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Z R Korszun

Publications and source records attributed to Z R Korszun.

13 recordsLinked to original sources
PubMed1998

Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of streptococcus pneumoniae bound to S-adenosylmethionine.

BACKGROUND: . Methyltransferases (Mtases) catalyze the transfer of methyl groups from S-adenosylmethionine (AdoMet) to a variety of small molecular and macromolecular substrates. These enzymes contain a characteristic alpha/beta structural fold. Four groups of DNA Mtases have been defined and representative structures have been determined for three groups. DpnM is a DNA Mtase that acts on adenine N6 in the sequence GATC; the enzyme represents group alpha DNA Mtases, for which no structures are known. RESULTS: . The structure of DpnM in complex with AdoMet was determined at 1.80 A resolution. The protein comprises a consensus Mtase fold with a helical cluster insert. DpnM binds AdoMet in a similar manner to most other Mtases and the enzyme contains a hollow that can accommodate DNA. The helical cluster supports a shelf within the hollow that may recognize the target sequence. Modeling studies indicate a potential site for binding the target adenine, everted from the DNA helix. Comparison of the DpnM structure and sequences of group alpha DNA Mtases indicates that the group is a genetically related family. Structural comparisons show DpnM to be most similar to a small-molecule Mtase and then to macromolecular Mtases, although several dehydrogenases show greater similarity than one DNA Mtase. CONCLUSIONS: . DpnM, and by extension the DpnM family or group alpha Mtases, contains the consensus fold and AdoMet-binding motifs found in most Mtases. Structural considerations suggest that macromolecular Mtases evolved from small-molecule Mtases, with different groups of DNA Mtases evolving independently. Mtases may have evolved from dehydrogenases. Comparison of these enzymes indicates that in protein evolution, the structural fold is most highly conserved, then function and lastly sequence.

Amino Acid Sequence↗
PubMed1997

A low-resolution low-temperature neutron diffraction study of myoglobin.

Diffraction data to 5 A resolution were collected on a myoglobin crystal at 80, 130, 180 and 240 K. The linear coefficient of thermal expansion for myoglobin was determined to be 45 x 10(-6) K(-1), based on the measured expansion of the unit-cell parameters. The nature of the hydration layers surrounding the protein in the crystal is described in terms of a shell solvent model, which was used to calculate the coefficient of thermal expansion in reasonable agreement with the measured value. Wilson statistics were calculated and discussed in terms of an averaged disorder model. [F(T(2)) - F(80 K) exp(-iphi)] Fourier maps were calculated where T(2) was taken as 130, 180 and 240 K, respectively. None of these difference maps showed any features above 2.0sigma in the protein region. The 130 and 240 K difference maps showed many small and widely distributed negative difference features and showed very few positive difference features above 2.5sigma in the solvent region. However, the 180 K difference map showed an extensive negative difference feature at the interface between symmetry-related molecules, occurring in the vicinity of residues 40-50 on one molecule and 76-80 on a symmetry-related molecule. These difference neutron Fourier maps indicate a concerted effect at 180 K, which is interpreted in terms of an onset of extended lattice disorder.

Journal Article↗
PubMed1996

Myoglobin solvent structure at different temperatures.

The structure of the solvent surrounding myoglobin crystals has been analyzed using neutron diffraction data, and the results indicate that the water around the protein is not disordered, but rather lies in well-defined hydration shells. We have analyzed the structure of the solvent surrounding the protein by collecting neutron diffraction data at four different temperatures, namely, 80, 130, 180, and 240K. Relative Wilson Statistics applied to low resolution data showed evidence of a phase transition in the region of 180K. A plot of the liquidity factor, Bsn, versus distance from the protein surface begins with a high plateau near the surface of the protein and drops to two minima at distances from the protein surface of about 2.35A and 3.85A. Two distinct hydration shells are observed. Both hydration shells are observed to expand as the temperature is increased.

Crystallography↗
PubMed1992

On the structure of the nickel/iron/sulfur center of the carbon monoxide dehydrogenase from Rhodospirillum rubrum: an x-ray absorption spectroscopy study.

The nickel/iron/sulfur center of the carbon monoxide dehydrogenase (carbon monoxide:(acceptor)oxidoreductase; EC 1.2.99.2) enzyme from Rhodospirillum rubrum (Rr-CODH) was studied by x-ray absorption spectroscopy at the Ni K edge. Extended x-ray absorption fine structure data show that the first Ni coordination shell consists of 2 S atoms at 2.23 A and 2-3 N/O atoms at 1.87 A. The edge structure indicates a distorted tetrahedral or five-coordinate Ni environment in both oxidized and reduced Rr-CODH. By comparing second-shell extended x-ray absorption fine structure data of Rr-CODH to that of (Et4N)3[NiFe3S4(SEt)4], a cubane-type cluster, it was clearly established that Ni in the Rr-CODH center is not involved in the core of a NiFe3S4 cubane cluster. One model consistent with the results is a mononuclear Ni2+ site, bridged by S-Cys or sulfide to one or both of the Fe4S4 clusters of the enzyme, with the remaining coordination sites occupied by additional S-Cys or N/O-liganding amino acid residues.

Absorptiometry, Photon↗
PubMed1989

Extended X-ray absorption fine structure study of Rhodospirillum rubrum and Rhodospirillum molischianum cytochromes c': relationship between heme stereochemistry and spin state.

An EXAFS study on the oxidized and reduced forms of cytochromes c' from Rhodospirillum rubrum and Rhodospirillum molischianum was performed at pH 7. The cytochromes c' have an apparent coordination number of 5 in both oxidation states. Average Fe-ligand bond lengths of 2.02 +/- 0.025 and 2.06 +/- 0.025 A are obtained in their oxidized and reduced forms, respectively. By use of suitable values for the Fe-NHis bond length and Fe out-of-plane displacement, as determined by small molecule crystallographic techniques, the Fe-Npyrrole bond lengths and the porphyrin center-to-Npyrrole distance have been estimated for cytochrome c' in both of its oxidation states. With this model, estimates of the Fe-Npyrrole bond lengths are 2.01 +/- 0.03 and 2.05 +/- 0.03 A, for the oxidized and reduced cytochromes c', respectively. The center-to-Npyrrole distance is estimated to be 1.99 +/- 0.03 A for oxidized cytochrome c' and 2.03 +/- 0.03 A for reduced cytochrome c'.

Cytochrome c Group↗
PubMed1988

The function and structure of the metal coordination sites within the glucocorticoid receptor DNA binding domain.

The glucocorticoid receptor enhances or represses transcription by binding to specific DNA sequences termed glucocorticoid response elements, or GREs. Studies of cloned glucocorticoid receptors reveal that the protein is organized as functional domains, in an arrangement that appears to be common among members of the steroid receptor family. A segment near the centre of the gene specifies DNA binding activity in vitro and contains two sequence motifs similar to 'zinc fingers' found in Xenopus transcription factor IIIA (TFIIIA). Such sequence motifs have been identified in nucleic acid binding proteins from a wide range of organisms. Steroid receptor protein fingers are proposed to bind zinc through two pairs of conserved cysteine residues. We report here that a protein of relative molecular mass 19,000 (Mr = 19 K) encompassing the DNA-binding domain of the glucocorticoid receptor that has been overexpressed in Escherichia coli and purified to homogeneity reversibly ligates two Zn(II) or Cd(II) ions. We show that metal ions are required for specific DNA binding and proper folding. Using EXAFS (extended X-ray absorption fine structure) and visible light spectroscopies, we find that each Zn atom is coordinated in a tetrahedral arrangement by four cysteines.

Amino Acid Sequence↗
PubMed1988

Simulation of launch and re-entry acceleration profiles for testing of shuttle and unmanned microgravity research payloads.

Microgravity experiments designed for execution in Get-Away Special canisters, Hitchhiker modules, and Reusable Re-entry Satellites will be subjected to launch and re-entry accelerations. Crew-dependent provisions for preventing acceleration damage to equipment or products will not be available for these payloads during flight; therefore, the effects of launch and re-entry accelerations on all aspects of such payloads must be evaluated prior to flight. A procedure was developed for conveniently simulating the launch and re-entry acceleration profiles of the Space Shuttle (3.3 and 1.7 x g maximum, respectively) and of two versions of NASA's proposed materials research Re-usable Re-entry Satellite (8 x g maximum in one case and 4 x g in the other). By using the 7 m centrifuge of the Gravitational Plant Physiology Laboratory in Philadelphia it was found possible to simulate the time dependence of these 5 different acceleration episodes for payload masses up to 59 kg. A commercial low-cost payload device, the "Materials Dispersion Apparatus" of Instrumentation Technology Associates was tested for (1) integrity of mechanical function, (2) retention of fluid in its compartments, and (3) integrity of products under simulated re-entry g-loads. In particular, the sharp rise from 1 g to maximum g-loading that occurs during re-entry in various unmanned vehicles was successfully simulated, conditions were established for reliable functioning of the MDA, and crystals of 5 proteins suspended in compartments filled with mother liquor were subjected to this acceleration load.

Acceleration↗
PubMed1987

The tertiary structure of azurin from Pseudomonas denitrificans as determined by Cu resonant diffraction using synchrotron radiation.

The structure of Pseudomonas denitrificans azurin has been solved at 3.0 A resolution by film data collection methods using synchrotron radiation. Bijvoet pairs of reflections were collected using 8.98 keV radiation where both delta f' and delta f", the real and imaginary corrections to azurin's Cu prosthetic group scattering, respectively, are large, and using 8.00 keV radiation where these corrections are smaller. The Cu atom was located by difference Patterson syntheses and used to phase the observed protein structure-factor moduli of selected reflections. An atomic model of the protein was built using a restricted data set and phases for all observed reflections to 3.0 A resolution were subsequently calculated from the initial model. The atomic model was subsequently rebuilt using all observed data. The results of this work are presented here and illustrate the utility of synchrotron radiation phasing techniques in solving the structures of metalloproteins without recourse to multiple isomorphous replacement.

Azurin↗
PubMed1986

Extended X-ray absorption fine structure studies of Zn2Fe2 hybrid hemoglobins: absence of heme bond length changes in half-ligated species.

Metal hybrid hemoglobins, in which Zn(II) replaces Fe(II), have been structurally characterized by extended X-ray absorption structure (EXAFS) studies. Since Zn and Fe have very different K absorption edge energies, the structures of the ligated (Fe) and unligated (Zn) sites could be examined independently within a single molecule that mimics an intermediate ligation state. The observed EXAFS spectra and associated structural parameters are compared among the ligand free (alpha Zn)2(beta Zn)2, half-ligated (alpha FeCO)2(beta Zn)2 and (alpha Zn)2(beta FeCO)2, and fully ligated (alpha FeCO)2(beta FeCO)2 systems.

Heme↗
PubMed1982

Extended X-ray absorption fine structure studies of cytochromes c: structural aspects of oxidation-reduction.

EXAFS fluorescence spectra were recorded for high-potential c-type cytochromes which range in oxidation-reduction potential from +145 to +365 mV. No average Fe-ligand bond length differences greater than 0.03 A were observed, for any cytochrome source of oxidation state. Least-squares analysis in combination with model calculations allowed limits to be set on the average Fe-N bond length (1.97-1.99 A) and the Fe-S bond length (2.29-2.32 A). A change of 0.05 A in either the average Fe-N or the Fe-S bond length is readily detectable with the range and quality of the data presented here. Two major conclusions are drawn from this study: In octahedrally coordinated iron porphyrin systems, Fe-N and Fe-S bond lengths are independent of oxidation-reduction potential, and they are also independent of oxidation state. A model for the regulation of oxidation-reduction potential in cytochrome c is proposed.

Animals↗
PubMed1977

Structure of cytochrome c555 of Chlorobium thiosulfatophilum: primitive low-potential cytochrome c.

Cytochrome c555 is an 86-residue type c cytochrome derived from Chlorobium thiosulfatophilum, an obligately anaerobic green sulfur bacterium which is among the most primitive of living organisms. Here is presented a preliminary structural description of the cytochrome c555 molecule based on its crystallographic structure determination at 2.7-A resolution by multiple isomorphous replacement methods. This structure is of interest not only because of its evolutionary significance but also because the cytochrome c555 molecule possesses an unusually low physiologic oxidoreduction potential (Em,7 = +145 mV) compared with related members of the cytochrome c family. Consequently, determination of its structure may permit a direct assessment of the structural factors responsible for prosthetic group redox potential regulation in type c cytochromes.

Bacteria↗