Faculty Opinions recommendation of Three-dimensional structural view of the central metabolic network of Thermotoga maritima.

A membrane-associated ATPase, PotA, is a component of the spermidine-preferential uptake system in prokaryotes that plays an important role in normal cell growth by regulating the cellular polyamine concentration. No three-dimensional structures of membrane-associated ATPases in polyamine-uptake systems have been determined to date. Here, the crystallization and preliminary X-ray diffraction analysis of PotA fromThermotoga maritimaare reported. Diffraction data were collected and processed to 2.7 Å resolution from both native and selenomethionine-labelled crystals. Preliminary crystallographic analysis revealed that the crystals belonged to the hexagonal space groupP3112 (orP3212), with unit-cell parametersa=b= 88.9,c= 221.2 Å, α = 90, β = 90, γ = 120°, indicating that a dimer was present in the asymmetric unit.

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Crystal structure of inactivated Thermotoga maritima invertase in complex with the trisaccharide substrate raffinose

Biochemical Journal ◽

10.1042/bj20051936 ◽

2006 ◽

Vol 395 (3) ◽

pp. 457-462 ◽

Cited By ~ 49

Author(s):

François Alberto ◽

Emmanuelle Jordi ◽

Bernard Henrissat ◽

Mirjam Czjzek

Keyword(s):

Crystal Structure ◽

Catalytic Domain ◽

Thermotoga Maritima ◽

Three Dimensional ◽

Catalytic Efficiency ◽

Dimensional Structure ◽

Glycoside Hydrolase Family ◽

Acid Base ◽

Hydrolase Family ◽

Binding Subsites

Thermotoga maritima invertase (β-fructosidase), a member of the glycoside hydrolase family GH-32, readily releases β-D-fructose from sucrose, raffinose and fructan polymers such as inulin. These carbohydrates represent major carbon and energy sources for prokaryotes and eukaryotes. The invertase cleaves β-fructopyranosidic linkages by a double-displacement mechanism, which involves a nucleophilic aspartate and a catalytic glutamic acid acting as a general acid/base. The three-dimensional structure of invertase shows a bimodular enzyme with a five bladed β-propeller catalytic domain linked to a β-sandwich of unknown function. In the present study we report the crystal structure of the inactivated invertase in interaction with the natural substrate molecule α-D-galactopyranosyl-(1,6)-α-D-glucopyranosyl-β-D-fructofuranoside (raffinose) at 1.87 Å (1 Å=0.1 nm) resolution. The structural analysis of the complex reveals the presence of three binding-subsites, which explains why T. maritima invertase exhibits a higher affinity for raffinose than sucrose, but a lower catalytic efficiency with raffinose as substrate than with sucrose.

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Glycerate 2-Kinase of Thermotoga maritima and Genomic Reconstruction of Related Metabolic Pathways

Journal of Bacteriology ◽

10.1128/jb.01469-07 ◽

2007 ◽

Vol 190 (5) ◽

pp. 1773-1782 ◽

Cited By ~ 25

Author(s):

Chen Yang ◽

Dmitry A. Rodionov ◽

Irina A. Rodionova ◽

Xiaoqing Li ◽

Andrei L. Osterman

Keyword(s):

Metabolic Pathways ◽

Thermotoga Maritima ◽

Three Dimensional ◽

Degradation Pathway ◽

Dimensional Structure ◽

Active Site Residues ◽

Hydroxypyruvate Reductase ◽

In Vitro Reconstitution

ABSTRACT Members of a novel glycerate-2-kinase (GK-II) family were tentatively identified in a broad range of species, including eukaryotes and archaea and many bacteria that lack a canonical enzyme of the GarK (GK-I) family. The recently reported three-dimensional structure of GK-II from Thermotoga maritima (TM1585; PDB code 2b8n) revealed a new fold distinct from other known kinase families. Here, we verified the enzymatic activity of TM1585, assessed its kinetic characteristics, and used directed mutagenesis to confirm the essential role of the two active-site residues Lys-47 and Arg-325. The main objective of this study was to apply comparative genomics for the reconstruction of metabolic pathways associated with GK-II in all bacteria and, in particular, in T. maritima. Comparative analyses of ∼400 bacterial genomes revealed a remarkable variety of pathways that lead to GK-II-driven utilization of glycerate via a glycolysis/gluconeogenesis route. In the case of T. maritima, a three-step serine degradation pathway was inferred based on the tentative identification of two additional enzymes, serine-pyruvate aminotransferase and hydroxypyruvate reductase (TM1400 and TM1401, respectively), that convert serine to glycerate via hydroxypyruvate. Both enzymatic activities were experimentally verified, and the entire pathway was validated by its in vitro reconstitution.

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Structure of the sodium-dependent phosphate transporter reveals insights into human solute carrier SLC20

Science Advances ◽

10.1126/sciadv.abb4024 ◽

2020 ◽

Vol 6 (32) ◽

pp. eabb4024

Author(s):

Jia-Yin Tsai ◽

Chen-Hsi Chu ◽

Min-Guan Lin ◽

Ying-Hsuan Chou ◽

Ruei-Yi Hong ◽

...

Keyword(s):

Thermotoga Maritima ◽

Three Dimensional ◽

Essential Element ◽

Phosphate Transport ◽

Phosphate Transporter ◽

Dimensional Structure ◽

Phosphate Binding ◽

Structure Based Drug Design ◽

Nucleotide Biosynthesis ◽

Sodium Dependent

Inorganic phosphate (Pi) is a fundamental and essential element for nucleotide biosynthesis, energy supply, and cellular signaling in living organisms. Human phosphate transporter (hPiT) dysfunction causes numerous diseases, but the molecular mechanism underlying transporters remains elusive. We report the structure of the sodium-dependent phosphate transporter from Thermotoga maritima (TmPiT) in complex with sodium and phosphate (TmPiT-Na/Pi) at 2.3-angstrom resolution. We reveal that one phosphate and two sodium ions (Pi-2Na) are located at the core of TmPiT and that the third sodium ion (Nafore) is located near the inner membrane boundary. We propose an elevator-like mechanism for sodium and phosphate transport by TmPiT, with the TmPiT-Na/Pi complex adopting an inward occluded conformation. We found that disease-related hPiT variants carry mutations in the corresponding sodium- and phosphate-binding residues identified in TmPiT. Our three-dimensional structure of TmPiT provides a framework for understanding PiT dysfunction and for future structure-based drug design.

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Crystal structure of levansucrase from the Gram-negative bacterium Gluconacetobacter diazotrophicus

Biochemical Journal ◽

10.1042/bj20050324 ◽

2005 ◽

Vol 390 (1) ◽

pp. 19-27 ◽

Cited By ~ 100

Author(s):

Carlos Martínez-Fleites ◽

Miguel Ortíz-Lombardía ◽

Tirso Pons ◽

Nicolas Tarbouriech ◽

Edward J. Taylor ◽

...

Keyword(s):

Thermotoga Maritima ◽

Three Dimensional ◽

Data Bank ◽

Dimensional Structure ◽

Glycoside Hydrolase Family ◽

Gluconacetobacter Diazotrophicus ◽

Negative Bacterium ◽

Sucrose Hydrolysis ◽

Gram Negative ◽

X Ray Crystallography

The endophytic Gram-negative bacterium Gluconacetobacter diazotrophicus SRT4 secretes a constitutively expressed levansucrase (LsdA, EC 2.4.1.10), which converts sucrose into fructooligosaccharides and levan. The enzyme is included in GH (glycoside hydrolase) family 68 of the sequence-based classification of glycosidases. The three-dimensional structure of LsdA has been determined by X-ray crystallography at a resolution of 2.5 Å (1 Å=0.1 nm). The structure was solved by molecular replacement using the homologous Bacillus subtilis (Bs) levansucrase (Protein Data Bank accession code 1OYG) as a search model. LsdA displays a five-bladed β-propeller architecture, where the catalytic residues that are responsible for sucrose hydrolysis are perfectly superimposable with the equivalent residues of the Bs homologue. The comparison of both structures, the mutagenesis data and the analysis of GH68 family multiple sequences alignment show a strong conservation of the sucrose hydrolytic machinery among levansucrases and also a structural equivalence of the Bs levansucrase Ca2+-binding site to the LsdA Cys339–Cys395 disulphide bridge, suggesting similar fold-stabilizing roles. Despite the strong conservation of the sucrose-recognition site observed in LsdA, Bs levansucrase and GH32 family Thermotoga maritima invertase, structural differences appear around residues involved in the transfructosylation reaction.

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Identification of the csp gene and molecular modelling of the CspA-like protein from Antarctic soil-dwelling psychrotrophic bacterium Psychrobacter sp. B6.

Acta Biochimica Polonica ◽

10.18388/abp.2009_2517 ◽

2009 ◽

Vol 56 (1) ◽

Cited By ~ 6

Author(s):

Agnieszka Kaufman-Szymczyk ◽

Arkadiusz Wojtasik ◽

Paweł Parniewski ◽

Aneta Białkowska ◽

Karolina Tkaczuk ◽

...

Keyword(s):

Escherichia Coli ◽

Cold Shock ◽

Thermotoga Maritima ◽

Protein A ◽

Three Dimensional ◽

Nmr Structure ◽

Cold Shock Protein ◽

Antarctic Soil ◽

Three Dimensional Model ◽

Sequence Identity

We cloned and sequenced the cspA-like gene from a psychrotrophic Antarctic soil-dwelling bacterial strain Psychrobacter sp. B6. The gene is 213 bp long and shows 99% and 98% sequence identity with the Psychrobacter cryohalolentis K5 gene encoding a cold-shock DNA-binding domain protein and the Psychrobacter arcticus transcriptional regulator-CspA gene, respectively. The protein encoded by the Psychrobacter sp. B6 cspA-like gene shows 100% identity with the two proteins mentioned above, and also 61% sequence identity with CspB from Bacillus subtilis and Csp from Bacillus caldolyticus, and 56% - with Escherichia coli CspA protein. A three-dimensional model of the CspA-like protein from Psychrobacter sp. B6 was generated based on three known structures of cold shock proteins: the crystal structure of the major cold shock protein from Escherichia coli (CspA), the NMR structure of the latter protein, and the NMR structure of Csp from Thermotoga maritima. The deduced structure of the CspA-like protein from Psychrobacter sp. B6 was found to be very similar to these known structures of Csp-like proteins.

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The orbit of Pluto over a long interval of time

Symposium - International Astronomical Union ◽

10.1017/s0074180900105509 ◽

1966 ◽

Vol 25 ◽

pp. 227-229 ◽

Cited By ~ 1

Author(s):

D. Brouwer

Keyword(s):

Periodic Orbit ◽

Numerical Integration ◽

Restricted Problem ◽

Three Dimensional ◽

The Third ◽

Circular Restricted Problem ◽

Resonance Relation

The paper presents a summary of the results obtained by C. J. Cohen and E. C. Hubbard, who established by numerical integration that a resonance relation exists between the orbits of Neptune and Pluto. The problem may be explored further by approximating the motion of Pluto by that of a particle with negligible mass in the three-dimensional (circular) restricted problem. The mass of Pluto and the eccentricity of Neptune's orbit are ignored in this approximation. Significant features of the problem appear to be the presence of two critical arguments and the possibility that the orbit may be related to a periodic orbit of the third kind.

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