scholarly journals Crystal structure of recombinant phosphoribosylpyrophosphate synthetase 2 fromThermus thermophilusHB27 complexed with ADP and sulfate ions

2017 ◽  
Vol 73 (6) ◽  
pp. 369-375 ◽  
Author(s):  
Vladimir I. Timofeev ◽  
Ekaterina V. Sinitsyna ◽  
Maria A. Kostromina ◽  
Tatiana I. Muravieva ◽  
Dmitry A. Makarov ◽  
...  
Keyword(s):  
Active Site ◽  
Thermus Thermophilus ◽  
Three Dimensional ◽  
Class I ◽  
Dimensional Structure ◽  
Sulfate Ions ◽  
Atp Binding Site ◽  
Allosteric Sites ◽  
Catalytic Loop ◽  
Phosphoribosylpyrophosphate Synthetase

Phosphoribosylpyrophosphate synthetase (PRPPS) from the thermophilic bacterial strainThermus thermophilusHB27 catalyzes the synthesis of phosphoribosylpyrophosphate from ribose 5-phosphate and ATP, and belongs to the class I PRPPSs. The three-dimensional structure of the recombinant enzyme was solved at 2.2 Å resolution using crystals grown in microgravity from protein solution containing ATP, magnesium and sulfate ions. An ADP molecule was located in the active site of each subunit of the hexameric enzyme molecule and sulfate ions were located in both the active and allosteric sites. It was found that the catalytic loop that restricts the active-site area and is usually missing from the electron-density map of class I PRPPSs adopts different conformations in three independent subunits inT. thermophilusPRPPS. A closed conformation of the active site was found in one of subunits where the highly ordered catalytic β-hairpin delivers the Lys and Arg residues that are essential for activity directly to the ADP molecule, which occupies the ATP-binding site. A comparison of the conformations of the catalytic loop in the three independent subunits reveals a possible mode of transition from the open to the closed state of the active site during the course of the catalyzed reaction.

scholarly journals Structural Features of a Bacteroidetes-Affiliated Cellulase Linked with a Polysaccharide Utilization Locus

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
A.E. Naas ◽  
A.K. MacKenzie ◽  
B. Dalhus ◽  
V.G.H. Eijsink ◽  
P.B. Pope
Keyword(s):  
Active Site ◽  
Three Dimensional ◽  
Structural Features ◽  
Structure And Function ◽  
Dimensional Structure ◽  
Active Site Cleft ◽  
Polysaccharide Utilization Locus ◽  
And Function ◽  
Rumen Metagenome

Abstract Previous gene-centric analysis of a cow rumen metagenome revealed the first potentially cellulolytic polysaccharide utilization locus, of which the main catalytic enzyme (AC2aCel5A) was identified as a glycoside hydrolase (GH) family 5 endo-cellulase. Here we present the 1.8 Å three-dimensional structure of AC2aCel5A and characterization of its enzymatic activities. The enzyme possesses the archetypical (β/α)8-barrel found throughout the GH5 family and contains the two strictly conserved catalytic glutamates located at the C-terminal ends of β-strands 4 and 7. The enzyme is active on insoluble cellulose and acts exclusively on linear β-(1,4)-linked glucans. Co-crystallization of a catalytically inactive mutant with substrate yielded a 2.4 Å structure showing cellotriose bound in the −3 to −1 subsites. Additional electron density was observed between Trp178 and Trp254, two residues that form a hydrophobic “clamp”, potentially interacting with sugars at the +1 and +2 subsites. The enzyme’s active-site cleft was narrower compared to the closest structural relatives, which in contrast to AC2aCel5A, are also active on xylans, mannans and/or xyloglucans. Interestingly, the structure and function of this enzyme seem adapted to less-substituted substrates such as cellulose, presumably due to the insufficient space to accommodate the side-chains of branched glucans in the active-site cleft.

PREDICTION OF THE THREE-DIMENSIONAL STRUCTURE OF THE ENZYMATIC PART OF T-PA

1987 ◽  
Author(s):  
A Heckel ◽  
K M Hasselbach
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Active Site ◽  
Serine Proteases ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
Salt Bridges ◽  
Three Dimensional Structure ◽  
Insertions And Deletions

Up to now the three-dimensional structure of t-PA or parts of this enzyme is unknown. Using computer graphical methods the spatial structure of the enzymatic part of t-PA is predicted on the hypothesis, the three-dimensional backbone structure of t-PA being similar to that of other serine proteases. The t-PA model was built up in three steps:1) Alignment of the t-PA sequence with other serine proteases. Comparison of enzyme structures available from Brookhaven Protein Data Bank proved elastase as a basis for modeling.2) Exchange of amino acids of elastase differing from the t-PA sequence. The replacement of amino acids was performed such that backbone atoms overlapp completely and side chains superpose as far as possible.3) Modeling of insertions and deletions. To determine the spatial arrangement of insertions and deletions parts of related enzymes such as chymotrypsin or trypsin were used whenever possible. Otherwise additional amino acid sequences were folded to a B-turn at the surface of the proteine, where all insertions or deletions are located. Finally the side chain torsion angles of amino acids were optimised to prevent close contacts of neigh bouring atoms and to improve hydrogen bonds and salt bridges.The resulting model was used to explain binding of arginine 560 of plasminogen to the active site of t-PA. Arginine 560 interacts with Asp 189, Gly 19 3, Ser 19 5 and Ser 214 of t-PA (chymotrypsin numbering). Furthermore interaction of chromo-genic substrate S 2288 with the active site of t-PA was studied. The need for D-configuration of the hydrophobic amino acid at the N-terminus of this tripeptide derivative could be easily explained.

scholarly journals The three-dimensional structure of a class-Pi glutathione S-transferase complexed with glutathione: the active-site hydration provides insights into the reaction mechanism

1998 ◽  
Vol 333 (3) ◽  
pp. 811-816 ◽  
Author(s):  
Antonio PÁRRAGA ◽  
Isabel GARCÍA-SÁEZ ◽  
Sinead B. WALSH ◽  
Timothy J. MANTLE ◽  
Miquel COLL
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Glutathione S Transferase ◽  
X Ray ◽  
The Right

The structure of mouse liver glutathione S-transferase P1-1 complexed with its substrate glutathione (GSH) has been determined by X-ray diffraction analysis. No conformational changes in the glutathione moiety or in the protein, other than small adjustments of some side chains, are observed when compared with glutathione adduct complexes. Our structure confirms that the role of Tyr-7 is to stabilize the thiolate by hydrogen bonding and to position it in the right orientation. A comparison of the enzyme–GSH structure reported here with previously described structures reveals rearrangements in a well-defined network of water molecules in the active site. One of these water molecules (W0), identified in the unliganded enzyme (carboxymethylated at Cys-47), is displaced by the binding of GSH, and a further water molecule (W4) is displaced following the binding of the electrophilic substrate and the formation of the glutathione conjugate. The possibility that one of these water molecules participates in the proton abstraction from the glutathione thiol is discussed.

scholarly journals Acmonidesite, a new ammonium sulfate chloride from La Fossa crater, Vulcano, Aeolian Islands, Italy

2018 ◽  
Vol 83 (1) ◽  
pp. 137-142 ◽  
Author(s):  
Francesco Demartin ◽  
Carlo Castellano ◽  
Italo Campostrini
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
New Mineral ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
Chlorine Atoms ◽  
Calculated Density ◽  
Sulfate Ions ◽  
Aeolian Islands ◽  
Fossa Crater

AbstractThe new mineral acmonidesite, (NH4,K,Pb2+,Na)9Fe42+(SO4)5Cl8, was found in an active fumarole (fumarole FA, temperature ~250°C) at La Fossa crater, Vulcano, Aeolian Islands, Sicily, Italy. It occurs on a pyroclastic breccia as brown prismatic crystals up to 0.10 mm long, in association with salammoniac, alunite and adranosite. The mineral is orthorhombic, space group C2221 (no. 20) with a = 9.841(1), b = 19.448(3) c = 17.847(3) Å, V = 3415.7(9) Å3 and Z = 4. The six strongest reflections in the powder X-ray diffraction pattern are: [dobs in Å(I)(hkl)] 8.766(100)(110), 1.805(88)(390), 5.178(45)(131), 4.250(42)(221), 2.926(42)(330) and 2.684(32)(261). The empirical formula (based on 28 anions per formula unit [pfu]) is (NH4)5.77K1.42Pb0.62Na1.24Fe3.96Mn0.08S5.04O20.16Cl7.97Br0.08. The idealised formula is (NH4,K,Pb2+,Na)9Fe42+(SO4)5Cl8. The calculated density is 2.551 g cm–3. Using single-crystal diffraction data, the structure was refined to a final R(F) = 0.0363 for 4614 independent observed reflections [I > 2σ(I)]. The structure contains two independent, distorted octahedral iron sites, Fe1 and Fe2, with the iron atoms in the 2+ oxidation state, as confirmed by the interatomic distances and bond-valence calculations (2.06 and 1.94 vu, respectively). Fe1 is surrounded by two chlorine atoms and four oxygens of the sulfate ions, with the following average distances (Å): Fe1–O 2.125 and Fe1–Cl 2.472; and Fe2 is surrounded by three chlorine atoms and three oxygens of the sulfate ions, with the following average distances (Å): Fe2–O 2.110 and Fe2–Cl 2.531. Three independent sulfate anions are also present and are connected with the iron polyhedra to form a three-dimensional structure containing voids occupied by four independent ammonium ions (two of them partially replaced by K+), one Na+/Pb2+ site and one Cl– ion.

scholarly journals Structure-function studies of the myosin motor domain: importance of the 50-kDa cleft.

1996 ◽  
Vol 7 (7) ◽  
pp. 1123-1136 ◽  
Author(s):  
K M Ruppel ◽  
J A Spudich
Keyword(s):  
Active Site ◽  
Three Dimensional ◽  
Point Mutations ◽  
Random Mutagenesis ◽  
Motor Domain ◽  
Actin Binding ◽  
Dimensional Structure ◽  
Null Cell ◽  
Myosin Motor Domain ◽  
Cell Phenotypes

We used random mutagenesis to create 21 point mutations in a highly conserved region of the motor domain of Dictyostelium myosin and classified them into three distinct groups based on the ability to complement myosin null cell phenotypes: wild type, intermediate, and null. Biochemical analysis of the mutated myosins also revealed three classes of mutants that correlated well with the phenotypic classification. The mutated myosins that were not fully functional showed defects ranging from ATP nonhydrolyzers to myosins whose enzymatic and mechanical properties are uncoupled. Placement of the mutations onto the three-dimensional structure of myosin showed that the mutated region lay along the cleft that separates the active site from the actin-binding domain and that has been shown to move in response to changes at the active site. These results demonstrate that this region of myosin plays a key role in transduction of chemical energy to mechanical displacement.

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