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At least 217 records · Page 12Linked to original sources
PubMed2004

Displacement of iron by zinc at the diiron site of Desulfovibrio vulgaris rubrerythrin: X-ray crystal structure and anomalous scattering analysis.

X-ray crystal structures of recombinant Desulfovibrio (D.) vulgaris rubrerythrin (Rbr) have shown a diiron site, whereas the crystal structure of Rbr "as-isolated" from D. vulgaris was reported to contain a mixed Zn,Fe binuclear site. To investigate the possibility that zinc had displaced iron during isolation or crystallization of the "as-isolated" D. vulgaris Rbr, the X-ray crystal structure of recombinant D. vulgaris all-iron Rbr that had been incubated with excess zinc sulfate prior to crystallization, yielding a protein labeled Zn,FeRbr, was solved. Analysis of the anomalous scattering data obtained at two different wavelengths showed that zinc had displaced a significant proportion of iron from both iron centers of the diiron site, and that no iron had been displaced from the [Fe(SCys)(4)] site. UV-visible absorption spectra of the redissolved Zn,FeRbr crystals showed 30-40% retention of oxo-bridged diferric sites, and the redissolved crystals had 37% of the peroxidase specific activity of the starting all-iron Rbr, which, together with the crystallographic results, indicate a predominant mixture of Fe1,Fe2 and Zn1,Zn2 sites. The structure of the Zn(Fe)1,Fe(Zn)2 binuclear site in the Zn,FeRbr crystals was very similar to that of the Zn,Fe binuclear site reported for the "as-isolated" D. vulgaris Rbr, including tetrahedral four-coordination at the Zn(Fe)1 site. The diiron sites in the recombinant Zn,FeRbr crystals were likely at least partially reduced during synchrotron irradiation. Our results suggest that the mixed-metal binuclear site reported for the "as-isolated" D. vulgaris Rbr could be due to displacement of iron from a native diiron site by adventitious zinc during isolation and/or crystallization, and that reduced diiron and dizinc sites can adopt very similar structures in Rbr.

Bacterial Proteins↗
PubMed2000

New rubidium zinc hydrogen phosphate, Rb2Zn2(HPO4)3: synthesis, crystal structure, and 31P single-crystal NMR.

A new rubidium zinc hydrogen phosphate, Rb2Zn2(HPO4)3, is prepared by an unusual method utilizing long nucleation times. This material is crystallized from a gel with an initial composition of 1.0 ZnO/0.94 P2O5/0.96 Rb2O/0.04 Li2O/41 H2O, while the phosphate concentration equals 1.6 M and pH = 3.5. The gel is placed in a sealed Pyrex flask at 52 degrees C, and after 4.5 months crystallization of Rb2Zn2(HPO4)3 is noticed. This new crystalline compound has a three-dimensional framework structure built from spiral chains of alternating PO4 and ZnO4 tetrahedra connected pairwise and assembled by other PO4 tetrahedra, rubidium ions, and hydrogen bonds. The two rubidium ions, Rb(1) and Rb(2), have an exceptionally low number of oxygen contacts in the first coordination sphere, five and seven, respectively. Crystal data: monoclinic, P2(1)/c (no. 14), a = 12.5880(4), b = 12.7170(8), c = 7.5827(8) A, beta = 96.100(1) degrees, Z = 4. A single-crystal 31P NMR investigation of Rb2Zn2(HPO4)3 was performed employing a two-axis goniometer probe and reveals the presence of three chemically and six magnetically nonequivalent phosphorus sites, in accordance with the crystal structure. 31P chemical shielding anisotropies and isotropic chemical shifts (-3.3(3), -2.6(3), and 2.0(3) ppm) have been determined for the three phosphorus sites.

Journal Article↗
PubMed2005

The structural basis of myotonic dystrophy from the crystal structure of CUG repeats.

Myotonic dystrophy (DM) type 1 is associated with an expansion of (>50) CTG repeats within the 3' untranslated region (UTR) of the dystrophin myotonin protein kinase gene (dmpk). In the corresponding mRNA transcript, the CUG repeats form an extended stem-loop structure. The double-stranded RNA of the stem sequesters RNA binding proteins away from their normal cellular targets resulting in aberrant transcription, alternative splicing patterns, or both, thereby leading to DM. To better understand the structural basis of DM type 1, we determined to 1.58-A resolution the x-ray crystal structure of an 18-bp RNA containing six CUG repeats. The CUG repeats form antiparallel double-stranded helices that stack end-on-end in the crystal to form infinite, pseudocontinuous helices similar to the long CUG stem loops formed by the expanded CUG repeats in DM type 1. The CUG helix is very similar in structure to A-form RNA with the exception of the unique U-U mismatches. This structure provides a high-resolution view of a toxic, trinucleotide repeat RNA.

3' Untranslated Regions↗
PubMed1998

Conformational changes in the crystal structure of rat glutathione transferase M1-1 with global substitution of 3-fluorotyrosine for tyrosine.

The structure of the tetradeca-(3-fluorotyrosyl) M1-1 GSH transferase (3-FTyr GSH transferase), a protein in which tyrosine residues are globally substituted by 3-fluorotyrosines has been determined at 2.2 A resolution. This variant was produced to study the effect on the enzymatic mechanism and the structure was undertaken to assess how the presence of the 3-fluorotyrosyl residue influences the protein conformation and hence its function. Although fluorinated amino acid residues have frequently been used in biochemical and NMR investigations of proteins, no structure of a protein that has been globally substituted with a fluorinated amino acid has previously been reported. Thus, this structure represents the first crystal structure of such a protein containing a library of 14 (28 crystallographically distinct) microenvironments from which the nature of the interactions of fluorine atoms with the rest of the protein can be evaluated. Numerous conformational changes are observed in the protein structure as a result of substitution of 3-fluorotyrosine for tyrosine. The results of the comparison of the crystal structure of the fluorinated protein with the native enzyme reveal that conformational changes are observed for most of the 3-fluorotyrosines. The largest differences are seen for residues where the fluorine, the OH, or both are directly involved in interactions with other regions of the protein or with a symmetry-related molecule. The fluorine atoms of the 3-fluorotyrosine interact primarily through hydrogen bonds with other residues and water molecules. In several cases, the conformation of a 3-fluorotyrosine is different in one of the monomers of the enzyme from that observed in the other, including different hydrogen-bonding patterns. Altered conformations can be related to differences in the crystal packing interactions of the two monomers in the asymmetric unit. The fluorine atom on the active-site Tyr6 is located near the S atom of the thioether product (9R,10R)-9-(S-glutathionyl)-10-hydroxy-9,10-dihydrophenanthrene and creates a different pattern of interactions between 3-fluorotyrosine 6 and the S atom. Studies of these interactions help explain why 3-FTyr GSH transferase exhibits spectral and kinetic properties distinct from the native GSH transferase.

Animals↗
PubMed2000

A convenient route to synthesize the fully conjugated bimetallic complex (Bu4N)2[tto[Ni(dmit)2]] (tto = tetrathiooxalate, C2S4(2-), and dmit = 1,3-dithiole-2-thione-4,5-dithiolate, C3S5(2-) and the crystal structure of a new crystal form.

A novel route for the conversion of (Bu4N)2[Ni(dmit)2] to (Bu4N)2[tto[Ni(dmit)2]] is reported here. This provides a much more efficient way of synthesizing (Bu4N)2[tto[Ni(dmit)2]] than the literature method. During the process, the conversion of dmit2- to tto2- was realized for the first time. This new synthesis should facilitate further research on the conducting bimetallic complexes [C]x[tto[Ni(dmit)2]]. In addition, a new crystal form of (Bu4N)2[tto[Ni(dmit)2]]. In addition, a new crystal form of (Bu4N)2[tto[Ni(dmit)2]] was determined by X-ray crystallographic analysis.

Journal Article↗
PubMed1999

Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes.

The oligopeptide-binding protein OppA provides a useful model system for studying the physical chemistry underlying noncovalent interactions since it binds a variety of readily synthesized ligands. We have studied the binding of eight closely related tripeptides of the type Lysine-X-Lysine, where X is an abnormal amino acid, by isothermal titration calorimetry (ITC) and X-ray crystallography. The tripeptides fall into three series of ligands, which have been designed to examine the effects of small changes to the central side chain. Three ligands have a primary amine as the second side chain, two have a straight alkane chain, and three have ring systems. The results have revealed a definite preference for the binding of hydrophobic residues over the positively charged side chains, the latter binding only weakly due to unfavorable enthalpic effects. Within the series of positively charged groups, a point of lowest affinity has been identified and this is proposed to arise from unfavorable electrostatic interactions in the pocket, including the disruption of a key salt bridge. Marked entropy-enthalpy compensation is found across the series, and some of the difficulties in designing tightly binding ligands have been highlighted.

Bacterial Proteins↗
PubMed2004

X-ray crystal structure of Desulfovibrio vulgaris rubrerythrin with zinc substituted into the [Fe(SCys)4] site and alternative diiron site structures.

The X-ray crystal structure of recombinant Desulfovibrio vulgaris rubrerythrin (Rbr) that was subjected to metal constitution first with zinc and then iron, yielding ZnS(4)Rbr, is reported. A [Zn(SCys)(4)] site with no iron and a diiron site with no appreciable zinc in ZnS(4)Rbr were confirmed by analysis of the anomalous scattering data. Partial reduction of the diiron site occurred during the synchrotron X-ray irradiation at 95 K, resulting in two different diiron site structures in the ZnS(4)Rbr crystal. These two structures can be classified as containing mixed-valent Fe1(III)(mu-OH(-))(mu-GluCO(2)(-))(2)Fe2(II) and Fe1(II)(mu-GluCO(2)(-))(2)Fe2(III)-OH(-) cores. The data do not show any evidence for alternative positions of the protein or solvent ligands. The iron and ligand positions of the solvent-bridged site are close to those of the diferric site in all-iron Rbr. The diiron site with only the two carboxylato bridges differs by an approximately 2 A shift in the position of Fe1, which changes from six- to four-coordination. The Fe1- - -Fe2 distance (3.6 A) in this latter site is significantly longer than that of the site with the additional solvent bridge (3.4 A) but significantly shorter than that previously reported for the diferrous site (4.0 A) in all-iron Rbr. The apparent redox-induced movement of Fe1 at 95 K in the ZnS(4)Rbr crystal implies an extremely low activation barrier, which is consistent with the rapid (approximately 30 s(-1)) room temperature turnover of the all-iron Rbr during its catalysis of two-electron reduction of hydrogen peroxide. ZnS(4)Rbr does not show peroxidase activity, presumably because the [Zn(SCys)(4)] site, unlike the [Fe(SCys)(4)] site, cannot mediate electron transfer to the diiron site. One or both of the diiron site structures in the cryoreduced ZnS(4)Rbr crystal are likely to represent that (those) of transient mixed-valent diiron site(s) that must occur upon return of the diferric to the diferrous oxidation level during peroxidase turnover.

Bacterial Proteins↗
PubMed2000

Crystal structure of recombinant trypsin-solubilized fragment of cytochrome b(5) and the structural comparison with Val61His mutant.

The crystal structure of the recombinant trypsin-solubilized fragment of the microsomal cytochrome b(5) from bovine liver has been determined at 1.9 A resolution and compared with the reported crystal structure of the lipase-solubilized fragment of the membrane protein cytochrome b(5). The two structures are similar to each other. However, some detailed structural differences are observed: the conformation of the segment Asn16-Ser20 is quite different, some helices around the heme and some segments between the helices are shifted slightly, the heme is rotated about the normal of the mean plane of heme, one of the propionates of the heme exhibits a different conformation. The average coordination distances between the iron and the two nitrogen atoms of the imidazole ligands are the same in the two structures. Most of the structural differences can be attributed to the different intermolecular interactions which result from the crystal packing. The wild-type protein structure is also compared with its Val61His mutant, showing that the heme binding and the main chain conformations are basically identical with each other except for the local area of the mutation site. However, when Val61 is mutated to histidine, the large side chain of His61 is forced to point away from the heme pocket toward the solvent region, disturbing the micro-environment of the heme pocket and influencing the stability and the redox potential of the protein.

Animals↗
PubMed1999

Difference density quality (DDQ): a method to assess the global and local correctness of macromolecular crystal structures.

Methods for the evaluation of the accuracy of crystal structures of proteins and nucleic acids are of general importance for structure-function studies as well as for biotechnological and biomedical research based upon three-dimensional structures of biomacromolecules. The structure-validation program DDQ (difference-density quality) has been developed to complement existing validation procedures. The DDQ method is based on the information present in a difference electron-density map calculated with the water molecules deliberately omitted from the structure-factor calculation. The quality of a crystal structure is reflected in this difference map by (i) the height of solvent peaks occurring at physical chemically reasonable positions with respect to protein and ligand atoms and (ii) the number and height of positive and negative 'shift' peaks next to protein atoms. The higher the solvent peaks and the lower the shift peaks, the better the structure is likely to be. Moreover, extraneous positive density due to an incomplete molecular model is also monitored, since this is another indicator of imperfections in the structure. Automated analysis of these types of features in difference electron densities is used to quantify the local as well as global accuracy of a structure. In the case of proteins, the DDQ structure-validation method is found to be very sensitive to small local errors, to omitted atoms and also to global errors in crystal structure determinations.

Crystallography, X-Ray↗
PubMed2001

Crystal structures of the peanut lectin-lactose complex at acidic pH: retention of unusual quaternary structure, empty and carbohydrate bound combining sites, molecular mimicry and crystal packing directed by interactions at the combining site.

The crystal structures of a monoclinic and a triclinic form of the peanut lectin-lactose complex, grown at pH 4.6, have been determined. They contain two and one crystallographically independent tetramers, respectively. The unusual "open" quaternary structure of the lectin, observed in the orthorhombic complex grown in neutral pH, is retained at the acidic pH. The sugar molecule is bound to three of the eight subunits in the monoclinic crystals, whereas the combining sites in four are empty. The lectin-sugar interactions are almost the same at neutral and acidic pH. A comparison of the sugar-bound and free subunits indicates that the geometry of the combining site is relatively unaffected by ligand binding. The combining site of the eighth subunit in the monoclinic crystals is bound to a peptide stretch in a loop from a neighboring molecule. The same interaction exists in two subunits of the triclinic crystals, whereas density corresponding to sugar exists in the combining sites of the other two subunits. Solution studies show that oligopeptides with sequences corresponding to that in the loop bind to the lectin at acidic pH, but only with reduced affinity at neutral pH. The reverse is the case with the binding of lactose to the lectin. A comparison of the neutral and acidic pH crystal structures indicates that the molecular packing in the latter is directed to a substantial extent by the increased affinity of the peptide loop to the combining site at acidic pH.

Carbohydrates↗
PubMed2002

Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations.

Crystal structures have shown that the HIV-1 protease flaps, domains that control access to the active site, are closed when the active site is occupied by a ligand. Although flap structures ranging from closed to semi-open are observed in the free protease, crystal structures reveal that even the semi-open flaps block access to the active site, indicating that the flaps are mobile in solution. The goals of this paper are to characterize the secondary structure and fast (sub-ns) dynamics of the flaps of the free protease in solution, to relate these results to X-ray structures and to compare them with predictions of dynamics calculations. To this end we have obtained nearly complete backbone and many sidechain signal assignments of a fully active free-protease construct that is stabilized against autoproteolysis by three point mutations. The secondary structure of this protein was characterized using the chemical shift index, measurements of (3h)J(NC') couplings across hydrogen bonds, and NOESY connectivities. Analysis of these measurements indicates that the protease secondary structure becomes irregular near the flap tips, residues 49-53. Model-free analysis of (15)N relaxation parameters, T(1), T(2) (T(1rho)) and (15)N-[(1)H] NOE, shows that residues in the flap tips are flexible on the sub-ns time scale, in contrast with previous observations on the inhibitor-bound protease. These results are compared with theoretical predictions of flap dynamics and the possible biological significance of the sub-ns time scale dynamics of the flap tips is discussed.

Amino Acid Sequence↗
PubMed2006

Structural changes of phenylalanine 338 and histidine 447 revealed by the crystal structures of tabun-inhibited murine acetylcholinesterase.

Organophosphorus compounds (OPs) interfere with the catalytic mechanism of acetylcholinesterase (AChE) by rapidly phosphorylating the catalytic serine residue. The inhibited enzyme can at least partly be reactivated with nucleophilic reactivators such as oximes. The covalently attached OP conjugate may undergo further intramolecular dealkylation or deamidation reactions, a process termed "aging" that results in an enzyme considered completely resistant to reactivation. Of particular interest is the inhibition and aging reaction of the OP compound tabun since tabun conjugates display an extraordinary resistance toward most reactivators of today. To investigate the structural basis for this resistance, we determined the crystal structures of Mus musculus AChE (mAChE) inhibited by tabun prior to and after the aging reaction. The nonaged tabun conjugate induces a structural change of the side chain of His447 that uncouples the catalytic triad and positions the imidazole ring of His447 in a conformation where it may form a hydrogen bond to a water molecule. Moreover, an unexpected displacement of the side chain of Phe338 narrows the active site gorge. In the crystal structure of the aged tabun conjugate, the side chains of His447 and Phe338 are reversed to the conformation found in the apo structure of mAChE. A hydrogen bond between the imidazole ring of His447 and the ethoxy oxygen of the aged tabun conjugate stabilizes the side chain of His447. The displacement of the side chain of Phe338 into the active site gorge of the nonaged tabun conjugate may interfere with the accessibility of reactivators and thereby contribute to the high resistance of tabun conjugates toward reactivation.

Acetylcholinesterase↗
PubMed1998

Structure-function relationships and flexible tetramer assembly in pyruvate decarboxylase revealed by analysis of crystal structures.

The crystal structures of pyruvate decarboxylase from the yeast Saccharomyces uvarum and Saccharomyces cerevisiae have been determined at 2.4 and 2.3 A resolution, respectively. These structures provide details about the protein fold and domain assembly within subunits, about subunit assembly to form dimers and about dimer assembly to form tetramers. They also provide a clear picture of the active site centered on the thiamin diphosphate cofactor, and have allowed amino acids critical for catalysis and involved in stabilization of the unusual cofactor conformation to be identified. The structural information has enabled identification of the site of allosteric activation to be centered on Cys-221, and suggests that a six residue segment leading from the regulatory site to the catalytic site may be involved in transmission of a binding signal. The importance of several amino acids within this segment in the regulatory process, as well as some involved in stabilizing and activating the cofactor has been confirmed by analyzing the behavior of recombinant enzymes with single point mutations introduced at these sites. Additional structures have been determined for pyruvate decarboxylase in multiple crystal forms, some of which were obtained from crystals grown with known allosteric activators present in the media. Currently four distinct types of tetramers have been observed, with each showing a different mode of association of dimers to form the tetramers. In some of the cases involving the presence of allosteric activators drastic changes in the mode of dimer assembly to form tetramers is seen.

Allosteric Regulation↗
PubMed1999

Modelling the crystal structure of the 2-hydronitronylnitroxide radical (HNN): observed and computer-generated polymorphs.

The crystal structures of two polymorphs of 4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazol-1-oxyl 3-oxide (the 2-hydronitronylnitroxide radical, HNN) are analyzed by packing energy criteria. Other unobserved polymorphic crystal structures are generated using a polymorph predictor package and three different force fields, one of which is without explicit Coulomb-type terms. The relative importance of several structural motifs (hydrogen-bonded dimers, shape-interlocking dimers or extended hydrogen-bonded chains) is discussed. As usual, many crystal structures within a narrow energy range are generated by the polymorph predictor, confirming that ab initio crystal-structure prediction is still problematic. Comparisons of powder patterns generated from the atomic coordinates of the X-ray structure and from computational crystal structures confirm that although the energy ranking depends on the force field used, the X-ray structure of the alpha polymorph was found to be among the most stable ones produced by the polymorph predictor, even using the chargeless force field.

Journal Article↗
PubMed1998

Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets.

Transcriptional regulation in papillomaviruses depends on sequence-specific binding of the regulatory protein E2 to several sites in the viral genome. Crystal structures of bovine papillomavirus E2 DNA targets reveal a conformational variant of B-DNA characterized by a roll-induced writhe and helical repeat of 10.5 bp per turn. A comparison between the free and the protein-bound DNA demonstrates that the intrinsic structure of the DNA regions contacted directly by the protein and the deformability of the DNA region that is not contacted by the protein are critical for sequence-specific protein/DNA recognition and hence for gene-regulatory signals in the viral system. We show that the selection of dinucleotide or longer segments with appropriate conformational characteristics, when positioned at correct intervals along the DNA helix, can constitute a structural code for DNA recognition by regulatory proteins. This structural code facilitates the formation of a complementary protein-DNA interface that can be further specified by hydrogen bonds and nonpolar interactions between the protein amino acids and the DNA bases.

Animals↗