The structure and properties of septin 3: a possible missing link in septin filament formation

2013 ◽  
Vol 450 (1) ◽  
pp. 95-105 ◽  
Author(s):  
Joci N. A. Macedo ◽  
Napoleão F. Valadares ◽  
Ivo A. Marques ◽  
Frederico M. Ferreira ◽  
Julio C. P. Damalio ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Sequence Similarity ◽  
Three Dimensional ◽  
Building Blocks ◽  
Structural Basis ◽  
Filament Assembly ◽  
Gtp Binding ◽  
Hydrolysis Of ◽  
Free Monomer ◽  
Septin Filament

The human genome codes for 13 members of a family of filament-forming GTP-binding proteins known as septins. These have been divided into four different subgroups on the basis of sequence similarity. The differences between the subgroups are believed to control their correct assembly into heterofilaments which have specific roles in membrane remodelling events. Many different combinations of the 13 proteins are theoretically possible and it is therefore important to understand the structural basis of specific filament assembly. However, three-dimensional structures are currently available for only three of the four subgroups. In the present study we describe the crystal structure of a construct of human SEPT3 which belongs to the outstanding subgroup. This construct (SEPT3-GC), which includes the GTP-binding and C-terminal domains, purifies as a nucleotide-free monomer, allowing for its characterization in terms of GTP-binding and hydrolysis. In the crystal structure, SEPT3-GC forms foreshortened filaments which employ the same NC and G interfaces observed in the heterotrimeric complex of human septins 2, 6 and 7, reinforcing the notion of ‘promiscuous’ interactions described previously. In the present study we describe these two interfaces and relate the structure to its tendency to form monomers and its efficiency in the hydrolysis of GTP. The relevance of these results is emphasized by the fact that septins from the SEPT3 subgroup may be important determinants of polymerization by occupying the terminal position in octameric units which themselves form the building blocks of at least some heterofilaments.

A new three-dimensional anionic cadmium(II) dicyanamide network

2014 ◽  
Vol 70 (11) ◽  
pp. 1054-1056 ◽  
Author(s):  
Qiang Li ◽  
Hui-Ting Wang
Keyword(s):  
Crystal Structure ◽  
Aqueous Solution ◽  
Unit Cell Volume ◽  
Three Dimensional ◽  
Building Blocks ◽  
The Other ◽  
Dimensional Structure ◽  
Cadmium Nitrate ◽  
Nitrate Tetrahydrate ◽  
Anionic Framework

A new cadmium dicyanamide complex, poly[tetramethylphosphonium [μ-chlorido-di-μ-dicyanamido-κ4N1:N5-cadmium(II)]], [(CH3)4P][Cd(NCNCN)2Cl], was synthesized by the reaction of tetramethylphosphonium chloride, cadmium nitrate tetrahydrate and sodium dicyanamide in aqueous solution. In the crystal structure, each CdIIatom is octahedrally coordinated by four terminal N atoms from four anionic dicyanamide (dca) ligands and by two chloride ligands. The dicyanamide ligands play two different roles in the building up of the structure; one role results in the formation of [Cd(dca)Cl]2building blocks, while the other links the building blocks into a three-dimensional structure. The anionic framework exhibits a solvent-accessible void of 673.8 Å3, amounting to 47.44% of the total unit-cell volume. The cavities in the network are occupied by pairs of tetramethylphosphonium cations.

Ammonium 4-chloropyridine-3-sulfonate

2006 ◽  
Vol 62 (4) ◽  
pp. o1488-o1489
Author(s):  
Tie-Han Li ◽  
Xin-Biao Mao ◽  
Qing-Bao Song ◽  
Chun-An Ma
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Three Dimensional ◽  
Dimensional Network ◽  
Hydrolysis Of

The title compound, NH4 +·C5H3ClNO3S−, was prepared by the hydrolysis of 4-chloropyridine-3-sulfonamide. In the crystal structure, a three-dimensional network is formed via N—H...O [H...O = 1.97 (3)–2.41 (2) Å] and N—H...N [H...N = 2.13 (3) Å] hydrogen bonds.

scholarly journals Biochemical and Structural Insights into Xylan Utilization by the Thermophilic Bacterium Caldanaerobius polysaccharolyticus

2012 ◽  
Vol 287 (42) ◽  
pp. 34946-34960 ◽  
Author(s):  
Yejun Han ◽  
Vinayak Agarwal ◽  
Dylan Dodd ◽  
Jason Kim ◽  
Brian Bae ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Gene Cluster ◽  
Plant Cell Wall ◽  
Hydrolytic Enzymes ◽  
Thermophilic Bacterium ◽  
Pentose Phosphate ◽  
Structural Basis ◽  
Resolution Analysis ◽  
Calorimetric Studies ◽  
Hydrolysis Of

Hemicellulose is the next most abundant plant cell wall component after cellulose. The abundance of hemicellulose such as xylan suggests that their hydrolysis and conversion to biofuels can improve the economics of bioenergy production. In an effort to understand xylan hydrolysis at high temperatures, we sequenced the genome of the thermophilic bacterium Caldanaerobius polysaccharolyticus. Analysis of the partial genome sequence revealed a gene cluster that contained both hydrolytic enzymes and also enzymes key to the pentose-phosphate pathway. The hydrolytic enzymes in the gene cluster were demonstrated to convert products from a large endoxylanase (Xyn10A) predicted to anchor to the surface of the bacterium. We further use structural and calorimetric studies to demonstrate that the end products of Xyn10A hydrolysis of xylan are recognized and bound by XBP1, a putative solute-binding protein, likely for transport into the cell. The XBP1 protein showed preference for xylo-oligosaccharides as follows: xylotriose > xylobiose > xylotetraose. To elucidate the structural basis for the oligosaccharide preference, we solved the co-crystal structure of XBP1 complexed with xylotriose to a 1.8-Å resolution. Analysis of the biochemical data in the context of the co-crystal structure reveals the molecular underpinnings of oligosaccharide length specificity.

scholarly journals Septin collar formation in budding yeast requires GTP binding and direct phosphorylation by the PAK, Cla4

2004 ◽  
Vol 164 (5) ◽  
pp. 701-715 ◽  
Author(s):  
Matthias Versele ◽  
Jeremy Thorner
Keyword(s):  
Wild Type ◽  
Gtp Hydrolysis ◽  
Filament Assembly ◽  
Gtp Binding ◽  
Type Mutant ◽  
Binding Residues ◽  
Septin Filament ◽  
Assembly Defect

Assembly at the mother–bud neck of a filamentous collar containing five septins (Cdc3, Cdc10, Cdc11, Cdc12, and Shs1) is necessary for proper morphogenesis and cytokinesis. We show that Cdc10 and Cdc12 possess GTPase activity and appropriate mutations in conserved nucleotide-binding residues abrogate GTP binding and/or hydrolysis in vitro. In vivo, mutants unable to bind GTP prevent septin collar formation, whereas mutants that block GTP hydrolysis do not. GTP binding-defective Cdc10 and Cdc12 form soluble heteromeric complexes with other septins both in yeast and in bacteria; yet, unlike wild-type, mutant complexes do not bind GTP and do not assemble into filaments in vitro. Absence of a p21-activated protein kinase (Cla4) perturbs septin collar formation. This defect is greatly exacerbated when combined with GTP binding-defective septins; conversely, the septin collar assembly defect of such mutants is suppressed efficiently by CLA4 overexpression. Cla4 interacts directly with and phosphorylates certain septins in vitro and in vivo. Thus, septin collar formation may correspond to septin filament assembly, and requires both GTP binding and Cla4-mediated phosphorylation of septins.

scholarly journals Crystal structure of diethanolbis(thiocyanato)bis(urotropine)cobalt(II) and tetraethanolbis(thiocyanato)cobalt(II)–urotropine (1/2)

2022 ◽  
Vol 78 (1) ◽  
pp. 1-0
Author(s):  
Christoph Krebs ◽  
Inke Jess ◽  
Magdalena Ceglarska ◽  
Christian Näther
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Building Blocks ◽  
Formula Unit ◽  
Wyckoff Position ◽  
Anionic Ligands ◽  
Hydrogen Bonded

The reaction of one equivalent Co(NCS)2 with four equivalents of urotropine (hexamethylenetetramine) in ethanol leads to the formation of two compounds, namely, bis(ethanol-κO)bis(thiocyanato-κN)bis(urotropine-κN)cobalt(II), [Co(NCS)2(C6H12N4)2(C2H6O)2] (1), and tetrakis(ethanol-κO)bis(thiocyanato-κN)cobalt(II)–urotropine (1/2), [Co(NCS)2(C2H6O)4]·2C6H12N4 (2). In 1, the Co cations are located on centers of inversion and are sixfold coordinated by two terminal N-bonded thiocyanate anions, two ethanol and two urotropine ligands whereas in 2 the cobalt cations occupy position Wyckoff position c and are sixfold coordinated by two anionic ligands and four ethanol ligands. Compound 2 contains two additional urotropine solvate molecules per formula unit, which are hydrogen bonded to the complexes. In both compounds, the building blocks are connected via intermolecular O—H...N (1 and 2) and C—H...S (1) hydrogen bonding to form three-dimensional networks.

Understanding the highly efficient catalysis of prokaryotic peptide deformylases by shedding light on the determinants specifying the low activity of the human counterpart

2014 ◽  
Vol 70 (2) ◽  
pp. 242-252 ◽  
Author(s):  
Sonia Fieulaine ◽  
Michel Desmadril ◽  
Thierry Meinnel ◽  
Carmela Giglione
Keyword(s):  
Sequence Similarity ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Dimensional Structure ◽  
Structural Basis ◽  
Human Counterpart ◽  
Low Activity

Peptide deformylases (PDFs), which are essential and ubiquitous enzymes involved in the removal of theN-formyl group from nascent chains, are classified into four subtypes based on the structural and sequence similarity of specific conserved domains. All PDFs share a similar three-dimensional structure, are functionally interchangeablein vivoand display similar propertiesin vitro, indicating that their molecular mechanism has been conserved during evolution. The human mitochondrial PDF is the only exception as despite its conserved fold it reveals a unique substrate-binding pocket together with an unusual kinetic behaviour. Unlike human PDF, the closely related mitochondrial PDF1As from plants have catalytic efficiencies and enzymatic parameters that are similar to those of other classes of PDFs. Here, the aim was to identify the structural basis underlying the properties of human PDF compared with all other PDFs by focusing on plant mitochondrial PDF1A. The construction of a chimaera composed of plant PDF1A with the nonrandom substitutions found in a conserved motif of its human homologue converted it into an enzyme with properties similar to the human enzyme, indicating the crucial role of these positions. The crystal structure of this human-like plant PDF revealed that substitution of two residues leads to a reduction in the volume of the ligand-binding site together with the introduction of negative charges, unravelling the origin of the weak affinity of human PDF for its substrate. In addition, the substitution of the two residues of human PDF modifies the transition state of the reaction through alteration of the network of interactions between the catalytic residues and the substrate, leading to an overall reduced reaction rate.

scholarly journals Molecular recognition at septin interfaces: the switches hold the key

2020 ◽  
Author(s):  
Higor Vinícius Dias Rosa ◽  
Diego Antonio Leonardo ◽  
Gabriel Brognara ◽  
José Brandão-Neto ◽  
Humberto D’Muniz Pereira ◽  
...  
Keyword(s):  
High Resolution ◽  
Molecular Recognition ◽  
Crystal Structures ◽  
Molecular Level ◽  
Small Gtpases ◽  
Structural Basis ◽  
List Type ◽  
Filament Assembly ◽  
New Interactions ◽  
Septin Filament

ABSTRACTThe assembly of a septin filament requires that homologous monomers must distinguish between one another in establishing appropriate interfaces with their neighbours. To understand this phenomenon at the molecular level, we present the first four crystal structures of heterodimeric septin complexes. We describe in detail the two distinct types of G-interface present within the octameric particles which must polymerize to form filaments. These are formed between SEPT2 and SEPT6 and between SEPT7 and SEPT3, and their description permits an understanding of the structural basis for the selectivity necessary for correct filament assembly. By replacing SEPT6 by SEPT8 or SEPT11, it is possible to rationalize Kinoshita’s postulate which predicts the exchangeability of septins from within a subgroup. Switches I and II, which in classical small GTPases provide a mechanism for nucleotide-dependent conformational change, have been repurposed in septins to play a fundamental role in molecular recognition. Specifically, it is switch I which holds the key to discriminating between the two different G-interfaces. Moreover, residues which are characteristic for a given subgroup play subtle, but pivotal, roles in guaranteeing that the correct interfaces are formed.HIGHLIGHTSHigh resolution structures of septin heterodimeric complexes reveal new interactionsSwitches of small GTPases are repurposed in septins to play key roles in interface contactsThe GTP present in catalytically inactive septins participates in molecular recognitionConservation of interface residues allows for subunit exchangeability from within septin subgroupsSpecific residues for each septin subgroup provide selectivity for proper filament assemblyGRAPHICAL ABSTRACT

scholarly journals Redetermination of [EuCl2(H2O)6]Cl

2014 ◽  
Vol 70 (6) ◽  
pp. i27-i27 ◽  
Author(s):  
Frank Tambornino ◽  
Philipp Bielec ◽  
Constantin Hoch
Keyword(s):  
Crystal Structure ◽  
Rotation Axis ◽  
Three Dimensional ◽  
Building Blocks ◽  
Structure Type ◽  
Chloride Anion ◽  
The Other ◽  
Water Molecules ◽  
Atomic Coordinates ◽  
The Eu

The crystal structure of the title compound, hexaaquadichloridoeuropium(III) chloride, was redetermined with modern crystallographic methods. In comparison with the previous study [Lepertet al.(1983).Aust. J. Chem.36, 477–482], it could be shown that the atomic coordinates of some O atoms had been confused and now were corrected. Moreover, it was possible to freely refine the positions of the H atoms and thus to improve the accurracy of the crystal structure. [EuCl2(H2O)6]Cl crystallizes with the GdCl3·6H2O structure-type, exhibiting discrete [EuCl2(H2O)6]+cations as the main building blocks. The main blocks are linked with isolated chloride anionsviaO—H...Cl hydrogen bonds into a three-dimensional framework. The Eu3+cation is located on a twofold rotation axis and is coordinated in the form of a Cl2O6square antiprism. One chloride anion coordinates directly to Eu3+, whereas the other chloride anion, situated on a twofold rotation axis, is hydrogen bonded to six octahedrally arranged water molecules.

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