scholarly journals Structure–Function Relationships in Yeast Tubulins

2000 ◽  
Vol 11 (5) ◽  
pp. 1887-1903 ◽  
Author(s):  
Kristy L. Richards ◽  
Kirk R. Anders ◽  
Eva Nogales ◽  
Katja Schwartz ◽  
Kenneth H. Downing ◽  
...  
Keyword(s):  
Synthetic Lethality ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Cold Sensitivity ◽  
Temperature Sensitive ◽  
Large Patch ◽  
Tubulin Dimer ◽  
The Core ◽  
Synthetically Lethal ◽  
Β Tubulin

A comprehensive set of clustered charged-to-alanine mutations was generated that systematically alter TUB1, the major α-tubulin gene of Saccharomyces cerevisiae. A variety of phenotypes were observed, including supersensitivity and resistance to the microtubule-destabilizing drug benomyl, lethality, and cold- and temperature-sensitive lethality. Many of the most benomyl-sensitivetub1 alleles were synthetically lethal in combination with tub3Δ, supporting the idea that benomyl supersensitivity is a rough measure of microtubule instability and/or insufficiency in the amount of α-tubulin. The systematictub1 mutations were placed, along with the comparable set of tub2 mutations previously described, onto a model of the yeast α–β-tubulin dimer based on the three-dimensional structure of bovine tubulin. The modeling revealed a potential site for binding of benomyl in the core of β-tubulin. Residues whose mutation causes cold sensitivity were concentrated at the lateral and longitudinal interfaces between adjacent subunits. Residues that affect binding of the microtubule-binding protein Bim1p form a large patch across the exterior-facing surface of α-tubulin in the model. Finally, the positions of the mutations suggest that proximity to the α–β interface may account for the finding of synthetic lethality of five viable tub1 alleles with the benomyl-resistant but otherwise entirely viable tub2-201allele.

scholarly journals Mutual Correction of Faulty PCNA Subunits in Temperature-Sensitive Lethal mus209 Mutants of Drosophila melanogaster

Genetics ◽  
2000 ◽  
Vol 154 (4) ◽  
pp. 1721-1733
Author(s):  
Daryl S Henderson ◽  
Ulrich K Wiegand ◽  
David G Norman ◽  
David M Glover
Keyword(s):  
Germ Line ◽  
Position Effect ◽  
Three Dimensional ◽  
Nuclear Antigen ◽  
Dimensional Structure ◽  
Female Sterility ◽  
Temperature Sensitive ◽  
Position Effect Variegation ◽  
Dna Double Strand Breaks ◽  
Mutant Genotype

Abstract Proliferating cell nuclear antigen (PCNA) functions in DNA replication as a processivity factor for polymerases δ and ε, and in multiple DNA repair processes. We describe two temperature-sensitive lethal alleles (mus209B1 and mus2092735) of the Drosophila PCNA gene that, at temperatures permissive for growth, result in hypersensitivity to DNA-damaging agents, suppression of position-effect variegation, and female sterility in which ovaries are underdeveloped and do not produce eggs. We show by mosaic analysis that the sterility of mus209B1 is partly due to a failure of germ-line cells to proliferate. Strikingly, mus209B1 and mus2092735 interact to restore partial fertility to heteroallelic females, revealing additional roles for PCNA in ovarian development, meiotic recombination, and embryogenesis. We further show that, although mus209B1 and mus2092735 homozygotes are each defective in repair of transposase-induced DNA double-strand breaks in somatic cells, this defect is substantially reversed in the heteroallelic mutant genotype. These novel mutations map to adjacent sites on the three-dimensional structure of PCNA, which was unexpected in the context of this observed interallelic complementation. These mutations, as well as four others we describe, reveal new relationships between the structure and function of PCNA.

The three-dimensional structure of interleukin-1β

1988 ◽  
Vol 16 (6) ◽  
pp. 949-953 ◽  
Author(s):  
JOHN P. PRIESTLE ◽  
HANS-PETER SCHÄR ◽  
MARKUS G. GRÜTTER
Keyword(s):  
Polypeptide Chain ◽  
Three Dimensional ◽  
Interleukin 1Β ◽  
Dimensional Structure ◽  
X Ray ◽  
Three Dimensional Structure ◽  
R Factor ◽  
The Core ◽  
Internal Sequence ◽  
Network Of Hydrogen Bonds

Summary The three-dimensional structure of human recombinant interleukin-1β has been determined at 0.24 nm resolution by X-ray crystallographic techniques. The partially refined model has a crystallographic R-factor of just under 19%. The structure is composed of 12 β-strands forming a complex network of hydrogen bonds. The core of the structure can best be described as a tetrahedron whose edges are each formed by two antiparallel β-strands. The interior of this structure is filled with hydrophobic side-chains. There is a 3-fold repeat in the folding of the polypeptide chain. Although this folding pattern suggests gene triplication, no significant internal sequence homology between topologically corresponding residues exists. The folding topology of interleukin-1β is very similar to that described by A. D. McLachlan [(1979) J. Mol. Biol. 133, 557–563] for soybean trypsin inhibitor.

scholarly journals Identification of a positive regulator of the cell cycle ubiquitin-conjugating enzyme Cdc34 (Ubc3).

1996 ◽  
Vol 16 (2) ◽  
pp. 677-684 ◽  
Author(s):  
J A Prendergast ◽  
C Ptak ◽  
D Kornitzer ◽  
C N Steussy ◽  
R Hodgins ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Amino Acid ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Temperature Sensitive ◽  
Reading Frame ◽  
Positive Regulator ◽  
Morphological Defects ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

The Cdc34 (Ubc3) ubiquitin-conjugating enzyme from Saccharomyces cerevisiae plays an essential role in the progression of cells from the G1 to S phase of the cell division cycle. Using a high-copy suppression strategy, we have identified a yeast gene (UBS1) whose elevated expression suppresses the conditional cell cycle defects associated with cdc34 mutations. The UBS1 gene encodes a 32.2-kDa protein of previously unknown function and is identical in sequence to a genomic open reading frame on chromosome II (GenBank accession number Z36034). Several lines of evidence described here indicate that Ubs1 functions as a general positive regulator of Cdc34 activity. First, overexpression of UBS1 suppresses not only the cell proliferation and morphological defects associated with cdc34 mutants but also the inability of cdc34 mutant cells to degrade the general amino acid biosynthesis transcriptional regulator, Gcn4. Second, deletion of the UBS1 gene profoundly accentuates the cell cycle defect when placed in combination with a cdc34 temperature-sensitive allele. Finally, a comparison of the Ubs1 and Cdc34 polypeptide sequences reveals two noncontiguous regions of similarity, which, when projected onto the three-dimensional structure of a ubiquitin-conjugating enzyme, define a single region situated on its surface. While cdc34 mutations corresponding to substitutions outside this region are suppressed by UBS1 overexpression, Ubs1 fails to suppress amino acid substitutions made within this region. Taken together with other findings, the allele specificity exhibited by UBS1 expression suggests that Ubs1 regulates Cdc34 by interaction or modification.

Conclusion

2021 ◽  
pp. 188-202
Author(s):  
Miikka Ruokanen
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Comprehensive Understanding ◽  
Major Work ◽  
Late Medieval ◽  
Strong Link ◽  
The Core ◽  
Effective Change ◽  
Magnum Opus ◽  
God's Grace

The present study has established a new understanding of Luther’s theological paradigm in his major work. Luther’s comprehensive understanding of the Trinitarian theology of grace, with special emphasis on Pneumatology, alongside the more obvious Christology, and together with a strong link with the theology of creation, is the fundamental thought structure of his magnum opus. The analysis has established an understanding of a three-dimensional structure of Luther’s Trinitarian doctrine of grace. Luther’s emphasis of prevenient grace and his combination of the forensic and participatory aspects of justification were his alternative to the Late Medieval doctrine of grace, which focused on the anthropological conditions for receiving God’s grace. Luther research has seen the participatory aspect (donum) as a term indicating an “effective change” in the believer; the present work shows that participation and forensic imputation (favor) belong together, enabling each other as the two complementary dimensions of the alien justice of Christ; the change, sanctification, comes as a fruit of that. Luther is a passionate defender of a radical doctrine of fully theocentric and monergistic Trinitarian grace; in order to maintain the clear principle of sola gratia, this doctrine must necessarily be Trinitarian. For Luther, this is the core of the Christian truth. The work at hand is the first piece of research revealing the centrality of Pneumatology and of the Trinitarian conception of grace, undermined in the previous research. The chapter includes a concluding encounter with Luther research. The Trinitarian doctrine of grace intensifies the ecumenical potential of Luther’s theology.

Refinement of the crystal structure of zoned philipsbornite–hidalgoite from the Tsumeb mine, Namibia, and hydrogen bonding in the D2+G3+3(T5+O4)(TO3OH)(OH)6 alunite structures

2012 ◽  
Vol 76 (4) ◽  
pp. 839-849 ◽  
Author(s):  
M. A. Cooper ◽  
F. C. Hawthorne
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Chemical Analysis ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
The Core ◽  
Core Composition ◽  
Ccd Detector ◽  
Bonding Scheme

AbstractThe crystal structure of zoned philipsbornite – hidalgoite, hexagonal (rhombohedral), Rm , Z = 3: a = 7.1142(4), c = 17.0973(9) A ˚ , V = 749.4(1) Å3, from the Tsumeb mine, Namibia, has been refined to R1 = 1.68% for 301 unique reflections collected on a Bruker D8 three-circle diffractometer equipped with a rotating-anode generator, multilayer optics and an APEX-II CCD detector. Chemical analysis by electron microprobe showed zoned crystals with a rim enriched in S and Fe relative to the core. The core composition is SO3 3.31, As2O5 30.57, Al2O3 23.05, FeO 1.44, PbO 33.94, H2Ocalc 9.58, total 101.79 wt.%, corresponding to Pb0.982+(Al2.92Fe0.132+)(AsO4)[(As0.72S0.27)O3.14(OH)0.85](OH)6; and the rim composition is SO3 8.88, As2O5 22.63, Al2O3 22.90, FeO 2.57, PbO 34.91, H2Ocalc 9.27, total 101.16 wt.%, corresponding to Pb0.992+(Al2.85Fe0.232+)(AsO4)[(As0.25S0.70)O3.30(OH)0.50](OH)6. Philipsbornite – hidalgoite has the alunite-type structure, sheets of corner-sharing octahedra, decorated on top and bottom by [(As,S)O4] and (AsO3OH) tetrahedra, that are linked into a three-dimensional structure by [12]-coordinated Pb2+ cations and hydrogen bonds. A new hydrogen-bonding scheme for the D2+G33+(T5+O4)(TO3OH)(OH)6 minerals is proposed.

scholarly journals Urkinase: Structure of Acetate Kinase, a Member of the ASKHA Superfamily of Phosphotransferases

2001 ◽  
Vol 183 (2) ◽  
pp. 680-686 ◽  
Author(s):  
Kathryn A. Buss ◽  
David R. Cooper ◽  
Cheryl Ingram-Smith ◽  
James G. Ferry ◽  
David Avram Sanders ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Acetate Kinase ◽  
Active Site Residues ◽  
Methanosarcina Thermophila ◽  
The Core ◽  
Binding Domains ◽  
The Common ◽  
Actin Superfamily

ABSTRACT Acetate kinase, an enzyme widely distributed in theBacteria and Archaea domains, catalyzes the phosphorylation of acetate. We have determined the three-dimensional structure of Methanosarcina thermophila acetate kinase bound to ADP through crystallography. As we previously predicted, acetate kinase contains a core fold that is topologically identical to that of the ADP-binding domains of glycerol kinase, hexokinase, the 70-kDa heat shock cognate (Hsc70), and actin. Numerous charged active-site residues are conserved within acetate kinases, but few are conserved within the phosphotransferase superfamily. The identity of the points of insertion of polypeptide segments into the core fold of the superfamily members indicates that the insertions existed in the common ancestor of the phosphotransferases. Another remarkable shared feature is the unusual, epsilon conformation of the residue that directly precedes a conserved glycine residue (Gly-331 in acetate kinase) that binds the α-phosphate of ADP. Structural, biochemical, and geochemical considerations indicate that an acetate kinase may be the ancestral enzyme of the ASKHA (acetate and sugar kinases/Hsc70/actin) superfamily of phosphotransferases.

GTPases: a family of molecular switches and clocks

1995 ◽  
Vol 349 (1329) ◽  
pp. 283-289 ◽  
Keyword(s):  
Single Gene ◽  
Three Dimensional ◽  
Molecular Switches ◽  
Eukaryotic Cells ◽  
Dimensional Structure ◽  
Gtpase Domain ◽  
Core Domain ◽  
The Core ◽  
Amino Acid Side Chains ◽  
Gtpase Cycle

Members of the GTPase superfamily share a core domain with a conserved three-dimensional structure and a common GTPase cycle, but perform a wide variety of regulatory tasks in eukaryotic cells. Evolution has created functional diversity from the conserved GTPase structure in two principal ways: (i) by combining in the product of a single gene the core GTPase domain attached to one or more additional folded domains; (ii) by building around a core GTPase an assembly of proteins encoded by different genes. Analysis of the patterns of conserved amino acid side chains on surfaces of Ga proteins reveals interfaces with other proteins in the G-protein signal linking device.

scholarly journals X-Ray Crystallographic and Mutational Studies of Fluoroacetate Dehalogenase from Burkholderia sp. Strain FA1

2009 ◽  
Vol 191 (8) ◽  
pp. 2630-2637 ◽  
Author(s):  
Keiji Jitsumori ◽  
Rie Omi ◽  
Tatsuo Kurihara ◽  
Atsushi Kurata ◽  
Hisaaki Mihara ◽  
...  
Keyword(s):  
Active Site ◽  
Three Dimensional ◽  
Chloride Ion ◽  
Catalytic Triad ◽  
Dimensional Structure ◽  
Active Site Residues ◽  
Density Peak ◽  
Core Domain ◽  
X Ray ◽  
The Core

ABSTRACT Fluoroacetate dehalogenase catalyzes the hydrolytic defluorination of fluoroacetate to produce glycolate. The enzyme is unique in that it catalyzes the cleavage of a carbon-fluorine bond of an aliphatic compound: the bond energy of the carbon-fluorine bond is among the highest found in natural products. The enzyme also acts on chloroacetate, although much less efficiently. We here determined the X-ray crystal structure of the enzyme from Burkholderia sp. strain FA1 as the first experimentally determined three-dimensional structure of fluoroacetate dehalogenase. The enzyme belongs to the α/β hydrolase superfamily and exists as a homodimer. Each subunit consists of core and cap domains. The catalytic triad, Asp104-His271-Asp128, of which Asp104 serves as the catalytic nucleophile, was found in the core domain at the domain interface. The active site was composed of Phe34, Asp104, Arg105, Arg108, Asp128, His271, and Phe272 of the core domain and Tyr147, His149, Trp150, and Tyr212 of the cap domain. An electron density peak corresponding to a chloride ion was found in the vicinity of the Nε1 atom of Trp150 and the Nε2 atom of His149, suggesting that these are the halide ion acceptors. Site-directed replacement of each of the active-site residues, except for Trp150, by Ala caused the total loss of the activity toward fluoroacetate and chloroacetate, whereas the replacement of Trp150 caused the loss of the activity only toward fluoroacetate. An interaction between Trp150 and the fluorine atom is probably an absolute requirement for the reduction of the activation energy for the cleavage of the carbon-fluorine bond.

scholarly journals Spectropolarimetry of Type Ibc Supernovae

2011 ◽  
Vol 7 (S279) ◽  
pp. 138-141
Author(s):  
Masaomi Tanaka ◽  
Koji S. Kawabata ◽  
Takashi Hattori ◽  
Paolo A. Mazzali ◽  
Kentaro Aoki ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Polarization Measurement ◽  
Dimensional Structure ◽  
Polarization Angle ◽  
High Quality ◽  
The Core ◽  
The Ideal

AbstractStudying a multi-dimensional structure of supernovae (SNe) gives important constraints on the mechanism of the SN explosion. Polarization measurement is one of the most powerful methods to study the explosion geometry of extragalactic SNe. Especially, Type Ib/c SNe are the ideal targets because the core of the explosion is bare. We have performed spectropolarimetric observations of Type Ib/c SNe with the Subaru telescope. We detect a rotation of the polarization angle across the line, which is seen as a loop in the Q - U plane. This indicates that axisymmetry is broken in the SN ejecta. Adding our new data to the sample of stripped-envelope SNe with high-quality spectropolarimetric data, five SNe out of six show a loop in the Q - U plane. This implies that the SN explosion commonly has a non-axisymmetric, three-dimensional geometry.

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