Multiple molecular recognition and catalysis. Nucleotide binding and ATP hydrolysis by a receptor molecule bearing an anion binding site, an intercalator group, and a catalytic site

1988 ◽  
pp. 596 ◽  
Author(s):  
Mir Wais Hosseini ◽  
A. John Blacker ◽  
Jean-Marie Lehn
Keyword(s):  
Molecular Recognition ◽  
Binding Site ◽  
Atp Hydrolysis ◽  
Nucleotide Binding ◽  
Catalytic Site ◽  
Anion Binding ◽  
Receptor Molecule

scholarly journals 3P157 Catalytic Site-Occupancy during ATP Hydrolysis of F_1-ATPase That Lacks Non-Catalytic Nucleotide Binding Site(Molecular motors,Poster Presentations)

2007 ◽  
Vol 47 (supplement) ◽  
pp. S242
Author(s):  
Rieko Shimo-Kon ◽  
Eiro Muneyuki ◽  
Kengo Adachi ◽  
Shou Furuike ◽  
Hiroshi Sakai ◽  
...  
Keyword(s):  
Binding Site ◽  
Molecular Motors ◽  
Atp Hydrolysis ◽  
Site Occupancy ◽  
Nucleotide Binding ◽  
Catalytic Site ◽  
Nucleotide Binding Site ◽  
Poster Presentations ◽  
Hydrolysis Of

scholarly journals Inner Workings of the UvrA·UvrB DNA Damage Sensor during Bacterial Nucleotide Excision Repair

2014 ◽  
Vol 70 (a1) ◽  
pp. C453-C453
Author(s):  
David Jeruzalmi
Keyword(s):  
Binding Site ◽  
Nucleotide Excision Repair ◽  
Atp Hydrolysis ◽  
Excision Repair ◽  
Protein Complexes ◽  
Nucleotide Binding ◽  
Dna Lesions ◽  
Early Stages ◽  
Deep Groove ◽  
Nucleotide Excision

Efficient elimination of DNA lesions by the nucleotide excision repair (NER) pathway is critical for all organisms. In bacteria, the NER pathway is implemented by the successive action of three proteins, UvrA, UvrB and UvrC via a series of large and dynamic multi-protein complexes. A large number of studies have defined three major stages associated with the early steps of the NER pathway. In stage 1, a large (300-400 kDa) complex of the UvrA and UvrB proteins (AB) scans the genome to identify lesion-containing DNA. This process requires rapid binding and release of DNA; moreover, damage must be specifically recognized, and distinguished from native DNA, despite the fact that the relevant lesions induce widely different DNA structures. Once lesion-containing DNA has been located, it is stably bound by a dimeric form of UvrA within the AB complex (Stage 2). A major reorganization then occurs in which UvrA is lost from the ensemble, and concomitantly, UvrB becomes localized at the site of damage (Stage 3). Following these early stages, additional events lead to excision of the damage on one strand, and repair of the resulting single-stranded gap. Over the past few years, we have determined three structures of UvrA and the UvrA·UvrB complex. Our first structure of isolated UvrA revealed its overall architecture, its DNA binding surface, and the arrangement of its four-nucleotide binding sites. In the structure of the complete UvrA·UvrB damage sensor, a central UvrA dimer is flanked by two UvrB molecules, all linearly arrayed along a DNA path predicted by biochemical studies. DNA is predicted to bind to UvrA in the complex within a narrow and deep groove that is compatible with native duplex DNA only. In contrast, the shape of the corresponding surface in our prior structure of UvrA is wide and shallow, and appears compatible with various types of lesion-deformed DNA. These differences point to conformation switching between the two forms as a component of the genome-scanning phase of damage sensing. We also show that the highly conserved signature domain II of UvrA, which is adjacent to the proximal nucleotide-binding site, mediates a critical nexus of contacts to UvrB and to DNA. Moreover, in the novel UvrA conformer, the disposition of this domain is altered such that association with either UvrB or DNA is precluded. Concomitantly, nucleotide is uniquely absent from the proximal binding site. Thus, the signature domain II is implicated in an ATP-hydrolysis-dependent conformational change that detaches UvrA from both UvrB and DNA after initial damage recognition. The disposition and number of UvrB molecules in the AB complex, both unanticipated, suggest that once UvrA departs, UvrB localizes to the site of damage by helicase-mediated tracking along the DNA. Together these results permit a high-resolution model for the dynamics of early stages in NER.

scholarly journals In Vivo Function of Hsp90 Is Dependent on ATP Binding and ATP Hydrolysis

1998 ◽  
Vol 143 (4) ◽  
pp. 901-910 ◽  
Author(s):  
Wolfgang M.J. Obermann ◽  
Holger Sondermann ◽  
Alicia A. Russo ◽  
Nikola P. Pavletich ◽  
F. Ulrich Hartl
Keyword(s):  
Crystal Structure ◽  
Atpase Activity ◽  
Binding Site ◽  
Atp Hydrolysis ◽  
Specific Inhibitor ◽  
Nucleotide Binding ◽  
Basic Mechanism ◽  
Atp Binding ◽  
Terminal Domain

Heat shock protein 90 (Hsp90), an abundant molecular chaperone in the eukaryotic cytosol, is involved in the folding of a set of cell regulatory proteins and in the re-folding of stress-denatured polypeptides. The basic mechanism of action of Hsp90 is not yet understood. In particular, it has been debated whether Hsp90 function is ATP dependent. A recent crystal structure of the NH2-terminal domain of yeast Hsp90 established the presence of a conserved nucleotide binding site that is identical with the binding site of geldanamycin, a specific inhibitor of Hsp90. The functional significance of nucleotide binding by Hsp90 has remained unclear. Here we present evidence for a slow but clearly detectable ATPase activity in purified Hsp90. Based on a new crystal structure of the NH2-terminal domain of human Hsp90 with bound ADP-Mg and on the structural homology of this domain with the ATPase domain of Escherichia coli DNA gyrase, the residues of Hsp90 critical in ATP binding (D93) and ATP hydrolysis (E47) were identified. The corresponding mutations were made in the yeast Hsp90 homologue, Hsp82, and tested for their ability to functionally replace wild-type Hsp82. Our results show that both ATP binding and hydrolysis are required for Hsp82 function in vivo. The mutant Hsp90 proteins tested are defective in the binding and ATP hydrolysis–dependent cycling of the co-chaperone p23, which is thought to regulate the binding and release of substrate polypeptide from Hsp90. Remarkably, the complete Hsp90 protein is required for ATPase activity and for the interaction with p23, suggesting an intricate allosteric communication between the domains of the Hsp90 dimer. Our results establish Hsp90 as an ATP-dependent chaperone.

An Attempt to Convert Noncatalytic Nucleotide Binding Site of F1-ATPase to the Catalytic Site: Hydrolysis of Tethered ATP by Mutated α Subunits in the Enzyme

1996 ◽  
Vol 220 (1) ◽  
pp. 94-97 ◽  
Author(s):  
Tadashi Matsui ◽  
Jean-Michel Jault ◽  
William S. Allison ◽  
Masasuke Yoshida
Keyword(s):  
Binding Site ◽  
Nucleotide Binding ◽  
Catalytic Site ◽  
Nucleotide Binding Site ◽  
F1 Atpase ◽  
Hydrolysis Of ◽  
Α Subunits

scholarly journals 3P147 Site occupancy and ATP hydrolysis activity of F_1-ATPase without noncatalytic nucleotide binding site

2004 ◽  
Vol 44 (supplement) ◽  
pp. S226
Author(s):  
R. Shimo-Kon ◽  
E. Muneyuki ◽  
N. Sakaki ◽  
K. Adachi ◽  
S. Furuike ◽  
...  
Keyword(s):  
Binding Site ◽  
Atp Hydrolysis ◽  
Site Occupancy ◽  
Nucleotide Binding ◽  
Nucleotide Binding Site ◽  
Hydrolysis Activity

Computational Identification of MicroRNA-targeted Nucleotide-Binding Site-Leucine-Rich Repeat Genes in Plants

BIO-PROTOCOL ◽  
2015 ◽  
Vol 5 (21) ◽  
Author(s):  
Zhu-Qing Shao ◽  
Yan-Mei Zhang ◽  
Bin Wang ◽  
Jian-Qun Chen
Keyword(s):  
Binding Site ◽  
Nucleotide Binding ◽  
Nucleotide Binding Site ◽  
Leucine Rich Repeat ◽  
Computational Identification
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