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Density Corresponding (density + corresponding)
Selected AbstractsCrystal structures of isomaltase from Saccharomyces cerevisiae and in complex with its competitive inhibitor maltoseFEBS JOURNAL, Issue 20 2010Keizo Yamamoto The structures of isomaltase from Saccharomyces cerevisiae and in complex with maltose were determined at resolutions of 1.30 and 1.60 Å, respectively. Isomaltase contains three domains, namely, A, B, and C. Domain A consists of the (,/,)8 -barrel common to glycoside hydrolase family 13. However, the folding of domain C is rarely seen in other glycoside hydrolase family 13 enzymes. An electron density corresponding to a nonreducing end glucose residue was observed in the active site of isomaltase in complex with maltose; however, only incomplete density was observed for the reducing end. The active site pocket contains two water chains. One water chain is a water path from the bottom of the pocket to the surface of the protein, and may act as a water drain during substrate binding. The other water chain, which consists of six water molecules, is located near the catalytic residues Glu277 and Asp352. These water molecules may act as a reservoir that provides water for subsequent hydrolytic events. The best substrate for oligo-1,6-glucosidase is isomaltotriose; other, longer-chain, oligosaccharides are also good substrates. However, isomaltase shows the highest activity towards isomaltose and very little activity towards longer oligosaccharides. This is because the entrance to the active site pocket of isomaltose is severely narrowed by Tyr158, His280, and loop 310,315, and because the isomaltase pocket is shallower than that of other oligo-1,6-glucosidases. These features of the isomaltase active site pocket prevent isomalto-oligosaccharides from binding to the active site effectively. [source] Rapid model building of ,-sheets in electron-density mapsACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2010Thomas C. Terwilliger A method for rapidly building ,-sheets into electron-density maps is presented. ,-Strands are identified as tubes of high density adjacent to and nearly parallel to other tubes of density. The alignment and direction of each strand are identified from the pattern of high density corresponding to carbonyl and C, atoms along the strand averaged over all repeats present in the strand. The ,-strands obtained are then assembled into a single atomic model of the ,-sheet regions. The method was tested on a set of 42 experimental electron-density maps at resolutions ranging from 1.5 to 3.8,Å. The ,-sheet regions were nearly completely built in all but two cases, the exceptions being one structure at 2.5,Å resolution in which a third of the residues in ,-sheets were built and a structure at 3.8,Å in which under 10% were built. The overall average r.m.s.d. of main-chain atoms in the residues built using this method compared with refined models of the structures was 1.5,Å. [source] Structure of the regulatory subunit of CK2 in the presence of a p21WAF1 peptide demonstrates flexibility of the acidic loopACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2004Loic Bertrand A truncated form of the regulatory subunit of the protein kinase CK2, (residues 1,178) has been crystallized in the presence of a fragment of the cyclin-dependent kinase inhibitor p21WAF1 (residues 46,65) and the structure solved at 2.9,Å resolution by molecular replacement. The core of the CK2, dimer shows a high structural similarity with that identified in previous structural analyses of the dimer and the holoenzyme. However, the electron density corresponding to the substrate-binding acidic loop (residues 55,64) indicates two conformations that differ from that of the holoenzyme structure [Niefind et al. (2001), EMBO J.20, 5320,5331]. Difference electron density near the dimerization region in each of the eight protomers in the asymmetric unit is attributed to between one and eight amino-acid residues of a complexed fragment of p21WAF1. This binding site corresponds to the solvent-accessible part of the conserved zinc-finger motif. [source] Structure of spinach acetohydroxyacid isomeroreductase complexed with its reaction product dihydroxymethylvalerate, manganese and (phospho)-ADP-riboseACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2000Karine Thomazeau Acetohydroxyacid isomeroreductase catalyses a two-step reaction composed of an alkyl migration followed by an NADPH-dependent reduction. Both steps require a divalent cation and the first step has a strong preference for magnesium. Manganese ions are highly unfavourable to the reaction: only 3% residual activity is observed in the presence of this cation. Acetohydroxyacid isomeroreductase has been crystallized with its substrate, 2-aceto-2-hydroxybutyrate (AHB), Mn2+ and NADPH. The 1.6,Å resolution electron-density map showed the reaction product (2,3-dihydroxy-3-methylvalerate, DHMV) and a density corresponding to (phospho)-ADP-ribose instead of the whole NADP+. This is one of the few structures of an enzyme complexed with its reaction product. The structure of this complex was refined to an R factor of 19.3% and an Rfree of 22.5%. The overall structure of the enzyme is very similar to that of the complex with the reaction-intermediate analogue IpOHA [N -hydroxy- N -isopropyloxamate; Biou et al. (1997), EMBO J.16, 3405,3415]. However, the active site shows some differences: the nicotinamide is cleaved and the surrounding amino acids have rearranged accordingly. Comparison between the structures corresponding to the reaction intermediate and to the end of the reaction allowed the proposal of a reaction scheme. Taking this result into account, the enzyme was crystallized with Ni2+ and Zn2+, for which only 0.02% residual activity were measured; however, the crystals of AHB/Zn/NADPH and of AHB/Ni/NADPH also contain the reaction product. Moreover, mass-spectrometry measurements confirmed the cleavage of nicotinamide. [source] The 1.9,Å structure of the branched-chain amino-acid transaminase (IlvE) from Mycobacterium tuberculosisACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 11 2009L. W. Tremblay Unlike mammals, bacteria encode enzymes that synthesize branched-chain amino acids. The pyridoxal 5,-phosphate-dependent transaminase performs the final biosynthetic step in these pathways, converting keto acid precursors into ,-amino acids. The branched-chain amino-acid transaminase from Mycobacterium tuberculosis (MtIlvE) has been crystallized and its structure has been solved at 1.9,Å resolution. The MtIlvE monomer is composed of two domains that interact to form the active site. The biologically active form of IlvE is a homodimer in which each monomer contributes a substrate-specificity loop to the partner molecule. Additional substrate selectivity may be imparted by a conserved N-terminal Phe30 residue, which has previously been observed to shield the active site in the type IV fold homodimer. The active site of MtIlvE contains density corresponding to bound PMP, which is likely to be a consequence of the presence of tryptone in the crystallization medium. Additionally, two cysteine residues are positioned at the dimer interface for disulfide-bond formation under oxidative conditions. It is unknown whether they are involved in any regulatory activities analogous to those of the human mitochondrial branched-chain amino-acid transaminase. [source] A lower-epiperimetric inequality for area-minimizing surfacesCOMMUNICATIONS ON PURE & APPLIED MATHEMATICS, Issue 12 2004Tristan Rivière The epiperimetric inequality introduced by E. R. Reifenberg in [3] gives a rate of decay at a point for the decreasing k -density of area of an area-minimizing integral k -cycle. While dilating the cycle at that point, this rate of decay holds once the configuration is close to a tangent cone configuration and above the limiting density corresponding to that configuration. This is why we propose to call the Reifenberg epiperimetric inequality an upper-epiperimetric inequality. A direct consequence of this upper-epiperimetric inequality is the statement that any point possesses a unique tangent cone. The upper-epiperimetric inequality was proven by B. White in [5] for area-minimizing 2-cycles in ,n. In the present paper we introduce the notion of a lower-epiperimetric inequality. This inequality gives this time a rate of decay for the decreasing k -density of area of an area-minimizing integral k -cycle, while dilating the cycle at a point once the configuration is close to a tangent cone configuration and below the limiting density corresponding to that configuration. Our main result in the present paper is to prove the lower-epiperimetric inequality for area-minimizing 2-cycles in ,n. As a consequence of this inequality we prove the "splitting before tilting" phenomenon for calibrated 2-rectifiable cycles, which plays a crucial role in the proof of the regularity of 1-1 integral currents in [4]. © 2004 Wiley Periodicals, Inc. [source] | ||||||||||