1518–26. http://dx.doi.org/10.1096/fasebj.9.15.8529830.

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Pegg, Scott C. H., Shoshana D. Brown, Sunil Ojha, Jennifer Seffernick, Elaine C. Meng, John H. Morris, Patricia J. Chang, Conrad C. Huang, Thomas E. Ferrin, and Patricia C. Babbitt. "Leveraging Enzyme Structure−Function Relationships for Functional Inference and Experimental Design: The Structure−Function Linkage Database†." Biochemistry 45, no. 8 (February 2006): 2545–55. http://dx.doi.org/10.1021/bi052101l.

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Michalska, Karolina, Jennifer Gale, Grazyna Joachimiak, Changsoo Chang, Catherine Hatzos-Skintges, Boguslaw Nocek, Stephen E. Johnston, et al. "Conservation of the structure and function of bacterial tryptophan synthases." IUCrJ 6, no. 4 (May 29, 2019): 649–64. http://dx.doi.org/10.1107/s2052252519005955.

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Tryptophan biosynthesis is one of the most characterized processes in bacteria, in which the enzymes from Salmonella typhimurium and Escherichia coli serve as model systems. Tryptophan synthase (TrpAB) catalyzes the final two steps of tryptophan biosynthesis in plants, fungi and bacteria. This pyridoxal 5′-phosphate (PLP)-dependent enzyme consists of two protein chains, α (TrpA) and β (TrpB), functioning as a linear αββα heterotetrameric complex containing two TrpAB units. The reaction has a complicated, multistep mechanism resulting in the β-replacement of the hydroxyl group of L-serine with an indole moiety. Recent studies have shown that functional TrpAB is required for the survival of pathogenic bacteria in macrophages and for evading host defense. Therefore, TrpAB is a promising target for drug discovery, as its orthologs include enzymes from the important human pathogens Streptococcus pneumoniae, Legionella pneumophila and Francisella tularensis, the causative agents of pneumonia, legionnaires' disease and tularemia, respectively. However, specific biochemical and structural properties of the TrpABs from these organisms have not been investigated. To fill the important phylogenetic gaps in the understanding of TrpABs and to uncover unique features of TrpAB orthologs to spearhead future drug-discovery efforts, the TrpABs from L. pneumophila, F. tularensis and S. pneumoniae have been characterized. In addition to kinetic properties and inhibitor-sensitivity data, structural information gathered using X-ray crystallography is presented. The enzymes show remarkable structural conservation, but at the same time display local differences in both their catalytic and allosteric sites that may be responsible for the observed differences in catalysis and inhibitor binding. This functional dissimilarity may be exploited in the design of species-specific enzyme inhibitors.

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Chen, Xin, and Janice A. Fischer. "In Vivo Structure/Function Analysis of the Drosophila fat facets Deubiquitinating Enzyme Gene." Genetics 156, no. 4 (December 1, 2000): 1829–36. http://dx.doi.org/10.1093/genetics/156.4.1829.

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Abstract The Drosophila Fat facets protein is a deubiquitinating enzyme required for patterning the developing compound eye. Ubiquitin, a 76-amino-acid polypeptide, serves as a tag to direct proteins to the proteasome, a protein degradation complex. Deubiquitinating enzymes are a large group of proteins that cleave ubiquitin-protein bonds. Fat facets belongs to a class of deubiquitinating enzymes called Ubps that share a conserved catalytic domain. Fat facets is unique among them in its large size and also because Fat facets is thought to deubiquitinate a specific substrate thereby preventing its proteolysis. Here we asked which portions of the Fat facets protein are essential for its function. P-element constructs that express partial Fat facets proteins were tested for function. In addition, the DNA sequences of 12 mutant fat facets alleles were determined. Finally, regions of amino acid sequence similarity in 18 Drosophila Ubps revealed by the Genome Project were identified. The results indicate functions for specific conserved amino acids in the catalytic region of Fat facets and also indicate that regions of the protein both N- and C-terminal to the catalytic region are required for Fat facets function.

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van Hijum, Sacha A. F. T., Slavko Kralj, Lukasz K. Ozimek, Lubbert Dijkhuizen, and Ineke G. H. van Geel-Schutten. "Structure-Function Relationships of Glucansucrase and Fructansucrase Enzymes from Lactic Acid Bacteria." Microbiology and Molecular Biology Reviews 70, no. 1 (March 2006): 157–76. http://dx.doi.org/10.1128/mmbr.70.1.157-176.2006.

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SUMMARY Lactic acid bacteria (LAB) employ sucrase-type enzymes to convert sucrose into homopolysaccharides consisting of either glucosyl units (glucans) or fructosyl units (fructans). The enzymes involved are labeled glucansucrases (GS) and fructansucrases (FS), respectively. The available molecular, biochemical, and structural information on sucrase genes and enzymes from various LAB and their fructan and α-glucan products is reviewed. The GS and FS enzymes are both glycoside hydrolase enzymes that act on the same substrate (sucrose) and catalyze (retaining) transglycosylation reactions that result in polysaccharide formation, but they possess completely different protein structures. GS enzymes (family GH70) are large multidomain proteins that occur exclusively in LAB. Their catalytic domain displays clear secondary-structure similarity with α-amylase enzymes (family GH13), with a predicted permuted (β/α)8 barrel structure for which detailed structural and mechanistic information is available. Emphasis now is on identification of residues and regions important for GS enzyme activity and product specificity (synthesis of α-glucans differing in glycosidic linkage type, degree and type of branching, glucan molecular mass, and solubility). FS enzymes (family GH68) occur in both gram-negative and gram-positive bacteria and synthesize β-fructan polymers with either β-(2→6) (inulin) or β-(2→1) (levan) glycosidic bonds. Recently, the first high-resolution three-dimensional structures have become available for FS (levansucrase) proteins, revealing a rare five-bladed β-propeller structure with a deep, negatively charged central pocket. Although these structures have provided detailed mechanistic insights, the structural features in FS enzymes dictating the synthesis of either β-(2→6) or β-(2→1) linkages, degree and type of branching, and fructan molecular mass remain to be identified.

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JITRAPAKDEE, Sarawut, and John C. WALLACE. "Structure, function and regulation of pyruvate carboxylase." Biochemical Journal 340, no. 1 (May 10, 1999): 1–16. http://dx.doi.org/10.1042/bj3400001.

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Pyruvate carboxylase (PC; EC 6.4.1.1), a member of the biotin-dependent enzyme family, catalyses the ATP-dependent carboxylation of pyruvate to oxaloacetate. PC has been found in a wide variety of prokaryotes and eukaryotes. In mammals, PC plays a crucial role in gluconeogenesis and lipogenesis, in the biosynthesis of neurotransmitter substances, and in glucose-induced insulin secretion by pancreatic islets. The reaction catalysed by PC and the physical properties of the enzyme have been studied extensively. Although no high-resolution three-dimensional structure has yet been determined by X-ray crystallography, structural studies of PC have been conducted by electron microscopy, by limited proteolysis, and by cloning and sequencing of genes and cDNA encoding the enzyme. Most well characterized forms of active PC consist of four identical subunits arranged in a tetrahedron-like structure. Each subunit contains three functional domains: the biotin carboxylation domain, the transcarboxylation domain and the biotin carboxyl carrier domain. Different physiological conditions, including diabetes, hyperthyroidism, genetic obesity and postnatal development, increase the level of PC expression through transcriptional and translational mechanisms, whereas insulin inhibits PC expression. Glucocorticoids, glucagon and catecholamines cause an increase in PC activity or in the rate of pyruvate carboxylation in the short term. Molecular defects of PC in humans have recently been associated with four point mutations within the structural region of the PC gene, namely Val145 → Ala, Arg451 → Cys, Ala610 → Thr and Met743 → Thr.

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Sakamoto, Hiroshi, Stéphanie Landais, Cécile Evrin, Christine Laurent-Winter, Octavian Bârzu, and Rod A. Kelln. "Structure–function relationships of UMP kinases from pyrH mutants of Gram-negative bacteria." Microbiology 150, no. 7 (July 1, 2004): 2153–59. http://dx.doi.org/10.1099/mic.0.26996-0.

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Bacterial uridine monophosphate (UMP) kinases are essential enzymes encoded by pyrH genes, and conditional-lethal or other pyrH mutants were analysed with respect to structure–function relationships. A set of thermosensitive pyrH mutants from Escherichia coli was generated and studied, along with already described pyrH mutants from Salmonella enterica serovar Typhimurium. It is shown that Arg-11 and Gly-232 are key residues for thermodynamic stability of the enzyme, and that Asp-201 is important for both catalysis and allosteric regulation. A comparison of the amino acid sequence of UMP kinases from several prokaryotes showed that these were conserved residues. Discussion on the enzyme activity level in relation to bacterial viability is also presented.

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Gloster, Tracey M. "Development of inhibitors as research tools for carbohydrate-processing enzymes." Biochemical Society Transactions 40, no. 5 (September 19, 2012): 913–28. http://dx.doi.org/10.1042/bst20120201.

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Carbohydrates, which are present in all domains of life, play important roles in a host of cellular processes. These ubiquitous biomolecules form highly diverse and often complex glycan structures without the aid of a template. The carbohydrate structures are regulated solely by the location and specificity of the enzymes responsible for their synthesis and degradation. These enzymes, glycosyltransferases and glycoside hydrolases, need to be functionally well characterized in order to investigate the structure and function of glycans. The use of enzyme inhibitors, which target a particular enzyme, can significantly aid this understanding, and may also provide insights into therapeutic applications. The present article describes some of the approaches used to design and develop enzyme inhibitors as tools for investigating carbohydrate-processing enzymes.

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Gao, Ruibo, Mengmeng Wang, Jiaoyan Zhou, Yuhang Fu, Meng Liang, Dongliang Guo, and Junlan Nie. "Prediction of Enzyme Function Based on Three Parallel Deep CNN and Amino Acid Mutation." International Journal of Molecular Sciences 20, no. 11 (June 11, 2019): 2845. http://dx.doi.org/10.3390/ijms20112845.

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During the past decade, due to the number of proteins in PDB database being increased gradually, traditional methods cannot better understand the function of newly discovered enzymes in chemical reactions. Computational models and protein feature representation for predicting enzymatic function are more important. Most of existing methods for predicting enzymatic function have used protein geometric structure or protein sequence alone. In this paper, the functions of enzymes are predicted from many-sided biological information including sequence information and structure information. Firstly, we extract the mutation information from amino acids sequence by the position scoring matrix and express structure information with amino acids distance and angle. Then, we use histogram to show the extracted sequence and structural features respectively. Meanwhile, we establish a network model of three parallel Deep Convolutional Neural Networks (DCNN) to learn three features of enzyme for function prediction simultaneously, and the outputs are fused through two different architectures. Finally, The proposed model was investigated on a large dataset of 43,843 enzymes from the PDB and achieved 92.34% correct classification when sequence information is considered, demonstrating an improvement compared with the previous result.

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Adjogatse, Eyram, Peter Erskine, Stephen A. Wells, John M. Kelly, Jonathan D. Wilden, A. W. Edith Chan, David Selwood, Alun Coker, Steve Wood, and Jonathan B. Cooper. "Structure and function of L-threonine-3-dehydrogenase from the parasitic protozoan Trypanosoma brucei revealed by X-ray crystallography and geometric simulations." Acta Crystallographica Section D Structural Biology 74, no. 9 (September 1, 2018): 861–76. http://dx.doi.org/10.1107/s2059798318009208.

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Two of the world's most neglected tropical diseases, human African trypanosomiasis (HAT) and Chagas disease, are caused by protozoan parasites of the genus Trypanosoma. These organisms possess specialized metabolic pathways, frequently distinct from those in humans, which have potential to be exploited as novel drug targets. This study elucidates the structure and function of L-threonine-3-dehydrogenase (TDH) from T. brucei, the causative pathogen of HAT. TDH is a key enzyme in the metabolism of L-threonine, and an inhibitor of TDH has been shown to have trypanocidal activity in the procyclic form of T. brucei. TDH is a nonfunctional pseudogene in humans, suggesting that it may be possible to rationally design safe and specific therapies for trypanosomiasis by targeting this parasite enzyme. As an initial step, the TDH gene from T. brucei was expressed and the three-dimensional structure of the enzyme was solved by X-ray crystallography. In multiple crystallographic structures, T. brucei TDH is revealed to be a dimeric short-chain dehydrogenase that displays a considerable degree of conformational variation in its ligand-binding regions. Geometric simulations of the structure have provided insight into the dynamic behaviour of this enzyme. Furthermore, structures of TDH bound to its natural substrates and known inhibitors have been determined, giving an indication of the mechanism of catalysis of the enzyme. Collectively, these results provide vital details for future drug design to target TDH or related enzymes.

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Maier, Timm, Marc Leibundgut, Daniel Boehringer, and Nenad Ban. "Structure and function of eukaryotic fatty acid synthases." Quarterly Reviews of Biophysics 43, no. 3 (August 2010): 373–422. http://dx.doi.org/10.1017/s0033583510000156.

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AbstractIn all organisms, fatty acid synthesis is achieved in variations of a common cyclic reaction pathway by stepwise, iterative elongation of precursors with two-carbon extender units. In bacteria, all individual reaction steps are carried out by monofunctional dissociated enzymes, whereas in eukaryotes the fatty acid synthases (FASs) have evolved into large multifunctional enzymes that integrate the whole process of fatty acid synthesis. During the last few years, important advances in understanding the structural and functional organization of eukaryotic FASs have been made through a combination of biochemical, electron microscopic and X-ray crystallographic approaches. They have revealed the strikingly different architectures of the two distinct types of eukaryotic FASs, the fungal and the animal enzyme system. Fungal FAS is a 2·6 MDa α6β6 heterododecamer with a barrel shape enclosing two large chambers, each containing three sets of active sites separated by a central wheel-like structure. It represents a highly specialized micro-compartment strictly optimized for the production of saturated fatty acids. In contrast, the animal FAS is a 540 kDa X-shaped homodimer with two lateral reaction clefts characterized by a modular domain architecture and large extent of conformational flexibility that appears to contribute to catalytic efficiency.

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Hai, Yang, Arthur M. Huang, and Yi Tang. "Structure-guided function discovery of an NRPS-like glycine betaine reductase for choline biosynthesis in fungi." Proceedings of the National Academy of Sciences 116, no. 21 (May 6, 2019): 10348–53. http://dx.doi.org/10.1073/pnas.1903282116.

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Nonribosomal peptide synthetases (NRPSs) and NRPS-like enzymes have diverse functions in primary and secondary metabolisms. By using a structure-guided approach, we uncovered the function of a NRPS-like enzyme with unusual domain architecture, catalyzing two sequential two-electron reductions of glycine betaine to choline. Structural analysis based on the homology model suggests cation-π interactions as the major substrate specificity determinant, which was verified using substrate analogs and inhibitors. Bioinformatic analysis indicates this NRPS-like glycine betaine reductase is highly conserved and widespread in kingdom fungi. Genetic knockout experiments confirmed its role in choline biosynthesis and maintaining glycine betaine homeostasis in fungi. Our findings demonstrate that the oxidative choline-glycine betaine degradation pathway can operate in a fully reversible fashion and provide insight in understanding fungal choline metabolism. The use of an NRPS-like enzyme for reductive choline formation is energetically efficient compared with known pathways. Our discovery also underscores the capabilities of the structure-guided approach in assigning functions of uncharacterized multidomain proteins, which can potentially aid functional discovery of new enzymes by genome mining.

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Vakili, Bahareh, Navid Nezafat, Manica Negahdaripour, Maryam Yari, Bijan Zare, and Younes Ghasemi. "Staphylokinase Enzyme: An Overview of Structure, Function and Engineered Forms." Current Pharmaceutical Biotechnology 18, no. 13 (March 29, 2018): 1026–37. http://dx.doi.org/10.2174/1389201019666180209121323.

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Krishnaswamy, Sudarsan, Giuseppe Verdile, David Groth, Limbikani Kanyenda, and Ralph N. Martins. "The structure and function of Alzheimer’s gamma secretase enzyme complex." Critical Reviews in Clinical Laboratory Sciences 46, no. 5-6 (December 2009): 282–301. http://dx.doi.org/10.3109/10408360903335821.

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40

Jacobson, Matthew P., Chakrapani Kalyanaraman, Suwen Zhao, and Boxue Tian. "Leveraging structure for enzyme function prediction: methods, opportunities, and challenges." Trends in Biochemical Sciences 39, no. 8 (August 2014): 363–71. http://dx.doi.org/10.1016/j.tibs.2014.05.006.

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Lozano, Pedro, Teresa De Diego, Said Gmouh, Michel Vaultier, and José L. Iborra. "Dynamic structure–function relationships in enzyme stabilization by ionic liquids." Biocatalysis and Biotransformation 23, no. 3-4 (January 2005): 169–76. http://dx.doi.org/10.1080/10242420500198657.

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ZHAO, Y. "Structure and Function of Angiotensin Converting Enzyme and Its Inhibitors." Chinese Journal of Biotechnology 24, no. 2 (February 2008): 171–76. http://dx.doi.org/10.1016/s1872-2075(08)60007-2.

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Hanoune, Jacques, Yves Pouille, Eleni Tzavara, Tiansheng Shen, Larissa Lipskaya, Norihiro Miyamoto, Yosuke Suzuki, and Nicole Defer. "Adenylyl cyclases: structure, regulation and function in an enzyme superfamily." Molecular and Cellular Endocrinology 128, no. 1-2 (April 1997): 179–94. http://dx.doi.org/10.1016/s0303-7207(97)04013-6.

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SHIMIZU, Toru. "Structure-function relationships of membrane-bound heme-enzyme, cytochrome P450." Seibutsu Butsuri 32, no. 1 (1992): 10–15. http://dx.doi.org/10.2142/biophys.32.10.

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Hermann, Johannes C., Ricardo Marti-Arbona, Alexander A. Fedorov, Elena Fedorov, Steven C. Almo, Brian K. Shoichet, and Frank M. Raushel. "Structure-based activity prediction for an enzyme of unknown function." Nature 448, no. 7155 (July 1, 2007): 775–79. http://dx.doi.org/10.1038/nature05981.

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Ondrechen, M. J., J. G. Clifton, and D. Ringe. "THEMATICS: A simple computational predictor of enzyme function from structure." Proceedings of the National Academy of Sciences 98, no. 22 (October 16, 2001): 12473–78. http://dx.doi.org/10.1073/pnas.211436698.

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Gascoyne, Peter. "The redox-mediated control of enzyme function and cellular structure." International Journal of Quantum Chemistry 28, S12 (June 19, 2009): 245–55. http://dx.doi.org/10.1002/qua.560280724.

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Liang, Meng, and Junlan Nie. "Prediction of Enzyme Function Based on a Structure Relation Network." IEEE Access 8 (2020): 132360–66. http://dx.doi.org/10.1109/access.2020.3010028.

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Schäfer, G., and S. Kardinahl. "Iron superoxide dismutases: structure and function of an archaic enzyme." Biochemical Society Transactions 31, no. 6 (December 1, 2003): 1330–34. http://dx.doi.org/10.1042/bst0311330.

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Iron and manganese superoxide dismutases are phylogenetically closely related. They are compared by in silico analysis with regard to their metal specificity and their three-dimensional structure. Special attention is given to the structure and properties of superoxide dismutases from archaeal prokaryotes. The mechanism and the extreme thermostability of superoxide dismutase from Sulfolobus acidocaldarius are discussed on the basis of its high-resolution X-ray structure. An alternating-site mechanism and an evolutionary origin of superoxide dismutases under the environmental conditions on the early Earth are proposed.

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SPORMANN, Dirk O., Jutta HEIM, and Dieter H. WOLF. "Carboxypeptidase yscS: gene structure and function of the vacuolar enzyme." European Journal of Biochemistry 197, no. 2 (April 1991): 399–405. http://dx.doi.org/10.1111/j.1432-1033.1991.tb15924.x.

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Journal articles on the topic 'Enzyme structure/function'

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