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Important Residues (important + residue)
Selected AbstractsCharacterization of the CuA center in the cytochrome c oxidase from Thermus thermophilus for the spectral range 1800,500 cm,1 with a combined electrochemical and Fourier transform infrared spectroscopic setupBIOPOLYMERS, Issue 1-2 2004M. Wolpert Abstract In this study we present the electrochemically induced Fourier transform infrared (FTIR) difference spectra of the CuA center derived from the ba3 -type cytochrome c oxidase of Thermus thermophilus in the spectral range from 1800 to 500 cm,1. The mid infrared is dominated by the ,(CO) vibrations of the amide I modes at 1688, 1660, and 1635 cm,1, reflecting the redox-induced perturbation of the predominantly ,-sheet type structure. The corresponding amide II signal is found at 1528 cm,1. In the lower frequency range below 800 cm,1, modes from amino acids liganding the CuA center are expected. On the basis of the absorbance spectrum of the isolated amino acids, methionine is identified as an important residue, displaying C,S vibrations at these frequencies. This spectral range was previously disregarded by protein IR spectroscopists, mainly due to the strong absorbance of the solvent, H2O. With an optimized setup, however, IR is found suitable for structure/function studies on proteins. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004 [source] Identification of catalytically important residues in the active site of Escherichia coli transaldolaseFEBS JOURNAL, Issue 8 2001Ulrich Schörken The roles of invariant residues at the active site of transaldolase B from Escherichia coli have been probed by site-directed mutagenesis. The mutant enzymes D17A, N35A, E96A, T156A, and S176A were purified from a talB -deficient host and analyzed with respect to their 3D structure and kinetic behavior. X-ray analysis showed that side chain replacement did not induce unanticipated structural changes in the mutant enzymes. Three mutations, N35A, E96A, and T156A resulted mainly in an effect on apparent kcat, with little changes in apparent Km values for the substrates. Residues N35 and T156 are involved in the positioning of a catalytic water molecule at the active site and the side chain of E96 participates in concert with this water molecule in proton transfer during catalysis. Substitution of Ser176 by alanine resulted in a mutant enzyme with 2.5% residual activity. The apparent Km value for the donor substrate, fructose 6-phosphate, was increased nearly fivefold while the apparent Km value for the acceptor substrate, erythrose 4-phosphate remained unchanged, consistent with a function for S176 in the binding of the C1 hydroxyl group of the donor substrate. The mutant D17A showed a 300-fold decrease in kcat, and a fivefold increase in the apparent Km value for the acceptor substrate erythrose 4-phosphate, suggesting a role of this residue in carbon,carbon bond cleavage and stabilization of the carbanion/enamine intermediate. [source] Protein,protein docking dealing with the unknownJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2010Irina S. Moreira Abstract Protein,protein binding is one of the critical events in biology, and knowledge of proteic complexes three-dimensional structures is of fundamental importance for the biochemical study of pharmacologic compounds. In the past two decades there was an emergence of a large variety of algorithms designed to predict the structures of protein,protein complexes,a procedure named docking. Computational methods, if accurate and reliable, could play an important role, both to infer functional properties and to guide new experiments. Despite the outstanding progress of the methodologies developed in this area, a few problems still prevent protein,protein docking to be a widespread practice in the structural study of proteins. In this review we focus our attention on the principles that govern docking, namely the algorithms used for searching and scoring, which are usually referred as the docking problem. We also focus our attention on the use of a flexible description of the proteins under study and the use of biological information as the localization of the hot spots, the important residues for protein,protein binding. The most common docking softwares are described too. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Structure and enzyme properties of Zabrotes subfasciatus ,-amylaseARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY (ELECTRONIC), Issue 2 2006Patrícia B. Pelegrini Abstract Digestive ,-amylases play an essential role in insect carbohydrate metabolism. These enzymes belong to an endo-type group. They catalyse starch hydrolysis, and are involved in energy production. Larvae of Zabrotes subfasciatus, the Mexican bean weevil, are able to infest stored common beans Phaseolus vulgaris, causing severe crop losses in Latin America and Africa. Their ,-amylase (ZSA) is a well-studied but not completely understood enzyme, having specific characteristics when compared to other insect ,-amylases. This report provides more knowledge about its chemical nature, including a description of its optimum pH (6.0 to 7.0) and temperature (20,30°C). Furthermore, ion effects on ZSA activity were also determined, showing that three divalent ions (Mn2+, Ca2+, and Ba2+) were able to enhance starch hydrolysis. Fe2+ appeared to decrease ,-amylase activity by half. ZSA kinetic parameters were also determined and compared to other insect ,-amylases. A three-dimensional model is proposed in order to indicate probable residues involved in catalysis (Asp204, Glu240, and Asp305) as well other important residues related to starch binding (His118, Ala206, Lys207, and His304). Arch. Insect Biochem. Physiol. 61:77,86, 2006. © 2006 Wiley-Liss, Inc. [source] Structure of a novel ribosome-inactivating protein from a hemi-parasitic plant inhabiting the northwestern HimalayasACTA CRYSTALLOGRAPHICA SECTION D, Issue 12-2 2004Vandana Mishra This is the first report of the structural studies of a novel ribosome-inactivating protein (RIP) obtained from the Himalayan mistletoe (Viscum album) (HmRip). HmRip is a type II heterodimeric protein consisting of a toxic enzyme (A-chain) with an active site for ribosome inactivation and a lectin subunit (B-chain) with well defined sugar-binding sites. The crystal structure of HmRip has been determined at 3.8,Å resolution and refined to a crystallographic R factor of 0.228 (Rfree = 0.271). A comparison of this structure with other type II RIPs reveals the presence of distinct structural features in the active site of the A-chain and in the 2, sugar-binding site of the B-chain. The conformation of the side chain of Tyr110, which is a conserved active-site residue in the A subunit, is strikingly different from those observed in other mistletoe RIPs, indicating its unique substrate-binding preference. The deletion of two important residues from the kink region after Ala231 in the 2, subdomain of the B-chain results in a significantly different conformation of the sugar-binding pocket. A ribosome-recognition site has also been identified in HmRip. The site is a shallow cavity, with the conserved residues Arg51, Asp70, Thr72 and Asn73 involved in the binding. The conformations of the antigenic epitopes of residues 1,20, 85,103 and 206,223 differ from those observed in other type II RIPs, resulting in the distinct antigenicity and pharmacological properties of HmRip. [source] Conformational change of the AcrR regulator reveals a possible mechanism of inductionACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2008Ruoyu Gu The Escherichia coli AcrR multidrug-binding protein represses transcription of acrAB and is induced by many structurally unrelated cytotoxic compounds. The crystal structure of AcrR in space group P2221 has been reported previously. This P2221 structure has provided direct information about the multidrug-binding site and important residues for drug recognition. Here, a crystal structure of this regulator in space group P31 is presented. Comparison of the two AcrR structures reveals possible mechanisms of ligand binding and AcrR regulation. [source] | |||||||||||||||||||