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Published Structure (published + structure)
Selected AbstractsFunctional implications of pigments bound to a cyanobacterial cytochrome b6f complexFEBS JOURNAL, Issue 2 2005Stephan-Olav Wenk A highly purified cytochrome b6f complex from the cyanobacterium Synechocystis sp. PCC 6803 selectively binds one chlorophyll a and one carotenoid in analogy to the recent published structure from two other b6f complexes. The unknown function of these pigments was elucidated by spectroscopy and site-directed mutagenesis. Low-temperature redox difference spectroscopy showed red shifts in the chlorophyll and carotenoid spectra upon reduction of cytochrome b6, which indicates coupling of these pigments with the heme groups and thereby with the electron transport. This is supported by the correlated kinetics of these redox reactions and also by the distinct orientation of the chlorophyll molecule with respect to the heme cofactors as shown by linear dichroism spectroscopy. The specific role of the carotenoid echinenone for the cytochrome b6f complex of Synechocystis 6803 was elucidated by a mutant lacking the last step of echinenone biosynthesis. The isolated mutant complex preferentially contained a carotenoid with 0, 1 or 2 hydroxyl groups (most likely 9- cis isomers of ,-carotene, a monohydroxy carotenoid and zeaxanthin, respectively) instead. This indicates a substantial role of the carotenoid , possibly for strucure and assembly , and a specificity of its binding site which is different from those in most other oxygenic photosynthetic organisms. In summary, both pigments are probably involved in the structure, but may also contribute to the dynamics of the cytochrome b6f complex. [source] Molecular docking studies of selected tricyclic and quinone derivatives on trypanothione reductase of Leishmania infantumJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2010Santhosh Kannan Venkatesan Abstract Visceral leishmaniasis, most lethal form of Leishmaniasis, is caused by Leishmania infantum in the Old world. Current therapeutics for the disease is associated with a risk of high toxicity and development of drug resistant strains. Thiol-redox metabolism involving trypanothione and trypanothione reductase, key for survival of Leishmania, is a validated target for rational drug design. Recently published structure of trypanothione reductase (TryR) from L. infantum, in oxidized and reduced form along with Sb(III), provides vital clues on active site of the enzyme. In continuation with our attempts to identify potent inhibitors of TryR, we have modeled binding modes of selected tricyclic compounds and quinone derivatives, using AutoDock4. Here, we report a unique binding mode for quinone derivatives and 9-aminoacridine derivatives, at the FAD binding domain. A conserved hydrogen bonding pattern was observed in all these compounds with residues Thr335, Lys60, His461. With the fact that these residues aid in the orientation of FAD towards the active site forming the core of the FAD binding domain, designing selective and potent compounds that could replace FAD in vivo during the synthesis of Trypanothione reductase can be deployed as an effective strategy in designing new drugs towards Leishmaniasis. We also report the binding of Phenothiazine and 9-aminoacridine derivatives at the Z site of the protein. The biological significance and possible mode of inhibition by quinone derivatives, which binds to FAD binding domain, along with other compounds are discussed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Towards a more reliable symmetry determination from powder diffraction: a redetermination of the low-temperature structure of 4-methylpyridine- N -oxideACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2009Palatinus The low-temperature structure of 4-methylpyridine- N -oxide was previously determined in symmetry P41 [Damay et al. (2006), Acta Cryst. B62, 627,633]. Using a recently published symmetry-determination method it was found that the true symmetry of the structure is P41212. The structure was refined in the new space group using X-ray and neutron data. The previously published structure is close to the newly refined structure, but the new structure is in agreement with the results of rotational tunneling spectroscopy, and, in contrast to the structure in symmetry P41, does not require a twofold degeneracy of the tunneling bands. [source] Strontium tetrafluoridoborate and barium tetrafluoridoborateACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2007Tina Buni In Sr(BF4)2, which is isomorphous with the previously published Ca(BF4)2, the metal atom possesses a coordination number of 8 with a square-antiprismatic environment. Each tetrafluoridoborate anion is bonded to four metal centers. In the barium derivative, the metal center, with symmetry 2/m, is surrounded by 14 F atoms. The B atom and two of the three independent F atoms occupy special positions with symmetry m. Each anion is connected to five Ba atoms. This structure differs significantly from an earlier published structure of Ba(BF4)2 [published as Ba2(BF4)4; Lin, Cheng, Chen & Huang (1998). Jiegon Huaxue, 17, 245]. The radial distribution functions for the present Ba(BF4)2 and earlier Ba2(BF4)4 structures differ significantly. [source] Structure of the thioredoxin-like domain of yeast glutaredoxin 3ACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2008Lydia M. Gibson Yeast glutaredoxin 3 (Grx3) is a cytosolic protein that regulates the activity of the iron-responsive transcriptional activator Aft1. This member of the monothiol glutaredoxin family contains a thioredoxin-like domain and a glutaredoxin-like domain, which both possess a monothiol active site. The crystal structure of the thioredoxin-like domain has been determined at 1.5,Å resolution and represents the first published structure of this domain for the monothiol glutaredoxin family. The loop containing the signature motif WAxxC is partially disordered, indicating a greater degree of flexibility in this region compared with classical dithiol thioredoxins with a WCGPC active-site motif. [source] A new crystal form of Lys48-linked diubiquitinACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2010Jean-François Trempe Lys48-linked polyubiquitin chains are recognized by the proteasome as a tag for the degradation of the attached substrates. Here, a new crystal form of Lys48-linked diubiquitin (Ub2) was obtained and the crystal structure was refined to 1.6,Å resolution. The structure reveals an ordered isopeptide bond in a trans configuration. All three molecules in the asymmetric unit were in the same closed conformation, in which the hydrophobic patches of both the distal and the proximal moieties interact with each other. Despite the different crystallization conditions and different crystal packing, the new crystal structure of Ub2 is similar to the previously published structure of diubiquitin, but differences are observed in the conformation of the flexible isopeptide linkage. [source] The 1.9,Å resolution structure of Mycobacterium tuberculosis 1-deoxy- d -xylulose 5-phosphate reductoisomerase, a potential drug targetACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2006Lena M. Henriksson 1-Deoxy- d -xylulose 5-phosphate reductoisomerase catalyzes the NADPH-dependent rearrangement and reduction of 1-deoxy- d -xylulose 5-phosphate to form 2- C -methyl- d -erythritol 4-phosphate, as the second step of the deoxyxylulose 5-phosphate/methylerythritol 4-phosphate pathway found in many bacteria and plants. The end product, isopentenyl diphosphate, is the precursor of various isoprenoids vital to all living organisms. The pathway is not found in humans; the mevalonate pathway is instead used for the formation of isopentenyl diphosphate. This difference, combined with its essentiality, makes the reductoisomerase an excellent drug target in a number of pathogenic organisms. The structure of 1-deoxy- d -xylulose 5-phosphate reductoisomerase from Mycobacterium tuberculosis (Rv2870c) was solved by molecular replacement and refined to a resolution of 1.9,Å. The enzyme exhibited an estimated kcat of 5.3,s,1 and Km and kcat/Km values of 7.2,µM and 7.4 × 105,M,1,s,1 for NADPH and 340,µM and 1.6 × 104,M,1,s,1 for 1-deoxy- d -xylulose 5-phosphate. In the structure, a sulfate is bound at the expected site of the phosphate moiety of the sugar substrate. The M. tuberculosis enzyme displays a similar fold to the previously published structures from Escherichia coli and Zymomonas mobilis. Comparisons offer suggestions for the design of specific drugs. Furthermore, the new structure represents an intermediate conformation between the open apo form and the closed holo form observed previously, giving insights into the conformational changes associated with catalysis. [source] Structural effects of monovalent anions on polymorphic lysozyme crystalsACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2001M. C. Vaney Understanding direct salt effects on protein crystal polymorphism is addressed by comparing different crystal forms (triclinic, monoclinic, tetragonal and orthorhombic) for hen, turkey, bob white quail and human lysozymes. Four new structures of hen egg-white lysozyme are reported: crystals grown in the presence of NapTS diffracted to 1.85,Å, of NaI to 1.6,Å, of NaNO3 to 1.45,Å and of KSCN to 1.63,Å. These new structures are compared with previously published structures in order to draw a mapping of the surface of different lysozymes interacting with monovalent anions, such as nitrate, chloride, iodide, bromide and thiocyanate. An analysis of the structural sites of these anions in the various lysozyme structures is presented. This study shows common anion sites whatever the crystal form and the chemical nature of anions, while others seem specific to a given geometry and a particular charge environment induced by the crystal packing. [source] | ||||||||||