scholarly journals Structural basis for cAMP-mediated allosteric control of the catabolite activator protein

2009 ◽  
Vol 106 (17) ◽  
pp. 6927-6932 ◽  
Author(s):  
Nataliya Popovych ◽  
Shiou-Ru Tzeng ◽  
Marco Tonelli ◽  
Richard H. Ebright ◽  
Charalampos G. Kalodimos
Keyword(s):  
Dna Binding ◽  
Structural Changes ◽  
Coiled Coil ◽  
Binding Pocket ◽  
Receptor Protein ◽  
Structural Basis ◽  
Allosteric Transition ◽  
Allosteric Control ◽  
Catabolite Activator Protein ◽  
Activator Protein

The cAMP-mediated allosteric transition in the catabolite activator protein (CAP; also known as the cAMP receptor protein, CRP) is a textbook example of modulation of DNA-binding activity by small-molecule binding. Here we report the structure of CAP in the absence of cAMP, which, together with structures of CAP in the presence of cAMP, defines atomic details of the cAMP-mediated allosteric transition. The structural changes, and their relationship to cAMP binding and DNA binding, are remarkably clear and simple. Binding of cAMP results in a coil-to-helix transition that extends the coiled-coil dimerization interface of CAP by 3 turns of helix and concomitantly causes rotation, by ≈60°, and translation, by ≈7 Å, of the DNA-binding domains (DBDs) of CAP, positioning the recognition helices in the DBDs in the correct orientation to interact with DNA. The allosteric transition is stabilized further by expulsion of an aromatic residue from the cAMP-binding pocket upon cAMP binding. The results define the structural mechanisms that underlie allosteric control of this prototypic transcriptional regulatory factor and provide an illustrative example of how effector-mediated structural changes can control the activity of regulatory proteins.

scholarly journals Catabolite activator protein: DNA binding and transcription activation

2004 ◽  
Vol 14 (1) ◽  
pp. 10-20 ◽  
Author(s):  
Catherine L Lawson ◽  
David Swigon ◽  
Katsuhiko S Murakami ◽  
Seth A Darst ◽  
Helen M Berman ◽  
...  
Keyword(s):  
Dna Binding ◽  
Transcription Activation ◽  
Catabolite Activator Protein ◽  
Activator Protein

scholarly journals The Molecular Basis of Specific DNA Binding by the BRG1 AT-hook and Bromodomain

2019 ◽  
Author(s):  
Julio C. Sanchez ◽  
Liyang Zhang ◽  
Stefania Evoli ◽  
Nicholas J. Schnicker ◽  
Maria Nunez-Hernandez ◽  
...  
Keyword(s):  
Dna Binding ◽  
Chromatin Remodeling ◽  
Critical Role ◽  
Binding Pocket ◽  
Structural Basis ◽  
Atpase Subunit ◽  
Baf Complex ◽  
Chromatin Remodeling Complex ◽  
Cancer Mutations ◽  
Dna Specificity

AbstractThe ATP-dependent BAF chromatin remodeling complex plays a critical role in gene regulation by modulating chromatin architecture, and is frequently mutated in cancer. Indeed, subunits of the BAF complex are found to be mutated in >20% of human tumors. The mechanism by which BAF properly navigates chromatin is not fully understood, but is thought to involve a multivalent network of histone and DNA contacts. We previously identified a composite domain in the BRG1 ATPase subunit that is capable of associating with both histones and DNA in a multivalent manner. Mapping the DNA binding pocket revealed that it contains several cancer mutations. Here, we utilize SELEX-seq to identify the DNA specificity of this composite domain and NMR spectroscopy and molecular modelling to determine the structural basis of DNA binding. Finally, we demonstrate that cancer mutations in this domain alter the mode of DNA association.

scholarly journals Phototaxis and Impaired Motility in Adenylyl Cyclase and Cyclase Receptor Protein Mutants of Synechocystis sp. Strain PCC 6803

2006 ◽  
Vol 188 (20) ◽  
pp. 7306-7310 ◽  
Author(s):  
Devaki Bhaya ◽  
Kenlee Nakasugi ◽  
Fariba Fazeli ◽  
Matthew S. Burriesci
Keyword(s):  
Cyclic Amp ◽  
Adenylyl Cyclase ◽  
Receptor Protein ◽  
Wild Type ◽  
Catabolite Activator Protein ◽  
Activator Protein ◽  
Protein Mutants ◽  
Synechocystis Sp ◽  
Pcc 6803

ABSTRACT We have carefully characterized and reexamined the motility and phototactic responses of Synechocystis sp. adenylyl cyclase (Cya1) and catabolite activator protein (SYCRP1) mutants to different light regimens, glucose, 3-(3,4-dichlorophenyl)-1,1-dimethylurea, and cyclic AMP. We find that contrary to earlier reports, cya1 and sycrp1 mutants are motile and phototactic but are impaired in one particular phase of phototaxis in comparison with wild-type Synechocystis sp.

scholarly journals Conformational dynamics of androgen receptors bound to agonists and antagonists

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hyo Jin Gim ◽  
Jiyong Park ◽  
Michael E. Jung ◽  
K. N. Houk
Keyword(s):  
Conformational Changes ◽  
Structural Changes ◽  
Structural Integrity ◽  
Structural Information ◽  
Close Contact ◽  
Conformational Dynamics ◽  
Principal Component ◽  
Binding Pocket ◽  
Structural Basis ◽  
Accelerated Molecular Dynamics

AbstractThe androgen receptor (AR) is critical in the progression of prostate cancer (PCa). Small molecule antagonists that bind to the ligand binding domain (LBD) of the AR have been successful in treating PCa. However, the structural basis by which the AR antagonists manifest their therapeutic efficacy remains unclear, due to the lack of detailed structural information of the AR bound to the antagonists. We have performed accelerated molecular dynamics (aMD) simulations of LBDs bound to a set of ligands including a natural substrate (dihydrotestosterone), an agonist (RU59063) and three antagonists (bicalutamide, enzalutamide and apalutamide) as well as in the absence of ligand (apo). We show that the binding of AR antagonists at the substrate binding pocket alter the dynamic fluctuations of H12, thereby disrupting the structural integrity of the agonistic conformation of AR. Two antagonists, enzalutamide and apalutamide, induce considerable structural changes to the agonist conformation of LBD, when bound close to H12 of AR LBD. When the antagonists bind to the pocket with different orientations having close contact with H11, no significant conformational changes were observed, suggesting the AR remains in the functionally activated (agonistic) state. The simulations on a drug resistance mutant F876L bound to enzalutamide demonstrated that the mutation stabilizes the agonistic conformation of AR LBD, which compromises the efficacy of the antagonists. Principal component analysis (PCA) of the structural fluctuations shows that the binding of enzalutamide and apalutamide induce conformational fluctuations in the AR, which are markedly different from those caused by the agonist as well as another antagonist, bicalutamide. These fluctuations could only be observed with the use of aMD.

scholarly journals Structural basis for two-way communication between dynein and microtubules

2019 ◽  
Author(s):  
Noritaka Nishida ◽  
Yuta Komori ◽  
Osamu Takarada ◽  
Atsushi Watanabe ◽  
Satoko Tamura ◽  
...  
Keyword(s):  
Disulfide Bond ◽  
Conformational Changes ◽  
Structural Changes ◽  
Coiled Coil ◽  
Cytoplasmic Dynein ◽  
Structural Basis ◽  
Atpase Domain ◽  
Directional Bias ◽  
Α Helix ◽  
Half Turn

AbstractThe movements of cytoplasmic dynein on microtubule (MT) tracks is achieved by two-way communication between the microtubule-binding domain (MTBD) and the ATPase domain of dynein via an a-helical coiled-coil stalk, but the structural basis of this communication remains elusive. Here, we regulated MTBD either in high-affinity or low-affinity states by introducing a disulfide bond between the coiled-coils and analyzed the resulting structures by NMRand cryo-EM. In the MT-unbound state, the affinity changes of MTBD were achieved by sliding of the N-terminal α-helix by one half-turn, which suggests that structural changes propagate from the ATPase-domain to MTBD. In addition, cryo-EM analysis showed that MT binding induced further sliding of the N-terminal α-helix even without the disulfide bond, which suggests the MT-induced conformational changes propagate toward the ATPase domain. Based on differences in the MT-binding surface between the high- and low-affinity states, we propose a potential mechanism for the directional bias of dynein movement on MT tracks.

scholarly journals Structural basis of mechano-chemical coupling by the mitotic kinesin KIF14

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Matthieu P.M.H. Benoit ◽  
Ana B. Asenjo ◽  
Mohammadjavad Paydar ◽  
Sabin Dhakal ◽  
Benjamin H. Kwok ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Structural Changes ◽  
Atp Hydrolysis ◽  
Nucleotide Binding ◽  
Binding Pocket ◽  
Bound State ◽  
Structural Basis ◽  
Coupling Mechanism ◽  
Developmental Defects ◽  
Microtubule Binding

AbstractKIF14 is a mitotic kinesin whose malfunction is associated with cerebral and renal developmental defects and several cancers. Like other kinesins, KIF14 couples ATP hydrolysis and microtubule binding to the generation of mechanical work, but the coupling mechanism between these processes is still not fully clear. Here we report 20 high-resolution (2.7–3.9 Å) cryo-electron microscopy KIF14-microtubule structures with complementary functional assays. Analysis procedures were implemented to separate coexisting conformations of microtubule-bound monomeric and dimeric KIF14 constructs. The data provide a comprehensive view of the microtubule and nucleotide induced KIF14 conformational changes. It shows that: 1) microtubule binding, the nucleotide species, and the neck-linker domain govern the transition between three major conformations of the motor domain; 2) an undocked neck-linker prevents the nucleotide-binding pocket to fully close and dampens ATP hydrolysis; 3) 13 neck-linker residues are required to assume a stable docked conformation; 4) the neck-linker position controls the hydrolysis rather than the nucleotide binding step; 5) the two motor domains of KIF14 dimers adopt distinct conformations when bound to the microtubule; and 6) the formation of the two-heads-bound-state introduces structural changes in both motor domains of KIF14 dimers. These observations provide the structural basis for a coordinated chemo-mechanical kinesin translocation model.

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