cDNA cloning and 1.75 Å crystal structure determination of PPL2, an endochitinase and N-acetylglucosamine-binding hemagglutinin from Parkia platycephala seeds

Parkia platycephala lectin 2 was purified from Parkia platycephala (Leguminosae, Mimosoideae) seeds by affinity chromatography and RP-HPLC. Equilibrium sedimentation and MS showed that Parkia platycephala lectin 2 is a nonglycosylated monomeric protein of molecular mass 29 407 ± 15 Da, which contains six cysteine residues engaged in the formation of three intramolecular disulfide bonds. Parkia platycephala lectin 2 agglutinated rabbit erythrocytes, and this activity was specifically inhibited by N-acetylglucosamine. In addition, Parkia platycephala lectin 2 hydrolyzed β(1-4) glycosidic bonds linking 2-acetoamido-2-deoxy-β-d-glucopyranose units in chitin. The full-length amino acid sequence of Parkia platycephala lectin 2, determined by N-terminal sequencing and cDNA cloning, and its three-dimensional structure, established by X-ray crystallography at 1.75 Å resolution, showed that Parkia platycephala lectin 2 is homologous to endochitinases of the glycosyl hydrolase family 18, which share the (βα) 8 barrel topology harboring the catalytic residues Asp125, Glu127, and Tyr182. © 2006 The Authors.

The 2.0-Å resolution crystal structure of a trimeric antibody fragment with noncognate VH–VL domain pairs shows a rearrangement of VH CDR3

The 2.0-Å resolution x-ray crystal structure of a novel trimeric antibody fragment, a “triabody,” has been determined. The trimer is made up of polypeptides constructed in a manner identical to that previously described for some “diabodies”: a VL domain directly fused to the C terminus of a VH domain—i.e., without any linker sequence. The trimer has three Fv heads with the polypeptides arranged in a cyclic, head-to-tail fashion. For the particular structure reported here, the polypeptide was constructed with a VH domain from one antibody fused to the VL domain from an unrelated antibody giving rise to “combinatorial” Fvs upon formation of the trimer. The structure shows that the exchange of the VL domain from antibody B1-8, a Vλ domain, with the VL domain from antibody NQ11, a Vκ domain, leads to a dramatic conformational change in the VH CDR3 loop of antibody B1-8. The magnitude of this change is similar to the largest of the conformational changes observed in antibody fragments in response to antigen binding. Combinatorial pairing of VH and VL domains constitutes a major component of antibody diversity. Conformationally flexible antigen-binding sites capable of adapting to the specific CDR3 loop context created upon VH–VL pairing may be employed by the immune system to maximize the structural diversity of the immune response.

Crystal structure of the SarR protein from Staphylococcus aureus

The expression of virulence determinants in Staphylococcus aureus is controlled by global regulatory loci (e.g., sarA and agr). The sar (Staphylococcus accessory regulator) locus is composed of three overlapping transcripts (sarA P1, P3, and P2, transcripts initiated from the P1, P3, and P2 promoters, respectively), all encoding the 124-aa SarA protein. The level of SarA, the major regulatory protein, is partially controlled by the differential activation of the sarA promoters. We previously partially purified a 13.6-kDa protein, designated SarR, that binds to the sarA promoter region to down-modulate sarA transcription from the P1 promoter and subsequently SarA expression. SarR shares sequence similarity to SarA, and another SarA homolog, SarS. Here we report the 2.3 Å-resolution x-ray crystal structure of the dimeric SarR-MBP (maltose binding protein) fusion protein. The structure reveals that the SarR protein not only has a classic helix–turn–helix module for DNA binding at the major grooves, but also has an additional loop region involved in DNA recognition at the minor grooves. This interaction mode could represent a new functional class of the “winged helix” family. The dimeric SarR structure could accommodate an unusually long stretch of ≈27 nucleotides with two or four bending points along the course, which could lead to the bending of DNA by 90° or more, similar to that seen in the catabolite activator protein (CAP)–DNA complex. The structure also demonstrates the molecular basis for the stable dimerization of the SarR monomers and possible motifs for interaction with other proteins.

Crystal structure at 2.6-A resolution of human macrophage migration inhibitory factor.

Macrophage migration inhibitory factor (MIF) was the first cytokine to be described, but for 30 years its role in the immune response remained enigmatic. In recent studies, MIF has been found to be a novel pituitary hormone and the first protein identified to be released from immune cells on glucocorticoid stimulation. Once secreted, MIF counterregulates the immunosuppressive effects of steroids and thus acts as a critical component of the immune system to control both local and systemic immune responses. We report herein the x-ray crystal structure of human MIF to 2.6 angstrom resolution. The protein is a trimer of identical subunits. Each monomer contains two antiparallel alpha-helices that pack against a four-stranded beta-sheet. The monomer has an additional two beta-strands that interact with the beta-sheets of adjacent subunits to form the interface between monomers. The three beta-sheets are arranged to form a barrel containing a solvent-accessible channel that runs through the center of the protein along a molecular 3-fold axis. Electrostatic potential maps reveal that the channel has a positive potential, suggesting that it binds negatively charged molecules. The elucidated structure for MIF is unique among cytokines or hormonal mediators, and suggests that this counterregulator of glucocorticoid action participates in novel ligand-receptor interactions.

Temperature dependence of the crystal structure and g-values of [(HC(Ph2PO)(3))(2)Cu] (ClO4)(2)center dot 2H(2)O: Influence of dynamic Jahn-Teller coupling and lattice strain interactions

The temperature dependence of the X-ray crystal structure and powder EPR spectrum of [(HC(Ph2PO)(3))(2)CU]-(ClO4)(2)center dot 2H(2)O is reported, and the structure at room temperature confirms that reported previously. Below similar to 100 K, the data imply a geometry with near elongated tetragonal symmetry for the [(HC(Ph2PO)(3))(2)Cu](2+) complex, but on warming the two higher Cu-O bond lengths and g-values progressively converge, and by 340 K the bond lengths correspond to a compressed tetragonal geometry. The data may be interpreted satisfactorily assuming an equilibrium among the energy levels of a Cu-O-6 polyhedron subjected to Jahn-Teller vibronic coupling and a lattice strain. However, agreement with the experiment is obtained only if the orthorhombic component of the lattice strain decreases to a negligible value as the temperature approaches 340 K.

Synthesis and characterization of Pd(II) and Pt(II) complexes with triazolopyrimidine derivatives: The crystal structure of [Pd2L2Cl4] where L=5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidine

The Pd(II) and Pt(II) complexes with triazolopyrimidine C-nucleosides L-1 (5,7-dimethyl-3-(2',3',5'-tri-O-benzoyl-beta-D-ribofuranosyl-s-triazolo)[4,3-a]pyrimidine), L-2 (5,7-dimethyl-3-beta-D-ribofuranosyl-s-triazolo [4,3-a]pyrimidine) and L-3 (5,7-dimethyl[1,5-a]-s-triazolopyrimidine), [Pd(en)(L-1)](NO3)(2), (Pd(bpy)(L-1)](NO3)(2), cis-Pd(L-3)(2)Cl-2, [Pd-2(L-3)(2)Cl-4]center dot H2O, cis-Pd(L-2)(2)Cl-2 and [Pt-3(L-1)(2)Cl-6] were synthesized and characterized by elemental analysis and NMR spectroscopy. The structure of the [Pd-2(L-3)(2)Cl-4]center dot H2O complex was established by Xray crystallography. The two L-3 ligands are found in a head to tail orientation, with a (PdPd)-Pd-... distance of 3.1254(17) angstrom.L-1 coordinates to Pd(II) through N8 and N1 forming polymeric structures. L-2 coordinates to Pd(II) through N8 in acidic solutions (0.1 M HCl) forming complexes of cis-geometry. The Pd(II) coordination to L-2 does not affect the sugar conformation probably due to the high stability of the C-C glycoside bond. (c) 2006 Elsevier B.V. All rights reserved.

Syntheses and characterization of trans-[NiL2(NCS)2][L = 2-(aminomethyl) pyridine], trans-[NiL02(NSC)2][L0 = 2-(2-aminoethyl)pyridine] and trans-[NiL00 2(NSC)2] [L00 = 2-(2-methylaminoethyl)pyridine] complexes: X-ray single crystal structure of trans-[NiL02(NSC)2] [L0 = 2-(2-aminoethyl)pyridine]

[NiL2(NCS)2] (1) [L = 2-(aminomethyl)pyridine], [NiL02(NCS)2] (2) [(L0) = 2-(2-aminoethyl)pyridine and [NiL00 2(NCS)2] (3) [L00 = 2-(2-methylaminoethyl)pyridine] have been synthesized from solution. All the complexes possess trans geometry as is evident from solid state UV–Vis spectral study and X-ray single crystal structure analysis of complex 2 unambiguously proves trans geometry of the species.

x-ray studies on crystalline complexes involving amino-acids and peptides .10. head-to-tail sequences in the crystal-structure of l-lysine acetate

l-Lysine acetate crystallises in the monoclinic space group P21 with a = 5.411 (1), b = 7.562(1), c= l2.635(2) Å and β = 91.7(1). The crystal structure was solved by direct methods and refined to an R value of 0.049 using the full matrix least squares method. The conformation and the aggregation of lysine molecules in the structure are similar to those found in the crystal structure of l-lysine l-aspartate. A conspicuous similarity between the crystal structures of l-arginine acetate and l-lysine acetate is that in both cases the strongly basic side chain, although having the largest pK value, interacts with the weakly acidic acetate group leaving the α-amino and the α-carboxylate groups to take part in head-to-tail sequences. These structures thus indicate that electrostatic effects are strongly modulated by other factors so as to give rise to head-to-tail sequences which have earlier been shown to be an almost universal feature of amino acid aggregation in the solid state.

X-ray crystal and molecular structure of a hydrated lithium picrate complex of benzo-15-crown-5; An example of non-chelation of the crown

Complexation of alkali and alkaline earth metal ions with crown ethers is well known (1) and chemical and crystallographic studies have been carried out for number of complexes (2,3). The interaction of the metal with the crown ether depends on the nature of the cation and particularly on the basicity of the anion (4) , In this paper we report the crystal and molecular structure of a lithium picrate complex of benzo-15-crown-5, the first x-ray crystallographic study of a lithlum-crown system.

X-ray studies of crystalline complexes involving amino acids. II. The crystal structure of L-arginine L-glutamate

Abstract is not available.

Hydrothermal synthesis and X-ray single crystal structure of bimetallic cluster complex [{Co(phen)(2)}(2)V4O12]center dot H2O

A new bimetallic cluster complex with the formula [{Co(phen)(2)}(2)V4O12](H2O)-H-. was synthesized from the hydrothermal reaction of V2O5, H2C2O4, Co(NO3)(2), 1,10-phenanthroline (phen), (C4H9)(4)NOH and water. The compound crystallizes in an orthorhombic system with space group Pbcn and unit cell parameters a = 19.106(3) Angstrom, b = 15.250(3) Angstrom, c = 16.321(2) Angstrom, V = 4755.4(13) Angstrom(3), Z = 4 and R = 0.0318. The bimetallic cluster complex [{Co(phen)(2)}(2)V4O12](H2O)-H-. is composed of a discrete V4O124- cluster eovalently attached to two [Co(phen)(2)](2+) fragments and the discrete hexanuclear bimetallic clusters of [{Co(phen)(2)}(V4O12)-V-2](H2O)-H-. are further extended into interesting three-dimensional supermolecular arrays via pi-pi stacking interactions of phen groups. Other characterizations by elemental analysis, IR, and thermal analysis are also described.

Vibrational properties, crystal X-ray diffraction structure and quantum chemical calculations on a divalent sulfur substituted phthalimide: 1H-Isoindole-1,3(2H)-dione, 2-[(methoxycarbonyl)thio]

Structural and conformational properties of 1H-Isoindole-1,3(2H)-dione, 2-[(methoxycarbonyl)thio] (S-phthalimido O-methyl thiocarbonate) are analyzed using a combined approach including X-ray diffraction, vibrational spectra and theoretical calculation methods. The vibrational properties have been studied by infrared and Raman spectroscopies along with quantum chemical calculations (B3LYP and B3PW91 functional in connection with the 6-311++G** and aug-cc-pVDZ basis sets). The crystal structure was determined by X-ray diffraction methods. The substance crystallizes in the monoclinic P2(1)/c space group with a = 6.795(1), b = 5.109(1), c = 30.011(3) angstrom, beta = 90.310(3)degrees and Z = 4 molecules per unit cell. The conformation adopted by the N-S-C=O group is syn (C=O double bond in synperiplanar orientation with respect to the N-S single bond). The experimental molecular structure is well reproduced by the MP2/aug-cc-pVDZ method. (C) 2010 Elsevier B.V. All rights reserved.

Crystal Structure Determination of Mebendazole Form A Using High-Resolution Synchrotron X-Ray Powder Diffraction Data

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)