Conformational changes and stabilization induced by phosphate binding to 5′-methylthioadenosine phosphorylase from the thermophilic archaeon Sulfolobus solfataricus

Extremophiles ◽  
2001 ◽  
Vol 5 (5) ◽  
pp. 295-302 ◽  
Author(s):  
Giovanna Cacciapuoti ◽  
Luigi Servillo ◽  
Maria Moretti ◽  
Marina Porcelli
Keyword(s):  
Conformational Changes ◽  
Sulfolobus Solfataricus ◽  
Phosphate Binding ◽  
Methylthioadenosine Phosphorylase ◽  
Thermophilic Archaeon

Orthorhombic lysozyme crystallization at acidic pH values driven by phosphate binding

2018 ◽  
Vol 74 (5) ◽  
pp. 480-489 ◽  
Author(s):  
Marina Plaza-Garrido ◽  
M. Carmen Salinas-Garcia ◽  
Ana Camara-Artigas
Keyword(s):  
Conformational Changes ◽  
Protein Function ◽  
Protein Crystallization ◽  
Amyloid Formation ◽  
Acidic Ph ◽  
Phosphate Binding ◽  
Cell Parameters ◽  
Ph Values ◽  
Phosphate Ion ◽  
Α Helix

The structure of orthorhombic lysozyme has been obtained at 298 K and pH 4.5 using sodium chloride as the precipitant and in the presence of sodium phosphate at a concentration as low as 5 mM. Crystals belonging to space groupP212121(unit-cell parametersa= 30,b= 56,c= 73 Å, α = β = γ = 90.00°) diffracted to a resolution higher than 1 Å, and the high quality of these crystals permitted the identification of a phosphate ion bound to Arg14 and His15. The binding of this ion produces long-range conformational changes affecting the loop containing Ser60–Asn74. The negatively charged phosphate ion shields the electrostatic repulsion of the positively charged arginine and histidine residues, resulting in higher stability of the phosphate-bound lysozyme. Additionally, a low-humidity orthorhombic variant was obtained at pH 4.5, and comparison with those previously obtained at pH 6.5 and 9.5 shows a 1.5 Å displacement of the fifth α-helix towards the active-site cavity, which might be relevant to protein function. Since lysozyme is broadly used as a model protein in studies related to protein crystallization and amyloid formation, these results indicate that the interaction of some anions must be considered when analysing experiments performed at acidic pH values.

A thioredoxin from the extreme thermophilic Archaeon Sulfolobus solfataricus

1994 ◽  
Vol 26 (3) ◽  
pp. 375-380 ◽  
Author(s):  
Annamaria Guagliardi ◽  
Valentina Nobile ◽  
Simonetta Bartolucci ◽  
Mose' Rossi
Keyword(s):  
Sulfolobus Solfataricus ◽  
Thermophilic Archaeon

scholarly journals Allosteric interactions of glycogen phosphorylase b. A crystallographic study of glucose 6-phosphate and inorganic phosphate binding to di-imidate-cross-linked phosphorylase b

1984 ◽  
Vol 218 (1) ◽  
pp. 45-60 ◽  
Author(s):  
A Lorek ◽  
K S Wilson ◽  
M S P Sansom ◽  
D I Stuart ◽  
E A Stura ◽  
...  
Keyword(s):  
Binding Site ◽  
Conformational Changes ◽  
Inorganic Phosphate ◽  
Glycogen Phosphorylase ◽  
Phosphate Binding ◽  
Binding Studies ◽  
Structural Explanation ◽  
Alpha Helices ◽  
Allosteric Effector ◽  
Glycogen Phosphorylase B

The binding to glycogen phosphorylase b of glucose 6-phosphate and inorganic phosphate (respectively allosteric inhibitor and substrate/activator of the enzyme) were studied in the crystal at 0.3 nm (3A) resolution. Glucose 6-phosphate binds in the alpha-configuration at a site that is close to the AMP allosteric effector site at the subunit-subunit interface and promotes several conformational changes. The phosphate-binding site of the enzyme for glucose 6-phosphate involves contacts to two cationic residues, Arg-309 and Lys-247. This site is also occupied in the inorganic-phosphate-binding studies and is therefore identified as a high-affinity phosphate-binding site. It is distinct from the weaker phosphate-binding site of the enzyme for AMP, which is 0.27 nm (2.7A) away. The glucose moiety of glucose 6-phosphate and the adenosine moiety of AMP do not overlap. The results provide a structural explanation for the kinetic observations that glucose 6-phosphate inhibition of AMP activation of phosphorylase b is partially competitive and highly co-operative. The results suggest that the transmission of allosteric conformational changes involves an increase in affinity at phosphate-binding sites and relative movements of alpha-helices. In order to study glucose 6-phosphate and phosphate binding it was necessary to cross-link the crystals. The use of dimethyl malondi-imidate as a new cross-linking reagent in protein crystallography is discussed.

The thermophilic archaeon Sulfolobus solfataricus is able to grow on phenol

2005 ◽  
Vol 156 (5-6) ◽  
pp. 677-689 ◽  
Author(s):  
Viviana Izzo ◽  
Eugenio Notomista ◽  
Alessandra Picardi ◽  
Francesca Pennacchio ◽  
Alberto Di Donato
Keyword(s):  
Sulfolobus Solfataricus ◽  
Thermophilic Archaeon

Structures of the deoxy and CO forms of haemoglobin from Dasyatis akajei, a cartilaginous fish

1999 ◽  
Vol 55 (7) ◽  
pp. 1291-1300 ◽  
Author(s):  
Khoon Tee Chong ◽  
Gentaro Miyazaki ◽  
Hideki Morimoto ◽  
Yutaka Oda ◽  
Sam-Yong Park
Keyword(s):  
Conformational Changes ◽  
Main Chain ◽  
Quaternary Structure ◽  
Three Dimensional ◽  
Oxygen Affinity ◽  
Organic Phosphate ◽  
Phosphate Binding ◽  
Phosphate Effect ◽  
Structural Differences ◽  
Dasyatis Akajei

The three-dimensional structures of the deoxy- and carbonmonoxyhaemoglobin (Hb) from Dasyatis akajei, a stingray, have been determined at 1.6 and 1.9 Å resolution, respectively. This is one of the most distantly related vertebrate Hbs to human HbA. Both structures resemble the respective forms of HbA, indicating that the α2β2-type tetramer and the mode of the quaternary structure change are common to Hbs of jawed vertebrates. Larger deviations between D. akajei Hb and human HbA are observed in various parts of the molecule, even in the E and F helices. Significant mutations and/or conformational changes are also observed around the haems, in the C-terminal region of the β subunit, in the α1β2 interface and in the organic phosphate-binding site of HbA. Despite these structural differences, the oxygen affinity, haem–haem interaction, Bohr effect and organic phosphate effect of D. akajei Hb are all only moderately reduced. Compared with human HbA, the overall r.m.s. deviation of main-chain atoms in the helical regions of bony fish Hbs is smaller than that of D. akajei Hb.

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