scholarly journals Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq

2011 ◽  
Vol 40 (4) ◽  
pp. 1856-1867 ◽  
Author(s):  
Tatsuhiko Someya ◽  
Seiki Baba ◽  
Mai Fujimoto ◽  
Gota Kawai ◽  
Takashi Kumasaka ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Bacillus Subtilis ◽  
Rna Binding ◽  
Rna Aptamer ◽  
Binding Properties ◽  
Insight Into

scholarly journals Insight into the sporulation phosphorelay: Crystal structure of the sensor domain of Bacillus subtilis histidine kinase, KinD

2013 ◽  
Vol 22 (5) ◽  
pp. 564-576 ◽  
Author(s):  
R. Wu ◽  
M. Gu ◽  
R. Wilton ◽  
G. Babnigg ◽  
Y. Kim ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Bacillus Subtilis ◽  
Histidine Kinase ◽  
Insight Into

scholarly journals Distinct effects of Q925 mutation on intracellular and extracellular Na+ and K+ binding to the Na+, K+-ATPase

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hang N. Nielsen ◽  
Kerri Spontarelli ◽  
Rikke Holm ◽  
Jens Peter Andersen ◽  
Anja P. Einholm ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Binding Sites ◽  
Functional Role ◽  
Transmembrane Helix ◽  
Binding Properties ◽  
Ion Translocation ◽  
Extracellular Side ◽  
Insight Into

Abstract Three Na+ sites are defined in the Na+-bound crystal structure of Na+, K+-ATPase. Sites I and II overlap with two K+ sites in the K+-bound structure, whereas site III is unique and Na+ specific. A glutamine in transmembrane helix M8 (Q925) appears from the crystal structures to coordinate Na+ at site III, but does not contribute to K+ coordination at sites I and II. Here we address the functional role of Q925 in the various conformational states of Na+, K+-ATPase by examining the mutants Q925A/G/E/N/L/I/Y. We characterized these mutants both enzymatically and electrophysiologically, thereby revealing their Na+ and K+ binding properties. Remarkably, Q925 substitutions had minor effects on Na+ binding from the intracellular side of the membrane – in fact, mutations Q925A and Q925G increased the apparent Na+ affinity – but caused dramatic reductions of the binding of K+ as well as Na+ from the extracellular side of the membrane. These results provide insight into the changes taking place in the Na+-binding sites, when they are transformed from intracellular- to extracellular-facing orientation in relation to the ion translocation process, and demonstrate the interaction between sites III and I and a possible gating function of Q925 in the release of Na+ at the extracellular side.

scholarly journals Crystal Structure and RNA Binding Properties of the RNA Recognition Motif (RRM) and AlkB Domains in Human AlkB Homolog 8 (ABH8), an Enzyme Catalyzing tRNA Hypermodification

2011 ◽  
Vol 287 (3) ◽  
pp. 2130-2143 ◽  
Author(s):  
Chiara Pastore ◽  
Irini Topalidou ◽  
Farhad Forouhar ◽  
Amy C. Yan ◽  
Matthew Levy ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Rna Binding ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Binding Properties ◽  
Recognition Motif

scholarly journals Crystal structure of heme A synthase from Bacillus subtilis

2018 ◽  
Vol 115 (47) ◽  
pp. 11953-11957 ◽  
Author(s):  
Satomi Niwa ◽  
Kazuki Takeda ◽  
Masayuki Kosugi ◽  
Erika Tsutsumi ◽  
Tatsushi Mogi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Bacillus Subtilis ◽  
Transmembrane Helix ◽  
Integral Membrane Protein ◽  
Heme Binding ◽  
Terminal Oxidases ◽  
Domain Structures ◽  
Heme A Synthase ◽  
Insight Into ◽  
Heme Molecule

Heme A is an essential cofactor for respiratory terminal oxidases and vital for respiration in aerobic organisms. The final step of heme A biosynthesis is formylation of the C-8 methyl group of heme molecule by heme A synthase (HAS). HAS is a heme-containing integral membrane protein, and its structure and reaction mechanisms have remained unknown. Thus, little is known about HAS despite of its importance. Here we report the crystal structure of HAS from Bacillus subtilis at 2.2-Å resolution. The N- and C-terminal halves of HAS consist of four-helix bundles and they align in a pseudo twofold symmetry manner. Each bundle contains a pair of histidine residues and forms a heme-binding domain. The C-half domain binds a cofactor-heme molecule, while the N-half domain is vacant. Many water molecules are found in the transmembrane region and around the substrate-binding site, and some of them interact with the main chain of transmembrane helix. Comparison of these two domain structures enables us to construct a substrate-heme binding state structure. This structure implies that a completely conserved glutamate, Glu57 in B. subtilis, is the catalytic residue for the formylation reaction. These results provide valuable suggestions of the substrate-heme binding mechanism. Our results present significant insight into the heme A biosynthesis.

Crystal structure of KBSi3O8 isostructural with danburite

1993 ◽  
Vol 57 (386) ◽  
pp. 157-164 ◽  
Author(s):  
Mitsuyoshi Kimata
Keyword(s):  
Crystal Structure ◽  
Direct Method ◽  
Crystal Chemical ◽  
Chemical Formula ◽  
Crystal Chemical Formula ◽  
3 Dimensional ◽  
Tetrahedral Sites ◽  
Structural Types ◽  
Coupled Substitution ◽  
Insight Into

AbstractThe crystal structure of KBSi3O8 (orthorhombic, Pnam, with a = 8.683(1), b = 9.253(1), c = 8.272(1) Å,, V = 664.4(1) Å3, Z = 4) has been determined by the direct method applied to 3- dimensional rcflection data. The structure of a microcrystal with the dimensions 20 × 29 × 37 μm was refined to an unweightcd residual of R = 0.031 using 386 non-zero structure amplitudes. KBSi3O8 adopts a structure essentially different from recdmergneritc NaBSi3O8, with the low albite (NaAlSi3O8) structure, and isotypic with danburite CaB2Si2Os which has the same topology as paracelsian BaAl2Si2O8. The chenfical relationship between this sample and danburitc gives insight into a new coupled substitution; K+ + Si4+ = Ca2+ + B3+ in the extraframework and tetrahedral sites. The present occupancy refinement revealed partial disordering of B and Si atoms which jointly reside in two kinds of general equivalent points, T(1) and T(2) sites. Thus the expanded crystal-chemical formula can be written in the form K(B0.44Si0.56)2(B0.06Si0.94)2O8The systematic trend among crystalline compounds with the M+T3+T4+3O8 formula suggests that they exist in one of four structural types; the feldspar structures with T3+/T4+ ordered and/or disordered forms, and the paracelsian and the hollandite structures.

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