finding the hammerhead ribozyme active site
Tài liệu Báo cáo khoa học: Crystal structure of Klebsiella sp. ASR1 phytase suggests substrate binding to a preformed active site that meets the requirements of a plant rhizosphere enzyme doc
... and mutant structure are in the same range as the differences between the two molecules of the asymmetric unit of the wild-type structure Neither the mutation nor the different crystallization ... well The hydrogen bond between the backbone nitrogen atom of Asp291 and the 3phosphate of the substrate is the only interaction with the protein backbone; all other contacts are formed using the ... similarity to PhyK in the a ⁄ b domain than in the a domain [20] This is also reflected in the rigidity of the protein The atomic displacement factors of the PhyK structure are smaller for the a ⁄ b domain...
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Tài liệu Báo cáo khoa học: Stefin A displaces the occluding loop of cathepsin B only by as much as required to bind to the active site cleft doc
... N-terminus, the active site C29 The C-terminal domain is based on a four-stranded b-barrel fold, contributing H199, the other active site residue The active site cleft is formed at the interface ... the inhibitors as well as to the packing constraints of the environment The larger and wider the features of the ligands that compete with the occluding loop for binding to the active site, the ... originating from the propeptide, termed the mini chain, which blocks the unprimed binding site [19] The mini loop in carboxypeptidase cathepsin X blocks the primed side of the active site, restricting...
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Tài liệu Báo cáo khoa học: Solution structure of hirsutellin A – new insights into the active site and interacting interfaces of ribotoxins docx
... the activity Given the 3D structure of the HtA active site, and the interactions between side chains, we propose that D40, H42, R95 and F126 also form part of it As in other ribotoxins, the active ... the structure of the remaining part is the same in both proteins, including a short segment (N56, C57 and D58) forming a turn of 310 helix (D75, C76 and D77 in a-sarcin) The active site The active ... the active site of the ribotoxins a-sarcin and restrictocin (Fig 3B) On the basis of its sequence alignment, which matched it with Y48 in a-sarcin, Y44 was proposed to be part of the active site...
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Tài liệu Báo cáo khoa học: Functional studies of active-site mutants from Drosophila melanogaster deoxyribonucleoside kinase Investigations of the putative catalytic glutamate–arginine pair and of residues responsible for substrate specificity docx
... binding of the feedback inhibitor dTTP and the position of Mg2+ in the active site Mg ion that coordinates the phosphates of dTTP (Fig 3) Discussion Mutation of residues in the active site was ... for the chemotherapeutic treatment of cancer and viral diseases because they catalyse the addition of the first phosphate group to the nucleoside analogue This primes the nucleoside for further ... functional group, the dramatically decreased catalytic rate is most likely due to the increased distance between the catalytic base and the 5¢-OH of either dThd or dCyd These results favour the reaction-mechanistic...
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Tài liệu Báo cáo khoa học: A tyrosinase with an abnormally high tyrosine hydroxylase/dopa oxidase ratio Role of the seventh histidine and accessibility to the active site docx
... is at pH These preferred activities of the two PPOs of R solanacearum are opposite to the names assigned to them when the genome of this bacterium was sequenced and the function of these conceptual ... respectively, the amounts of protein (lg) in the TH and DO activity peaks Yields were calculated with the values in parentheses, which are the three most active fractions from the purification ... Comparison of the amino acid sequences at the active site with other tyrosinases and catechol oxidases allows us to propose correlations between key residues in the catalytic patterns of these enzymes...
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Tài liệu Báo cáo khóa học: The effect of mutations surrounding and within the active site on the catalytic activity of ricin A chain pptx
... 234 and 235 [9] Of theses residues, only Arg213 is in the vicinity of the active site of RTA In order to establish the role of arginyl residues around the active site of RTA in the binding of rRNA, ... facilitate docking into the active site of RTA Here, two of the models proposed [10] have been examined (Fig 1) The third model in which the hexanucleotide is bound to the active site of RTA in an ... between the base G4 and the sidechain of Asn122 In the second model (Fig 1B) the structure of the hexanucelotide is, on the whole, unchanged and the majority of the interactions that were seen in the...
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Tài liệu Báo cáo khóa học: Active-site residues and amino acid specificity of the bacterial 4¢-phosphopantothenoylcysteine synthetase CoaB pptx
... (Thr) (Fig 6); the G-A transition concurs with the use of hydroxylamine as the mutagenic agent [14] Therefore, the dfp-1 mutation is within the AAVAD motif of the C-terminal PPC synthetase (CoaB) ... 4¢-phosphopantetheine and coenzyme A biosynthesis With the used assay, it is difficult to evaluate the PPC synthetase activity at different temperatures, because the enzymatic activity of the present pantothenate ... 4¢-phosphopantothenic acid, CTP and cysteine The synthesis of PPC occurs in two half reactions starting with the formation of 4¢-phosphopantothenoyl-CMP (activation of the carboxyl group of 4¢-phosphopantothenate)...
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Tài liệu Báo cáo khoa học: Effect of deletion of the DNase I hypersensitive sites on the transcription of chicken Ig-b gene and on the maintenance of active chromatin state in the Ig-b locus docx
... both the acetylation state of the promoter region of the active b-globin gene [19] and the DNase I general sensitivity in the b-globin locus are the same as the wild type control [17] Thus, there ... the chromatin state of the cells with any deletion in the regions I–IV in the Ig-b locus, judged by DHSs as the indicator, was the same as that in predeletion cells, the region required for the ... and each of these regions was deleted in DT40 cells The roles of the DHSs on Ig-b gene expression and the maintenance of active chromatin state in the Ig-b locus were examined in the deletion...
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Tài liệu Báo cáo khoa học: Enlarging the gas access channel to the active site renders the regulatory hydrogenase HupUV of Rhodobacter capsulatus O2 sensitive without affecting its transductory activity docx
... the deeply buried active site [23–25] As both molecular H2 and O2 are hydrophobic gases, they probably use the same access pathway to the hydrogenase active site The amino-acid sequences of the ... during the activation step of the ready enzyme increases the lag phase without preventing the activation [29] On the other hand, when added to the active enzyme, O2 would react directly with the active ... the active site to O2 In the mutated protein, O2 has access to the active bimetallic site, which would remain in the inactive form, and, consequently, this protein exhibits some features of the...
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Tài liệu Báo cáo khoa học: Site-directed mutagenesis of a loop at the active site of E1 (a2b2) of the pyruvate dehydrogenase complex A possible common sequence motif docx
... properly as a lid for the active site, thereby granting easier access for the cofactor ThDP to its binding site The lower thermal stability of the mutant E1s and the increased Vmax in the DCPIP assay, ... with the E1 crystal structures in that the arginine residues corresponding to E1aR282 of the B stearothermophilus E1 are not pointing towards the active site, identified by the C2-carbon of the ... decarboxylase; one active site was found to be in an open conformation, with two loop regions disordered, whereas in the other these loop regions were well-ordered and shielded the active site from the bulk...
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Tài liệu Báo cáo Y học: Expression and characterization of active site mutants of hevamine, a chitinase from the rubber tree Hevea brasiliensis docx
... colloidal chitin and the enzyme influences the active site properties The cause of these differences is not known Km and kcat measurements of hevamine and mutants Comparison of the steady-state kinetic ... shows that the use of chitohexaose in the cocrystallization experiments resulted only in a chitotetraose molecule being bound in the active site (at subsites )1 to )4) In contrast, the cocrystallization ... and Asp125 In the mutants, the hydrogen bond of the amide nitrogen with the Asp125 side chain is not possible anymore, and the )1 N-acetyl group points away from the C1 atom of the )1 sugar (Fig...
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Báo cáo khoa học: Binding of ATP at the active site of human pancreatic glucokinase – nucleotide-induced conformational changes with possible implications for its kinetic cooperativity doc
... simulations of the modelled binary GK–ATP complex revealed that the global rmsd of the structure converged at the end of the 2-ns simulation period (Fig S2A) The dynamic changes in the active site cleft ... conformation The MD simulations indicate that the binding triggers molecular motion of the flexible surface ⁄ active site loop and partial closure of the interdomain active site cleft The modelled ... ATP-binding site in the MD simulated model structure of the binary hGK–ATP complex and the domain motion induced by ATP binding to the hGK apoenzyme (A) Close-up view of the ATPbinding site in the MD...
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Báo cáo khoa học: Insights into substrate and product traffic in the Drosophila melanogaster acetylcholinesterase active site gorge by enlarging a back channel ppt
... shift of the pS curve towards higher substrate concentrations due to the lower affinity of both the free and acetylated mutated active sites If choline could leave the active site by the back ... replacing the loop from amino acids 103–136 This external loop is at the opposite side of the molecule with respect to the active site entrance and its deletion does not affect the activity or the ... the case of the Glu mutation, the b value is linked to the k2 value and thus both cannot be estimated independently However, if b is set to (i.e the symmetry of the pS curve supporting it), the...
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Báo cáo khoa học: Interactions of imidazoline ligands with the active site of purified monoamine oxidase A potx
... the I2BS stereospecificities would be useful Interestingly, the lowest-energy orientation for each of the three ligands in the large active site of MAO-A put them in the middle of the active site ... for the active site than reported values for I2BS It seems clear that the active site of MAO is not the site to which I2BS ligands bind with nanomolar affinity However, imidazolines bind at the active ... the binding site The initial energy-minimized orientations for guanabenz, 2-BFI and idazoxan placed the compounds at the entrance of the active site cavity near amino acid residues found in the...
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Báo cáo khoa học: Site-directed mutagenesis of selected residues at the active site of aryl-alcohol oxidase, an H2O2-producing ligninolytic enzyme pot
... nidulans, and the activities of the site- directed variants (when active) could be directly detected in filtrates of 48 h cultures of the transformants harbouring the mutated aao sequences The first ... residue affects the FAD environment, even without being located in the near vicinity of the cofactor, but further studies are required 4882 Conserved histidines at the AAO active site AAO His502 ... formation) by an active site base contributing to the transfer of a hydride from the substrate a-carbon to the flavin cofactor [40–46] Site- directed mutagenesis suggested that the conserved histidine...
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Báo cáo khóa học: Mutational and computational analysis of the role of conserved residues in the active site of a family 18 chitinase docx
... that the carboxylic groups in the Asp140-Asp142-Glu144 triad contain two protons at the pH where the enzyme is most active The basic arm of the pH-activity profile must be determined by the loss ... the D140N, D142N, E144Q and D215N mutants, the pH-dependency of specific activity was recorded for these four mutants and the four corresponding alanine mutants The least active mutants (i.e the ... in the preceding run Some of the pH profiles differed strongly from the wildtype profile, however, the profiles for the amide and corresponding alanine mutants were similar in all cases Together these...
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Báo cáo khoa học: The signature amidase from Sulfolobus solfataricus belongs to the CX3C subgroup of enzymes cleaving both amides and nitriles Ser195 and Cys145 are predicted to be the active site nucleophiles pot
... Discussion The characterization of the SsAH enzyme described here strongly suggests that the Ser171–cisSer195–Lys96 catalytic triad, similarly to other members of this family, forms the active site ... synthesized Forward and reverse primers correspond to the first 20 nucleotides at the 5¢- and 3¢- of the gene coding sequence and include the NcoI and BamHI sites, at each end, respectively The ... more efficiently than the SsAH-WT (Table 1) The behaviour of this mutant can be rationally explained on the basis of the homology model, as the increased occupancy deriving from the arginine side...
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Báo cáo khoa học: Homoadenosylcobalamins as probes for exploring the active sites of coenzyme B12-dependent diol dehydratase and ethanolamine ammonia-lyase docx
... AdePeCbl at the cobalamin moiety without cleavage of the Co-C bond Center, The same superimposition at both the cobalamin moiety and the adenine ring with the Co-C bond cleaved and the Co-C distance ... been synthesized [24–26] These analogues might be useful as probes for exploring the active sites of AdoCbl-dependent enzymes In this paper, we have investigated the coenzymic properties of these ... property of these coenzyme analogues would be reasonably explained by the fact that adenine-anchored radicals are formed by photolysis of their Co-C bond and kept associated with the active site The...
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Báo cáo khoa học: Auto-methylation of the mouse DNA-(cytosine C5)-methyltransferase Dnmt3a at its active site cysteine residue pot
... to the methyl group of AdoMet and is the most reactive residue in the catalytic center of the enzyme To test whether the catalytic cysteine is the target for auto-methylation, we purified the ... leads to the formation of a covalent bond between the enzyme and the substrate base The formation of the cysteine–cytosine bond increases the negative charge density at the C5 atom of the cytosine, ... type The distance between the sulfhydryl atom of the catalytic cysteine side chain and sulfur ˚ atom of AdoHcy (7.66 A) is indicated On the other hand, they harbor a cysteine residue in their active...
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Báo cáo khoa học: Kinetic and crystallographic analyses of the catalytic domain of chitinase from Pyrococcus furiosus – the role of conserved residues in the active site pdf
... that these residues stabilize the distortion of the NAG3 residue In these interactions, we particularly focused on the Trp664 residue, which is located at the bottom of the active site cleft The ... conformational changes, but of the removal of negative charge at these residues Conformation of chito-oligosaccharides bound to the active site cleft For the structural determination of the AD2–substrate ... on the b4-strand (Fig 1) The Glu (E) in this motif acts as the catalytic proton donor, and the second Asp (D2) is supposed to contribute to the stabilization of the essential distortion of the...
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