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PubMed2000

New alternating ferro- and antiferromagnetic one-dimensional complexes. Synthesis, characterization, crystal structure, and magnetic properties of.

The preparation, X-ray crystal structure, and magnetic properties of alternating 1,1- and 1,3-azido-bridged copper(II) complex [Cu(4,4'-dmbpy)(N3)2]n (1, 4,4'-dmbpy = 4,4'-dimethylbipyridine) have been reported. It crystallizes in triclinic system, space group P1, a = 7.9903(1) A, b = 9.3545(9) A, c = 10.754(2) A, alpha = 113.485(1) degrees, beta = 101.399(1) degrees, gamma = 101.897(1) degrees, Z = 2. The magnetic properties of 1 have been investigated in the temperature range 1.5-300 K. Alternating antiferromagnetic (-J = 191.0 cm(-1)) interaction through a 1,3-N3- bridge and ferromagnetic (J = 297.1 cm(-1)) interaction through a 1,1-N3- bridge are obtained for 1 by analyzing the magnetic susceptibility data with the Hamiltonian H = -Jsigma(S2iS2i-1--alphaS2iS2i+1). It's derivatives ([Mn(4,4'-dmbpy)(N3)2]n (2), [Ni(4,4'-dmbpy)(N3)2]n (3), and [Fe(4,4'-dmbpy)(N3)2]n (4) and the heterometallic derivatives [NiMn(4,4'-dmbpy)2(N3)4]n (5) and [CuMn(4,4'-dmbpy)2(N3)4]n (6) have also been synthesized and characterized by electronic and IR spectra. The X-ray powder diffraction and the magnetic properties of 6 have also been discussed.

Journal Article↗
PubMed1996

Synthesis, Crystal Structure, and EPR Studies of the Five-Coordinate [CuCl(3)(H(2)O)(2)](-) Complex in (dabcoH(2))(2)Cl(3)[CuCl(3)(H(2)O)(2)].H(2)O.

The compound (dabcoH(2))(2)Cl(3)[CuCl(3)(H(2)O)(2)].H(2)O, where dabco = 1,4-diazabicyclo[2.2.2]octane, has been synthesized, its structure has been determined by single-crystal structural analysis, and its properties have been investigated by powder and single-crystal EPR spectroscopy. The compound crystallizes in space group Pnma at room temperature with unit cell dimensions of a = 15.227(1) Å, b = 7.467(1) Å, and c = 20.166(2) Å with Z = 4. The structure was solved by the Patterson method and refined by full-matrix least-squares to R = 4.3% for 1681 observed reflections (I > 2sigma(I)). The [CuCl(3)(H(2)O)(2)](-) anion exists with a slightly distorted trigonal bipyramidal geometry in which the three Cl atoms lie in equatorial positions and the two water molecules are in axial positions. The distortion appears to be driven by the presence of N-H.Cl hydrogen bonds. The EPR spectra are also consistent with the presence of only a small distortion from trigonal bipyramidal geometry since g(1) approximately g(2) > g(3) approximately 2.0. Analysis of the geometry indicates the distortion consists primarily of a "negative" C(2)(v)() type. Analysis of the thermal parameters supports the supposition that the observed geometry corresponds to disorder over two "positive" C(2)(v)() distortions.

Journal Article↗
PubMed2005

Crystal structure and DNA binding functions of ERCC1, a subunit of the DNA structure-specific endonuclease XPF-ERCC1.

Human XPF-ERCC1 is a DNA endonuclease that incises a damaged DNA strand on the 5' side of a lesion during nucleotide excision repair and has additional role(s) in homologous recombination and DNA interstrand crosslink repair. We show that a truncated form of XPF lacking the N-terminal helicase-like domain in complex with ERCC1 exhibits a structure-specific endonuclease activity with similar specificity to that of full-length XPF-ERCC1. Two domains of ERCC1, a central domain and a C-terminal tandem helix-hairpin-helix (HhH2) dimerization domain, bind to ssDNA. The central domain of ERCC1 binds ssDNA/dsDNA junctions with a defined polarity, preferring a 5' single-stranded overhang. The XPF-ERCC1 HhH2 domain heterodimer contains two independent ssDNA-binding surfaces, which are revealed by a crystal structure of the protein complex. A crystal structure of the central domain of ERCC1 shows its fold is strikingly similar to that of the nuclease domains of the archaeal Mus81/XPF homologs, despite very low sequence homology. A groove lined with basic and aromatic residues on the surface of ERCC1 has apparently been adapted to interact with ssDNA. On the basis of these crystallographic and biochemical studies, we propose a model in which XPF-ERCC1 recognizes a branched DNA substrate by binding the two ssDNA arms with the two HhH2 domains of XPF and ERCC1 and by binding the 5'-ssDNA arm with the central domain of ERCC1.

Animals↗
PubMed2003

Crystal structure of soybean 11S globulin: glycinin A3B4 homohexamer.

Most plant seeds contain 11S globulins as major storage proteins for their nutrition. Soybean glycinin belongs to the 11S globulin family and consists of five kinds of subunits. We determined the crystal structure of a homohexamer of the glycinin A3B4 subunit at 2.1-A resolution. The crystal structure shows that the hexamer has 32-point group symmetry formed by face-to-face stacking of two trimers. The interface buries the highly conserved interchain disulfide. Based on the structure, we propose that an ingenious face-to-face mechanism controls the hexamer formation of the 11S globulin by movement of a mobile disordered region to the side of the trimer after posttranslational processing. Electrostatic analysis of the faces suggests that the interchain disulfide-containing face has high positive potential at acidic pH, which induces dissociation of the hexamer into trimers that may be susceptible to proteinases after seed imbibition. This dissociation might result in the degradation and mobilization of 11S globulins as storage proteins in embryos during germination and seedling growth.

Amino Acid Sequence↗
PubMed2005

Expression, purification and crystal structure of a truncated acylpeptide hydrolase from Aeropyrum pernix K1.

Acylpeptide hydrolase (APH) catalyzes the N-terminal hydrolysis of Nalpha-acylpeptides to release Nalpha-acylated amino acids. The crystal structure of recombinant APH from the thermophilic archaeon Aeropyrum pernix K1 (apAPH) was reported recently to be at a resolution of 2.1 Angstrom; using X-ray diffraction. A truncated mutant of apAPH that lacks the first short alpha-helix at the N-terminal, apAPH-delta(1-21), was cloned, expressed, characterized and crystallized. Data from biochemical experiments indicate that the optimum temperature of apAPH is decreased by 15 degrees C with the deletion of the N-terminal alpha-helix. However, the enzyme activity at the optimal temperature does not change. It suggests that this N-terminal alpha-helix is essential for thermostability. Here, the crystal structure of apAPH-delta(1-21) has been determined by molecular replacement to 2.5 Angstrom;. A comparison between the two structures suggests a difference in thermostability, and it can be concluded that by adding or deleting a linking structure (located over different domains), the stability or even the activity of an enzyme can be modified.

Aeropyrum↗
PubMed2000

Crystal structure of cambialistic superoxide dismutase from porphyromonas gingivalis.

The crystal structure of cambialistic superoxide dismutase (SOD) from Porphyromonas gingivalis, which exhibits full activity with either Fe or Mn at the active site, has been determined at 1.8-A resolution by molecular replacement and refined to a crystallographic R factor of 17.9% (Rfree 22.3%). The crystals belong to the space group P212121 (a = 75.5 A, b = 102.7 A, c = 99.6 A) with four identical subunits in the asymmetric unit. Each pair of subunits forms a compact dimer, but not a tetramer, with 222 point symmetry. Each subunit has 191 amino-acid residues most of which are visible in electron density maps, and consists of seven alpha helices and one three-stranded antiparallel beta sheet. The metal ion, a 3 : 1 mixture of Fe and Mn, is coordinated with five ligands (His27, His74, His161, Asp157, and water) arranged at the vertices of a trigonal bipyramid. Although the overall structural features, including the metal coordination geometry, are similar to those found in other single-metal containing SODs, P. gingivalis SOD more closely resembles the dimeric Fe-SODs from Escherichia coli rather than another cambialistic SOD from Propionibacterium shermanii, which itself is rather similar to other tetrameric SODs.

Amino Acid Sequence↗
PubMed2004

Crystal structure of phosphotransacetylase from the methanogenic archaeon Methanosarcina thermophila.

Phosphotransacetylase (Pta) [EC 2.3.1.8] is ubiquitous in the carbon assimilation and energy-yielding pathways in anaerobic prokaryotes where it catalyzes the reversible transfer of the acetyl group from acetyl phosphate to CoA forming acetyl CoA and inorganic phosphate. The crystal structure of Pta from the methane-producing archaeon Methanosarcina thermophila, representing the first crystal structure of any Pta, was determined by multiwavelength anomalous diffraction at 2.7 A resolution. In solution and in the crystal, the enzyme forms a homodimer. Each monomer consists of two alpha/beta domains with a cleft along the domain boundary, which presumably contains the substrate binding sites. Comparison of the four monomers present in the asymmetric unit indicates substantial variations in the relative orientation of the two domains and the structure of the putative active site cleft. A search for structural homologs revealed the NADP(+)-dependent isocitrate and isopropylmalate dehydrogenases as the only homologs with a similar two-domain architecture.

Archaeal Proteins↗
PubMed2001

Crystal structures and freezing of dipolar fluids.

We investigate the crystal structure of classical systems of spherical particles with an embedded point dipole at T=0. The ferroelectric ground state energy is calculated using generalizations of the Ewald summation technique. Due to the reduced symmetry compared to the nonpolar case the crystals are never strictly cubic. For the Stockmayer (i.e., Lennard-Jones plus dipolar) interaction three phases are found upon increasing the dipole moment: hexagonal, body-centered orthorhombic, and body-centered tetragonal. An even richer phase diagram arises for dipolar soft spheres with a purely repulsive inverse power law potential approximately r(-n). A crossover between qualitatively different sequences of phases occurs near the exponent n=12. The results are applicable to electro- and magnetorheological fluids. In addition to the exact ground state analysis we study freezing of the Stockmayer fluid by density-functional theory.

Journal Article↗
PubMed1992

Refined 2.3 A X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA. A starting point for improving antithrombotics.

Well-diffracting crystals of bovine epsilon-thrombin in complex with several "non-peptidic" benzamidine and arginine-based thrombin inhibitors have been obtained by co-crystallization. The 2.3 A crystal structures of three complexes formed either with NAPAP, 4-TAPAP, or MQPA, were solved by Patterson search methods and refined to crystallographic R-values of 0.167 to 0.178. The active-site environment of thrombin is only slightly affected by binding of the different inhibitors; in particular, the exposed "60-insertion loop" essentially maintains its typical projecting structure. The D-stereoisomer of NAPAP and the L-stereoisomer of MQPA bind to thrombin with very similar conformations, as previously inferred from their binding to bovine trypsin; the arginine side-chain of the latter inserts into the specificity pocket in a "non-canonical" manner. The L-stereoisomer of 4-TAPAP, whose binding geometry towards trypsin was only poorly defined, is bound to the thrombin active-site in a compact conformation. In contrast to NAPAP, the distal p-amidino/guanidino groups of 4-TAPAP and MQPA do not interact with the carboxylate group of Asp189 in the thrombin specificity pocket in a "symmetrical" twin N-twin O manner, but through "lateral" single N-twin O contacts; in contrast to the p-amidino group of 4-TAPAP, however, the guanidyl group of MQPA packs favourably in the pocket due to an elaborate hydrogen bond network, which includes two entrapped water molecules. These thrombin structures confirm previous conclusions of the important role of the intermolecular hydrogen bonds formed with Gly216, and of the good sterical fit of the terminal bulky hydrophobic inhibitor groups with the hydrophobic aryl binding site and the S2-cavity, respectively, for tight thrombin active site binding of these non-peptidic inhibitors. These accurate crystal structures are presumed to be excellent starting points for the design and the elaboration of improved antithrombotics.

Amidines↗
PubMed2002

Crystal structure of the inclusion complex of beta-cyclodextrin with mefenamic acid from high-resolution synchrotron powder-diffraction data in combination with molecular-mechanics calculations.

The crystal structure of the inclusion complex of beta-cyclo-dextrin with mefenamic acid has been determined from a combination of high-resolution synchrotron powder-diffraction data and molecular-mechanics calculations. A grid search indicates two possible solutions, which are corroborated by molecular-mechanics calculations, while Rietveld-refinement results suggest the crystal structure that is more likely to be formed in the solid state. Mefenamic acid is partially included in beta-cyclodextrin with either the xylyl or the benzoic-acid moiety being inside its cavity. In both solutions mefenamic acid and beta-cyclodextrin form a monomeric complex in a herringbone packing scheme.

Journal Article↗
PubMed1997

The role of DNA in the mechanism of NFkappaB dimer formation: crystal structures of the dimerization domains of the p50 and p65 subunits.

BACKGROUND: Members of the rel/NFkappaB family of transcription factors play a vital role in the regulation of rapid cellular responses, such as those required to fight infection or react to cellular stress. Members of this family of proteins form homo- and heterodimers with differing affinities for dimerization. They share a structural motif known as the rel homology region (RHR), the C-terminal one third of which mediates protein dimerization. Crystal structures of the rel/NFkappaB family members p50 and p65 in their DNA-bound homodimeric form have been solved. These structures showed that the residues from the dimerization domains of both p50 and p65 participate in DNA binding and that the DNA-protein and protein dimerization surfaces form one continuous overlapping interface. We desired to investigate the contribution of DNA to NFkappaB dimerization and to identify the mechanism for the selective association of rel/NFkappaB family peptides into transcriptionally active dimers. RESULTS: We report here the crystal structures of the dimerization domains of murine p50 and p65 at 2.2 A and 2.0 A resolution, respectively. A comparison of these two structures suggests that conservative amino acid changes at three positions are responsible for the differences in their dimer interfaces. The presence of the target DNA does not change the dimer interface of either protein in any significant manner. CONCLUSIONS: These two structures suggest that the rel/NFkappaB family of transcription factors use only a few conservative changes in their amino acid sequences to form a host of dimers with varying affinities for dimerization. Amino acids at positions corresponding to 254, 267, and 307 of murine p50, function as primary determinants for the observed differences in dimerization affinity. The DNA-contacting charged amino acid sidechains from the dimerization domains are held in a similar conformation in both the DNA-bound and free states, therefore, no major structural rearrangement is required to bring these residues into contact with the DNA.

Amino Acid Sequence↗
PubMed1997

Molecular recognition at the thrombin active site: structure-based design and synthesis of potent and selective thrombin inhibitors and the X-ray crystal structures of two thrombin-inhibitor complexes.

BACKGROUND: The serine protease thrombin is central in the processes of hemostasis and thrombosis. To be useful, thrombin inhibitors should combine potency towards thrombin with selectivity towards other related enzymes such as trypsin. We previously reported the structure-based design of thrombin inhibitors with rigid, bicyclic core structures. These compounds were highly active towards thrombin, but showed only modest selectivity. RESULTS: Here, we describe the rational design of selective thrombin inhibitors starting from the X-ray crystal structure of the complex between the previously generated lead molecule and thrombin. The lead molecule bound with a Ki value of 90nM and a selectivity of 7.8 for thrombin over trypsin. Our design led to inhibitors with improved activity and greatly enhanced selectivity. The binding mode for two of the new inhibitors was determined by X-ray crystallography of their complexes with thrombin. The results confirmed the structures predicted by molecular modeling and, together with the binding assays, provided profound insight into molecular recognition phenomena at the thrombin active site. CONCLUSIONS: A novel class of nonpeptidic, selective thrombin inhibitors has resulted from structure-based design and subsequent improvement of the initial lead molecule. These compounds, which are preorganized for binding to thrombin through a rigid, bicyclic or tricyclic central core, could aid in the development of new antithrombotic drugs. Correlative binding and X-ray structural studies within a series of related, highly preorganized inhibitors, which all prefer similar modes of association to thrombin, generate detailed information on the strength of individual intermolecular bonding interactions and their contribution to the overall free energy of complexation.

Antithrombins↗
PubMed1999

Crystal structure of mistletoe lectin I from Viscum album.

The crystal structure of the ribosome-inactivating protein (RIP) mistletoe lectin I (ML-I) from Viscum album has been solved by molecular replacement techniques. The structure has been refined to a crystallographic R-factor of 24.5% using X-ray diffraction data to 2.8 A resolution. The heterodimeric 63-kDa protein consists of a toxic A subunit which exhibits RNA-glycosidase activity and a galactose-specific lectin B subunit. The overall protein fold is similar to that of ricin from Ricinus communis; however, unlike ricin, ML-I is already medically applied as a component of a commercially available misteltoe extract with immunostimulating potency and for the treatment of human cancer. The three-dimensional structure reported here revealed structural details of this pharmaceutically important protein. The comparison to the structure of ricin gives more insights into the functional mechanism of this protein, provides structural details for further protein engineering studies, and may lead to the development of more effective therapeutic RIPs.

Abrin↗
PubMed2002

Crystal structure of a thermostable lipase from Bacillus stearothermophilus P1.

We describe the first lipase structure from a thermophilic organism. It shares less than 20% amino acid sequence identity with other lipases for which there are crystal structures, and shows significant insertions compared with the typical alpha/beta hydrolase canonical fold. The structure contains a zinc-binding site which is unique among all lipases with known structures, and which may play a role in enhancing thermal stability. Zinc binding is mediated by two histidine and two aspartic acid residues. These residues are present in comparable positions in the sequences of certain lipases for which there is as yet no crystal structural information, such as those from Staphylococcal species and Arabidopsis thaliana. The structure of Bacillus stearothermophilus P1 lipase provides a template for other thermostable lipases, and offers insight into mechanisms used to enhance thermal stability which may be of commercial value in engineering lipases for industrial uses.

Amino Acid Sequence↗
PubMed1994

Crystal structure of a free radical enzyme, galactose oxidase.

The crystal structure of the copper-containing enzyme, galactose oxidase, has been solved by multiple isomorphous replacement and refined to a resolution of 1.7 A. The X-ray structure reveals a unique polypeptide fold. The protein can be divided into three domains, all of which consist almost entirely of beta-strands. The structure of the second domain is particularly striking, 28 beta-strands arranged in a pseudo 7-fold symmetry. The copper site is on the surface of the protein and extremely rich in aromatic side-chains. The copper ion has two histidines, two tyrosines, and one external ligand in distorted square pyramidal coordination. The presence of pyrroloquinoline quinone as a covalently bound cofactor in GOase has been excluded. Instead, an unexpected covalent linkage between Tyr272 and Cys228 has been observed, whose functional role may relate to the presence of a tyrosine free radical at Tyr272. The tyrosine free radical could be stabilized by delocalization to Cys228 and stacking interactions with Trp290. A structural model for substrate binding is proposed that offers an explanation for the substrate specificity of the enzyme and many of the spectroscopic and enzymological data. Although the model lacks direct confirmation at present, it should provide a stimulus for further spectroscopic and crystallographic studies.

Amino Acid Sequence↗
PubMed1984

Backbone side chain interactions in peptides. I. Crystal structures of model dipeptides with the Pro-Ser sequence.

The preferential occurrence of amino-acid residues having short polar side-chain within beta-folded regions of crystallized proteins suggests the existence of some stabilizing interaction involving the side polar function. Three model dipeptides tBuCO-L-Pro-L-Ser-NHMe 1, tBuCO-L-Pro-D-Ser-NHMe 2 in the pure enantiomeric a and racemic b forms, and iPrCO-L-Pro-D-Ser-OMe 3 have been investigated in the solid state by X-ray crystallography. Homo and heterochiral sequences 1 and 2 are folded in the beta I and beta II types, respectively, whereas 3 obviously accommodates an open conformation. Besides the i + 3 leads to i hydrogen bond typical of beta-bends in 1, 2a, and 2b, the Ser NH group in all four crystal structures is a proton donor to the lone orbitals of the Ser O gamma oxygen atom. The result is that the disposition of the Ser C alpha--C beta bond corresponds to the rotamer III (chi 1 congruent to 60 degrees). As shown by the crystal structure of 3, the intra-Ser NH. . .O gamma hydrogen bonding is not restricted to beta-folded Pro-Ser sequences. Therefore, this interaction is not only a stabilizing factor for beta-turns but it is also probably responsible for the already mentioned stability of rotamer III for the Ser C alpha--C beta bond in peptides and protein.

Dipeptides↗
PubMed1995

Crystal structure of doisynolic acid and the structure of other products formed during its synthesis.

The crystal structure of the D-seco-estrogen doisynolic acid shows it to have the natural S configuration at the position derived from C-14 in estrone. Two major by-products during the synthesis of doisynolic acid from estrone are shown to be dimeric steroids. One is an aldol condensation product, and the other appears to arise from an alkaline cleavage of the aldol product.

Crystallization↗
PubMed2000

Crystal structure of a DNA.RNA hybrid duplex with a polypurine RNA r(gaagaagag) and a complementary polypyrimidine DNA d(CTCTTCTTC).

DNA.RNA hybrid duplexes are substrates of RNase H and reverse transcriptase. The crystal structure of a hybrid duplex, d(5'-CTCTTCTTC-3').r(5'-gaagaagag-3') (the uppercase letters indicate DNA and lowercase letters RNA), with a polypurine RNA strand and a complementary DNA strand has been determined at 1.8 A resolution. The structure was refined first at 1.9 A by XPLOR and subsequently by CNS at 1.8 A. The hybrid is found in a standard A-form conformation with all the sugars in the C3'-endo puckering. The 5'-terminal base dC of the DNA strand was clearly visible in the electron density map of the present structure, in contrast to the previously reported structure d(TTCTTBr(5)CTTC).r(gaagaagaa) where the 5'-terminal base dT was not visible, leaving the terminal rA unpaired. Thus, the comparison of the terminal base pairs, C.g versus T.a, in the two hybrid crystal structures provides information on the stability of these base pairs in hydrogen bonding (three versus two) and base stacking interactions. The differences in the terminal base pairs produce different kinks in the two structures. Minor groove widening is observed in the present structure at a distinctive kink in the lower half of the duplex, in contrast to the small widening of the minor groove and a very slight bend in the upper half of the T.a structure.

Base Composition↗