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At least 19 recordsLinked to original sources
PubMed1990

Enzymatic mechanism of creatine amidinohydrolase as deduced from crystal structures.

Crystal structures of the enzyme creatine amidinohydrolase (creatinase, EC 3.5.3.3) with two different inhibitors, the reaction product sarcosine and the substrate creatine, bound have been analyzed by X-ray diffraction methods. With the inhibitor carbamoyl sarcosine, two different crystal forms at different pH values have been determined. An enzymatic mechanism is proposed on the basis of the eight structures analyzed. The enzyme binds substrate and inhibitor in a distorted geometry where the urea resonance is broken. His232 is the general base and acid, and acts as a proton shuttle. It withdraws a proton from water 377 and donates it to the N(3) atom of the guanidinium group. OH- 377 adds to the C(1) atom of the guanidinium group to form a urea hydrate. Proton withdrawal by His232 leads to products. The reaction product sarcosine binds to the active site in a reverse orientation. The free enzyme was found to have a bicarbonate bound to the active site.

Binding Sites↗
PubMed1990

Preliminary investigation of the phage phi X174 crystal structure.

Crystals of the single-stranded DNA bacteriophage phi X174 have been grown. They have a monoclinic unit cell with space group P2(1), unit cell dimensions of a = 306.0 (+/- 0.2) A, b = 361.1 (+/- 0.2) A, c = 299.7 (+/- 0.2 degrees) A, beta = 92.91 degrees (+/- 0.02 degrees) and diffract to at least 2.7 A resolution. There are two virus particles per unit cell. Packing considerations show that the mean diameter of the virus particles is 280 A. The virus separates into two bands in a sucrose gradient. The ratio between the absorbance at 260 nm and 280 nm is 1.45 to 1.65 for the faster and 1.15 to 1.35 for the slower bands, but both bands contain intact particles. Crystals derived from these bands are isomorphous and there is no detectable difference in their structure amplitudes.

Bacteriophage phi X 174↗
PubMed1992

Alpha-beta-dehydro-amino acid residues in the design of peptide structures. Molecular and crystal structures of two folded dehydro peptides.

The molecular and crystal structures of two N alpha-protected tripeptide amides, containing in the central position the alpha-beta-dehydro-amino acid residue delta Phe (Z-configurational isomer), were determined by X-ray diffraction. While Z-Gly-delta Phez-L-Pro-NH2 is characterized in the crystal state by the presence of a type I beta-bend conformation (at the delta Phez-L-Pro sequence), Z-D-Ala-delta Phez-Gly-NH2 is folded into two consecutive beta-bends (type II' followed by type I), at the D-Ala-delta Phez and delta Phez-Gly sequences, respectively. In both cases the achiral delta Phez residue adopts a set of phi, psi angles typical of the right-handed helical conformation. The delta Phe residue may be exploited to design aromatic peptides with preferred secondary structures.

Amino Acid Sequence↗
PubMed1987

Crystal structure of two crystal forms of 9 alpha-fluorocortisol acetate: variation of the conformation of the A ring of steroids due to crystal packing.

This paper reports the crystal structure of the propanol solvate of 9 alpha-fluorocortisol acetate, which crystallizes in the monoclinic space group P21 [a = 7.470 (6), b = 14.78 (1), c = 12.310 (9), beta = 105.2 degrees, Z = 2, R = 0.061, and the tetragonal unsolvated crystal form (a = b = 9.208 (2), c = 49.284 (9), P4(1)2(1)2, Z = 8, R = 0.050)]. The molecular structure of fluorocortisol acetate in the two crystal forms differs primarily in the A ring and acetoxy orientation. The A ring of the steroid in the tetragonal crystal was found to be disordered, and exists in both a normal and inverted conformation. The A ring of the steroid in the monoclinic propanol solvate has the normal (1 alpha, 2 beta half-chain) conformation. The differences in the conformation of the side chain and the A ring appear to reflect the conformational variability in 9 alpha-fluorocortisol acetate.

Fludrocortisone↗
PubMed1991

Refined crystal structure of ytterbium-substituted carp parvalbumin 4.25 at 1.5 A, and its comparison with the native and cadmium-substituted structures.

The crystal structure of carp parvalbumin 4.25 containing a 1:1 molar ratio of ytterbium chloride to protein has been refined at 1.5 A resolution by restrained least-squares methods to a crystallographic R value of 0.199. The crystal structure confirms the NMR studies, which suggest that low concentrations of ytterbium cause an extensive displacement of calcium from the EF metal binding site. A comparison of the ytterbium-substituted model with the native and cadmium-substituted structure show no significant differences, except around the substituted EF metal-binding region. The displacement of calcium by ytterbium at the EF site has caused a movement in the polypeptide backbone of Ser-91 and Asp-92. This movement resulted in an increase in the number of oxygen ligands bound to ytterbium in the EF site from seven to eight.

Amino Acid Sequence↗
PubMed1987

Crystal structures of [Met5] and [(4-bromo)Phe4,Met5]enkephalins: formation of a dimeric antiparallel beta-structure.

The crystal structure of [(4-bromo)Phe4,Met5]enkephalin (Tyr-Gly-Gly-(4-bromo)-Phe-Met) shows two independent molecular conformations. The molecules are arranged in parallel in a head-to-tail fashion and form an antiparallel beta-sheet structure involving intermolecular hydrogen bonds. This dimeric beta-structure is also observed in the [Met5]enkephalin crystal, in spite of their different crystal packing environments, which shows the energetic stability of this molecular conformation. The three-dimensional similarity between the dimeric beta-structure and the beta-turn form is discussed in the relation to the opioid delta and mu receptors.

Crystallography↗
PubMed1990

Cardiotoxin VII4 from Naja mossambica mossambica. The refined crystal structure.

The crystal structure of cardiotoxin VII4 from Naja mossambica mossambica was refined to 2.5 A resolution. Fifty ordered solvent sites were localized and included in the refinement. The final R factor is 0.197 (lambda/(2sin theta) less than 5 A; F greater than 3 sigma). The three-dimensional structure is characterized by two beta-sheets. Of particular interest is the two-stranded beta-sheet in the N-terminal region. This shows a large right-handed twist and, though strongly connected to the core of the molecule, and in particular to the C-terminal end, protrudes out of the bulk of the molecule. The segment of four amino acid residues connecting the two strands of this sheet is particularly exposed. It contains an invariant proline residue that has probably an important structural role, and is completely hydrophobic. Two other conserved hydrophobic zones were identified; the largest extends over the second and third loops, on one side only of the molecule. All side-chains of invariant hydrophobic character (except proline residues) belong to one of these three zones. Also discussed are the dimeric assembly and the rather loose packing in the crystal. The three-dimensional structure is compared with that of short and long alpha-neurotoxins. Comparison with two-dimensional nuclear magnetic resonance results on the 68% homologous cardiotoxin CT X IIb shows an excellent overall agreement. A few differences are probably genuine.

Amino Acid Sequence↗
PubMed1977

Molecular structure of thyroxine analogues. Crystal structure of 3,5,3'-triiodothyroacetic and 3,5,3',5'-tetraoiodothyroacetic acid N-diethanolamine (1:1) complexes.

Crystallographic data demonstrated that conformations of thyroid hormones and their derivatives in which the phenyl rings are either skewed (phi,phi'; +/-90,0 degrees) or twist-skewed (phi,phi'; +/-108, +/-28 degrees) are energetically favored. Acetic acid metabolites are consistently observed in the skewed conformation whereas their parent hormones are observed in the twist-skewed conformation. These preferences are manifestations of long-range conformational transmission and together with plasma protein binding data may indicate a site-specific preference for the skewed vs. twist-skewed conformation. These findings result in part from the crystal structure determinations of the N-diethanolamine (1:1) complexes of the active thyroxine metabolites 3,5,3'-triiodothyroacetic acid (T3AA) and 3,5,3'5'-tetraiodothyroacetic acid (T4AA) which are reported here. The conformation of the 3'-iodine in the hypocholestermic agent T3AA is distal, the biologically preferred conformation, and the overall conformation of T3AA is transoid, while that of T4AA is cisoid.

Chemical Phenomena↗
PubMed1990

Protein-DNA conformational changes in the crystal structure of a lambda Cro-operator complex.

The structure of a complex of bacteriophage lambda Cro protein with a 17-base-pair operator has been determined at 3.9-A resolution. Isomorphous derivatives obtained by the synthesis of site-specific iodinated DNA oligomers were of critical importance in solving the structure. The crystal structure contains three independent Cro-operator complexes that have very similar, although not necessarily identical, conformations. In the complex, the protein dimer undergoes a large conformational change relative to the crystal structure of the free protein. One monomer rotates by about 40 degrees relative to the other, this being accomplished primarily by a twisting of the two beta-sheet strands that connect one monomer with the other. In the complex, the DNA is bent by about 40 degrees into the shape of a boomerang but maintains essentially Watson-Crick B-form. In contrast to other known protein-DNA complexes, the DNA is not stacked end-to-end. The structure confirms the general features of the model previously proposed for the interaction of Cro with DNA.

Amino Acid Sequence↗
PubMed1989

Platelet activating factor antagonist design. 3. X-ray crystal structure and intermolecular crystal lattice interactions of methyl trans-4-acetoxymethyl-4,5-dihydro-2,5-bis(3,4-methylenedioxyphenyl)- 3-furancarboxylate.

C23H20O9, Mr = 440.41, monoclinic, P21/c, a = 11.433 (1), b = 7.808 (2), c = 23.313 (3) A, beta = 99.67 (1) degree, V = 2052 A3, Z = 4, Dx = 1.43 g cm-3, lambda(MoK alpha) = 0.71073 A, mu = 0.69 cm-1, F(000) = 920, T = 293 K, final R = 0.048 for 1645 observed [Fo greater than or equal to 5 sigma(Fo)] reflections. The observed structure reveals a trans relationship for the 4-acetoxymethyl and 5-aryl substituents. The 4,5-dihydrofuran ring system adopts an envelope conformation. There is no crystallographically imposed symmetry. Several intermolecular van der Waals interactions occur in the cell lattice of this compound.

Chemical Phenomena↗
PubMed1987

Ribonuclease structure and catalysis: crystal structure of sulfate-free native ribonuclease A at 1.5-A resolution.

The structure of native bovine pancreatic ribonuclease A, without the inhibitory sulfate anion normally bound at the active site, has been determined by X-ray diffraction at 1.53-A resolution. Treatment of a crystal of ribonuclease containing sulfate with an alkaline buffer released most of the sulfate anions. On return to active pH, few of the side chains moved, and the backbone structure remained unchanged. The active site conformation was essentially unchanged except for the replacement of the sulfate anion by a water molecule, which is hydrogen-bonded to histidine-12 and to another water, and for a small movement of the side chain of lysine-41. Histidines-12 and -119, the catalytic basic and acidic residues, have not moved. Thus the distance between them, and the presence of an intervening water, prohibits the possibility of their being hydrogen-bonded together. The structure has been refined by restrained least squares to an R factor of 0.17. Analysis of individual atomic temperature factors indicates that the molecule has become less rigid in general but that some regions were particularly affected by loss of the sulfate, while others were relatively unaffected. The active site geometry of native ribonuclease A supports the original in-line mechanism of Rabin and co-workers and is in disagreement with the adjacent mechanism of Witzel and co-workers.

Models, Molecular↗
PubMedDate not supplied

Structure investigations of agonists of the natural neurotransmitter acetylcholine, V. Structure-activity correlations for cholinergic stimulants derived from crystal structures of their halides.

General features of crystal structures of halide salts of cholinergic stimulants can be interpreted in terms of substrate-receptor interactions. The monoatomic counterions in the crystal structures are discussed as models for the binding site of the receptor with respect to the ammonium group of the cholinergic neurotransmitters. In the crystal structures the anions occupy the tetrahedral faces of the quaternary trimethylammonio methyl or related groups in a specific geometry. Crystallographic and pharmacological evidence indicates that these groups should preferentially interact with the receptor via a specific face type (B-type face). The directionality of the interaction is derived from the vectors joining N+ with the anions occupying B-type faces. So called "activity triangles", formed by the nitrogen of the ammonium group, a second polar centre of the neurotransmitter cation and a counterion occupying a B-face of the ammonium group, provide a structural criterion for the differentiation between muscarinic and nicotinic activity. It is shown that structure-activity relationships of cholinergic stimulants do not depend on the conformational details of the neurotransmitter cations, but primarily on the relative positions of the polar centres of the cations with respect to the anionic binding site of the receptor.

Acetylcholine↗
PubMed1979

Crystal structure analysis of the tetragonal crystal form are preliminary molecular model of pig-heart citrate synthase.

The crystal structure of pig heart citrate synthase was analyzed at 0.35-nm resolution. Chain tracing was possible and an initial molecular model constructed. The dimensions of the dimer molecule (located on a crystallographic diad) are 7.5 x 6.0 x 9.0 nm. The chain folding is characterized by the predominance of helices and the absence of sheet structure. The electron density accounts for 355 residues per monomer, so that about 80 residues must be disordered in the crystal. The disordered segment in probably N-terminal. The ordered part consists of two closely associated domains, a large domain with 300 residues and a C-terminal domain of 55 residues consisting of 3(anti)parallel helices. The large domain is built from 12 helical segments, some of which are buried in the interior of the molecule. Inhibitor binding studies with citrate and CoA revealed citrate binding sites but showed no electron density for CoA. It is suggested that CoA binds to the disordered, flexible N-terminal domain. Experiments of limited proteolysis with trypsin showed that under conditions a segment of Mr 9000 is cleaved off selectively. The remaining 35 000-Mr part is dimeric.

Animals↗
PubMed1992

Molecular and crystal structure of konjac glucomannan in the mannan II polymorphic form.

A probable crystal structure of konjac glucomannan (mannose:glucose ratio = 1.6) is proposed based on X-ray data and constrained linked-atom least-squares model refinement. The structure crystallizes in the mannan II polymorphic form, in an orthorhombic unit-cell with a = 9.01 A, b = 16.73 A, c (fiber axis) = 10.40 A, and a probable space group I222. The backbone conformation of the chain is a two-fold helix stabilized by intramolecular O-3-O-5' hydrogen bonds, with the O-6 rotational position gt. The unit cell contains four chains with antiparallel packing polarity and eight water molecules which reside in crystallographic positions. Intermolecular hydrogen bonds occur exclusively between chains and water molecules, establishing a three-dimensional hydrogen-bond network in the crystal structure. The glucose residues replace mannoses in the structure in isomorphous fashion, although some disorder appears possible. A structure having alternating gg-gt O-6 rotational positions and conforming to space group P222 appears to describe the disorder regions of the crystal. The reliability of the structure analysis is indicated by the X-ray residuals R = 0.276 and R" = 0.223.

Carbohydrate Conformation↗
PubMed1992

Comparison of the NMR solution structure and the x-ray crystal structure of rat metallothionein-2.

Metallothioneins are small cysteine-rich proteins capable of binding heavy metal ions such as Zn2+ and Cd2+. They are ubiquitous tissue components in higher organisms, which tentatively have been attributed both unspecific protective functions against toxic metal ions and highly specific roles in fundamental zinc-regulated cellular processes. In this paper a detailed comparison of the NMR solution structure [Schultze, P., Wörgötter, E., Braun, W., Wagner, G., Vasák, M., Kägi, J. H. R. & Wüthrich, K. (1988) J. Mol. Biol. 203, 251-268] and a recent x-ray crystal structure [Robbins, A. H., McRee, D. E., Williamson, M., Collett, S. A., Xoung, N. H., Furey, W. F., Wang, B. C. & Stout, C. D. (1991) J. Mol. Biol. 221, 1269-1293] of rat metallothionein-2 shows that the metallothionein structures in crystals and in solution have identical molecular architectures. The structures obtained with both techniques now present a reliable basis for discussions on structure-function correlations in this class of metalloproteins.

Amino Acid Sequence↗
PubMed1987

The crystal structures of octyl alpha-D-glucopyranoside monohydrate and hemihydrate: mesogenic structures with interdigitizing alkyl chains.

The crystal structure of octyl alpha-D-glucopyranoside monohydrate, C14H28O6.H2O, is monoclinic, C2, with Z = 4, a = 17.896(2), b = 5.154(1), c = 18.303(2) A, beta = 90.30(1) degrees. The hemihydrate, C14H28O6.0.5 H2O, is also monoclinic, C2, with Z = 4, a = 15.190(5), b = 5.136(3), c = 19.944(7), beta = 92.74(3) degrees. The crystal structures were solved using SHELXTL and refined to R values of 0.037 and 0.052 for 1224 and 1231 observed structure amplitudes, respectively. The crystal structures have bilayer head-to-head molecular packing with interdigitizing alkyl chains similar to those observed in other long-chain alkyl pyranosides. The carbohydrate moieties are hydrogen-bonded in infinite chains which exclude the ring and glycosidic oxygen atoms. Both crystal structures transform to a smectic A liquid crystal at 72.3 degrees, which has a clearing point at 116.5 degrees.

Carbohydrate Conformation↗