The structure of the H107R variant of the extracellular domain of the mouse natural killer cell receptor NKR-P1A has been determined by X-ray diffraction at 2.3 Å resolution from a merohedrally twinned crystal. Unlike the structure of the wild-type receptor in space group I4(1)22 with a single chain per asymmetric unit, the crystals of the variant belonged to space group I4(1) with a dimer in the asymmetric unit. Different degrees of merohedral twinning were detected in five data sets collected from different crystals. The mutation does not have a significant impact on the overall structure, but led to the binding of an additional phosphate ion at the interface of the molecules.

• MeSH
• extracelulární prostor chemie   MeSH
• krystalografie rentgenová MeSH
• kvarterní struktura proteinů MeSH
• lektinové receptory NK-buněk - podrodina B chemie   genetika   MeSH
• molekulární modely MeSH
• mutace MeSH
• myši MeSH
• terciární struktura proteinů MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The endonuclease TBN1 from Solanum lycopersicum (tomato) was expressed in Nicotiana benthamiana leaves and purified with suitable quality and in suitable quantities for crystallization experiments. Two crystal forms (orthorhombic and rhombohedral) were obtained and X-ray diffraction experiments were performed. The presence of natively bound Zn2+ ions was confirmed by X-ray fluorescence and by an absorption-edge scan. X-ray diffraction data were collected from the orthorhombic (resolution of 5.2 Å) and rhombohedral (best resolution of 3.2 Å) crystal forms. SAD, MAD and MR methods were applied for solution of the phase problem, with partial success. TBN1 contains three Zn2+ ions in a similar spatial arrangement to that observed in nuclease P1 from Penicillium citrinum.

• MeSH
• deoxyribonukleasy chemie   genetika   MeSH
• ionty chemie   MeSH
• konformace proteinů MeSH
• krystalizace MeSH
• krystalografie rentgenová MeSH
• molekulární sekvence - údaje MeSH
• rekombinantní proteiny chemie   genetika   MeSH
• rostlinné proteiny chemie   genetika   MeSH
• Solanum lycopersicum chemie   genetika   MeSH
• zinek chemie   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The paper reports the structure of the small laccase from Streptomyces coelicolor determined from a crystal soaked with potassium hexacyanoferrate [K4Fe(CN)6]. The decolorization of the natively blue crystal observed upon soaking indicates the reduction of the enzyme in the crystal. The ligand binds between laccase molecules and stabilizes the crystal. The increased diffraction limit of the diffraction data collected from this crystal enabled the refinement of the small laccase structure at 2.3 Å resolution, which is the highest resolution obtained to date.

• MeSH
• bakteriální proteiny chemie   MeSH
• barva MeSH
• ferrikyanidy chemie   MeSH
• konformace proteinů MeSH
• krystalografie rentgenová MeSH
• lakasa chemie   MeSH
• měď chemie   MeSH
• molekulární modely MeSH
• molekulární sekvence - údaje MeSH
• stabilita enzymů MeSH
• Streptomyces coelicolor enzymologie   MeSH
• vazebná místa MeSH
• železo chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The structure of the Fc fragment of monoclonal antibody IgG2b from hybridom M75 of Mus musculus has been determined by single crystal X-ray diffraction. This is the first report of the structure of the murine immunoglobulin isotype IgG2b. The structure refined at 2.1 A resolution provides more detailed structural information about native oligosaccharides than was previously available. High-quality Fourier maps provide a clear identification of alpha-l-fucose with partial occupancy in the first branch of the antennary oligosaccharides. A unique Fc:Fc interaction was observed at the C(H)2-C(H)3 interface.

• MeSH
• financování organizované MeSH
• glykosylace MeSH
• imunoglobulin G chemie   MeSH
• imunoglobuliny - Fc fragmenty chemie   MeSH
• imunokomplex chemie   MeSH
• krystalizace MeSH
• krystalografie rentgenová metody   MeSH
• monoklonální protilátky chemie   MeSH
• myši MeSH
• oligosacharidy chemie   MeSH
• sekundární struktura proteinů MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH

The structure of the extracellular domain of human CD69 has been determined by single-crystal X-ray diffraction. The structure refined to 1.37 A resolution provides further details of the overall structure and the asymmetric interface between the monomers in the native dimer. The protein was crystallized using di[poly(ethylene glycol)] adipate, which also served as a cryoprotectant. This is the first report of a crystal structure determined using crystals grown with this polymer.

• MeSH
• CD antigeny chemie   MeSH
• diferenciační antigeny T-lymfocytů chemie   MeSH
• konformace proteinů MeSH
• krystalografie rentgenová MeSH
• lektiny typu C chemie   MeSH
• lidé MeSH
• molekulární modely MeSH
• polymery chemie   MeSH
• rekombinantní proteiny MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• práce podpořená grantem MeSH

Glycosylation of IgG-Fc plays an important role in the activation of the immune system response. Effector functions are modulated by different degrees of deglycosylation of IgG-Fc. However, the geometry of oligosaccharides covalently bound to IgG-Fc does not seem to be in good agreement with electron density in most of the structures deposited in the Protein Data Bank. Our study of correlation between the oligosaccharide geometry, connectivity, and electron density shows several discrepancies, mainly for L-fucose. Revision of refinement of two structures containing the Fc-fragment solved at the highest resolution brings clear evidence for ?-L-fucosylation instead of ß-L-fucosylation as it was claimed in most of the deposited structures in the Protein Data Bank containing the Fc-fragment, and also in the original structures selected for re-refinement. Our revision refinement results in a decrease in R factors, better agreement with electron density, meaningful contacts, and acceptable geometry of L-fucose.

• MeSH
• fukosa chemie   MeSH
• imunoglobuliny - Fc fragmenty MeSH
• krystalizace MeSH
• vazebná místa MeSH
• vztahy mezi strukturou a aktivitou MeSH

Enzymes from cold-adapted species are significantly more active at low temperatures, even those close to zero Celsius, but the rationale of this adaptation is complex and relatively poorly understood. It is commonly stated that there is a relationship between the flexibility of an enzyme and its catalytic activity at low temperature. This paper gives the results of a study using molecular dynamics simulations performed for five pairs of enzymes, each pair comprising a cold-active enzyme plus its mesophilic or thermophilic counterpart. The enzyme pairs included alpha-amylase, citrate synthase, malate dehydrogenase, alkaline protease and xylanase. Numerous sites with elevated flexibility were observed in all enzymes; however, differences in flexibilities were not striking. Nevertheless, amino acid residues common in both enzymes of a pair (not present in insertions of a structure alignment) are generally more flexible in the cold-active enzymes. The further application of principle component analysis to the protein dynamics revealed that there are differences in the rate and/or extent of opening and closing of the active sites. The results indicate that protein dynamics play an important role in catalytic processes where structural rearrangements, such as those required for active site access by substrate, are involved. They also support the notion that cold adaptation may have evolved by selective changes in regions of enzyme structure rather than in global change to the whole protein.

• MeSH
• amylasy chemie   MeSH
• bakteriální proteiny chemie   MeSH
• citrátsynthasa chemie   MeSH
• endo-1,4-beta-xylanasy chemie   MeSH
• endopeptidasy chemie   MeSH
• enzymy chemie   metabolismus   MeSH
• financování organizované MeSH
• malátdehydrogenasa chemie   MeSH
• molekulární modely MeSH
• nízká teplota MeSH
• počítačová simulace MeSH
• sekundární struktura proteinů MeSH
• Publikační typ
• srovnávací studie MeSH

The small bacterial laccase from the actinobacterium Streptomyces coelicolor which lacks the second of the three domains of the laccases structurally characterized to date was crystallized. This multi-copper phenol oxidase crystallizes in a primitive tetragonal lattice, with unit-cell parameters a = b = 179.8, c = 175.3 A. The crystals belong to either space group P4(1)2(1)2 or P4(3)2(1)2. The self-rotation function shows the presence of a noncrystallographic threefold axis in the structure. Phases will be determined from the anomalous signal of the natively present copper ions.

• MeSH
• difrakce rentgenového záření MeSH
• financování organizované MeSH
• krystalizace MeSH
• lakasa genetika   chemie   metabolismus   MeSH
• molekulová hmotnost MeSH
• Streptomyces coelicolor enzymologie   genetika   MeSH

Two new X-ray structures of an HIV-1 protease mutant (A71V, V82T, I84V) in complex with inhibitors SE and SQ, pseudotetrapeptide inhibitors with an acyclic S-hydroxyethylamine isostere, were determined. Comparison of eight structures exploring the binding of four similar inhibitors--SE, SQ (S-hydroxyethylamine isostere), OE (ethyleneamine), and QF34 (hydroxyethylene)--to wild-type and A71V/V82T/I84V HIV-1 protease elucidates the principles of altered interaction with changing conditions. The A71V mutation, which is distant from the active site, causes changes in the structure of the enzyme detectable by the means of X-ray structure analysis, and a route of propagation of the effect toward the active site is proposed.

• MeSH
• ethanolamin chemie   MeSH
• financování organizované MeSH
• HIV-proteasa genetika   chemie   MeSH
• inhibitory HIV-proteasy chemie   MeSH
• krystalografie rentgenová MeSH
• ligandy MeSH
• molekulární modely MeSH
• molekulární struktura MeSH
• mutace MeSH
• oligopeptidy chemie   MeSH
• vazebná místa MeSH
• vodíková vazba MeSH
• vztahy mezi strukturou a aktivitou MeSH

Peptidomimetic inhibitors of human immunodeficiency virus-1 protease are successful lead substances for the development of virostatic drugs against HIV as the causative agent of acquired immunodeficiency syndrome (AIDS). The hydroxyethylamine isostere of the proteolytic cleavage intermediate provides a suitable replacement for the peptide bond. A series of acyclic pseudopeptide inhibitors with the hydroxyethylamine isostere varying in chiral carbon configuration and P'2 residue type were structurally analysed by single-crystal X-ray crystallography. The compounds inhibit HIV protease with subnanomolar inhibition constants and block viral replication in tissue cultures. Here, the structure of such a complex with the R configuration of the isosteric group (PDB code 1zsf) is presented together with newly available synchrotron data for a complex with the S stereoisomer of the inhibitor (PDB code 1zsr). Comparison of the structure and binding with other complexes of HIV-1 protease and similar inhibitors contributes to the understanding of how these molecules bind to the wild-type form of this enzyme. The hydroxy group of the R stereoisomer interacts with one of the catalytic aspartic acids by a short hydrogen bond with rather extreme geometry. The change of configuration of the chiral carbon bearing the hydroxyl from S to R does not influence the inhibition efficiency in this case.

• MeSH
• ethanolaminy chemie   MeSH
• financování organizované MeSH
• HIV-1 enzymologie   MeSH
• HIV-proteasa chemie   metabolismus   MeSH
• inhibitory HIV-proteasy chemie   MeSH
• krystalografie rentgenová MeSH
• molekulární modely MeSH
• oligopeptidy chemie   MeSH
• stereoizomerie MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• vodíková vazba MeSH