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D Suck

Publications and source records attributed to D Suck.

At least 55 records · Page 3Linked to original sources
PubMed1985

Crystallization of cytoplasmic actin in complex with deoxyribonuclease I.

Crystals of cytoplasmic (porcine liver) actin in complex with deoxyribonuclease I (DNAase I) were prepared for structural determination by X-ray-diffraction analysis. The crystallization of porcine liver actin-DNAase I complex is preceded by a brief treatment with immobilized trypsin, whereby a C-terminal tri- or di-peptide including cysteine-374 is removed from the actin without any noticeable degradation of both proteins as judged by sodium dodecyl-sulphate/polyacrylamide-gel electrophoresis. Analysis of the crystals obtained does not reveal any differences in the three-dimensional structure of porcine liver actin from its skeletal compartment at up to 0.6 nm resolution. However, in contrast with crystalline skeletal-muscle actin-DNAase I complex, heavy-atom substitution of crystals of porcine liver actin-DNAase I complex could not be achieved with methyl mercuriacetate. Evidence is presented that, in porcine liver actin, the N-terminal cysteine residue is not located at position no. 10, as in skeletal- and smooth-muscle actin, but most probably at position no. 17. Thus, because this site is covered by DNAase I, the cysteine becomes inaccessible to titration with 5,5'-dithiobis-(2-nitrobenzoic acid) after complex-formation with DNAase I.

Actins↗
PubMed1985

Three-dimensional structure of the complex of actin and DNase I at 4.5 A resolution.

The shape of an actin subunit has been derived from an improved 6 A map of the complex of rabbit skeletal muscle actin and bovine pancreatic DNase I obtained by X-ray crystallographic methods. The three-dimensional structure of DNase I determined independently at 2.5 A resolution was compared with the DNase I electron density in the actin:DNase map. The two structures are very similar at 6 A resolution thus leading to an unambiguous identification of actin as well as DNase I electron density. Furthermore the correct hand of the actin structure is determined from the DNase I atomic structure. The resolution of the actin structure was extended to 4.5 A by using a single heavy-atom derivative and the knowledge of the atomic coordinates of DNase I. The dimensions of an actin subunit are 67 A X 40 A X 37 A. It consists of a small and a large domain, the small domain containing the N terminus. Actin is an alpha,beta-protein with a beta-pleated sheet in each domain. These sheets are surrounded by several alpha-helices, comprising at least 40% of the structure. The phosphate peak of the adenine nucleotide is located between the two domains. The complex of actin and DNase I as found in solution (i.e., the actin:DNase I contacts which do not depend on crystal packing) was deduced from a comparison of monoclinic with orthorhombic crystals. Residues 44-46, 51, 52, 60-62 of DNase I are close to a loop region in the small domain of actin. At a distance of approximately 15 A there is a second contact in the large domain in which Glu13 of DNase I is involved. A possible binding region for myosin is discussed.

Actins↗
PubMed1984

Three-dimensional structure of fungal proteinase K reveals similarity to bacterial subtilisin.

The three-dimensional structure of the fungal serine protease proteinase K has been determined at 3.3 A resolution by single crystal X-ray diffraction analysis. The enzyme crystallizes in the tetragonal space group P4(3)2(1)2 with cell constants a = b = 68.3 A, c = 108.5 A. The asymmetric unit consists of one monomer of 27 000 daltons mol. wt., approximately 50% higher than the so far assumed value of 18 500 daltons. The main chain fold of proteinase K shows a high degree of tertiary homology with the corresponding bacterial subtilisin BPN'. Proteinase K is the second enzyme in this family of serine proteases to be studied by X-ray diffraction, thus confirming the existence of two unrelated families of serine proteases in pro-and eukaryotes.

Bacteria↗
PubMed1984

Three-dimensional structure of bovine pancreatic DNase I at 2.5 A resolution.

The three-dimensional structure of bovine pancreatic deoxyribonuclease I (DNase I) has been determined at 2.5 A resolution by X-ray diffraction from single crystals. An atomic model was fitted into the electron density using a graphics display system. DNase I is an alpha, beta-protein with two 6-stranded beta-pleated sheets packed against each other forming the core of a 'sandwich'-type structure. The two predominantly anti-parallel beta-sheets are flanked by three longer alpha-helices and extensive loop regions. The carbohydrate side chain attached to Asn 18 is protruding by approximately 15 A from the otherwise compact molecule of approximate dimensions 45 A X 40 A. The binding site of CA2+-deoxythymidine-3',5'-biphosphate (Ca-pdTp) has been determined by difference Fourier techniques confirming biochemical results that the active centre is close to His 131. Ca-pdTp binds at the surface of the enzyme between the two beta-pleated sheets and seems to interact with several charged amino acid side chains. Active site geometry and folding pattern of DNase I are quite different from staphylococcal nuclease, the only other Ca2+-dependent deoxyribonuclease whose structure is known at high resolution. The electron density map indicates that two Ca2+ ions are bound to the enzyme under crystallization conditions.

Animals↗
PubMed1981

Three-dimensional structure of the complex of skeletal muscle actin and bovine pancreatic DNAse I at 6-A resolution.

The structure of rabbit skeletal muscle actin complexed with bovine pancreatic DNase I has been determined by x-ray crystallographic methods at 6-A resolution. The analysis was based on a new orthorhombic crystal form, space group P212121, with one complex in the asymmetric unit. Six isomorphous heavy-atom derivatives yielding an overall figure of merit of 0.72 have been used to calculate the electron-density map. Molecular models for actin and DNase I derived from this map have dimensions 67 X 40 X 37 A and 50 X 50 X 40 A, respectively. The actin molecule is elongated and consists of a larger and a smaller domain, each containing density regions resembling a central beta-pleated sheet surrounded by alpha-helices. The highest electron-density peak is found in the cleft between the two domains, perhaps indicating the bound ATP. Observed crystal contacts between actin molecules and a model for the F-actin filament are discussed. Two high-affinity Ca2+-binding sites which also bind Ba2+ have been located at the surface of the DNase I molecule.

Actins↗