scholarly journals The crystal structure of the global anaerobic transcriptional regulator FNR explains its extremely fine-tuned monomer-dimer equilibrium

2015 ◽  
Vol 1 (11) ◽  
pp. e1501086 ◽  
Author(s):  
Anne Volbeda ◽  
Claudine Darnault ◽  
Oriane Renoux ◽  
Yvain Nicolet ◽  
Juan C. Fontecilla-Camps
Keyword(s):  
Crystal Structure ◽  
Coiled Coil ◽  
Binding Domain ◽  
Salt Bridges ◽  
Dimer Interface ◽  
Amino Terminal ◽  
Oxygen Sensitive ◽  
Aliivibrio Fischeri ◽  
Carboxyl Terminal ◽  
Terminal Cluster

The structure of the dimeric holo–fumarate and nitrate reduction regulator (FNR) from Aliivibrio fischeri has been solved at 2.65 Å resolution. FNR globally controls the transition between anaerobic and aerobic respiration in facultative anaerobes through the assembly/degradation of its oxygen-sensitive [4Fe-4S] cluster. In the absence of O2, FNR forms a dimer and specifically binds to DNA, whereas in its presence, the cluster is degraded causing FNR monomerization and DNA dissociation. We have used our crystal structure and the information previously gathered from numerous FNR variants to propose that this process is governed by extremely fine-tuned interactions, mediated by two salt bridges near the amino-terminal cluster-binding domain and an “imperfect” coiled-coil dimer interface. [4Fe-4S] to [2Fe-2S] cluster degradation propagates a conformational signal that indirectly causes monomerization by disrupting the first of these interactions and unleashing the “unzipping” of the FNR dimer in the direction of the carboxyl-terminal DNA binding domain.

scholarly journals The Ubiquitin-associated Domain of hPLIC-2 Interacts with the Proteasome

2003 ◽  
Vol 14 (9) ◽  
pp. 3868-3875 ◽  
Author(s):  
Maurits F. Kleijnen ◽  
Rodolfo M. Alarcón ◽  
Peter M. Howley
Keyword(s):  
Proteasomal Degradation ◽  
Binding Domain ◽  
Full Length ◽  
Degradation Pathways ◽  
Wild Type ◽  
Amino Terminal ◽  
Uba Domain ◽  
Carboxyl Terminal ◽  
Protein Ligases

The ubiquitin-like hPLIC proteins can associate with proteasomes, and hPLIC overexpression can specifically interfere with ubiquitin-mediated proteolysis ( Kleijnen et al., 2000 ). Because the hPLIC proteins can also interact with certain E3 ubiquitin protein ligases, they may provide a link between the ubiquitination and proteasomal degradation machineries. The amino-terminal ubiquitin-like (ubl) domain is a proteasome-binding domain. Herein, we report that there is a second proteasome-binding domain in hPLIC-2: the carboxyl-terminal ubiquitin-associated (uba) domain. Coimmunoprecipitation experiments of wild-type and mutant hPLIC proteins revealed that the ubl and uba domains each contribute independently to hPLIC-2–proteasome binding. There is specificity for the interaction of the hPLIC-2 uba domain with proteasomes, because uba domains from several other proteins failed to bind proteasomes. Furthermore, the binding of uba domains to polyubiquitinated proteins does not seem to be sufficient for the proteasome binding. Finally, the uba domain is necessary for the ability of full-length hPLIC-2 to interfere with the ubiquitin-mediated proteolysis of p53. The PLIC uba domain has been reported to bind and affect the functions of proteins such as GABAAreceptor and presenilins. It is possible that the function of these proteins may be regulated or mediated through proteasomal degradation pathways.

scholarly journals Structural Arrangement Produced by Concanavalin A Binding to Homomeric GluK2 Receptors

Membranes ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 613
Author(s):  
Cuauhtemoc U. Gonzalez ◽  
Elisa Carrillo ◽  
Vladimir Berka ◽  
Vasanthi Jayaraman
Keyword(s):  
Concanavalin A ◽  
Binding Domain ◽  
Kainate Receptors ◽  
Kainate Receptor ◽  
Agonist Binding ◽  
Con A ◽  
Dimer Interface ◽  
Amino Terminal ◽  
Receptor Modulation ◽  
Monovalent Ions

Kainate receptors are members of the ionotropic glutamate receptor family. They form cation-specific transmembrane channels upon binding glutamate that desensitize in the continued presence of agonists. Concanavalin A (Con-A), a lectin, stabilizes the active open-channel state of the kainate receptor and reduces the extent of desensitization. In this study, we used single-molecule fluorescence resonance energy transfer (smFRET) to investigate the conformational changes underlying kainate receptor modulation by Con-A. These studies showed that Con-A binding to GluK2 homomeric kainate receptors resulted in closer proximity of the subunits at the dimer–dimer interface at the amino-terminal domain as well as between the subunits at the dimer interface at the agonist-binding domain. Additionally, the modulation of receptor functions by monovalent ions, which bind to the dimer interface at the agonist-binding domain, was not observed in the presence of Con-A. Based on these results, we conclude that Con-A modulation of kainate receptor function is mediated by a shift in the conformation of the kainate receptor toward a tightly packed extracellular domain.

scholarly journals Determination of the Multimerization State of the Hepatitis Delta Virus Antigens In Vivo

2003 ◽  
Vol 77 (19) ◽  
pp. 10314-10326 ◽  
Author(s):  
Cromwell T. Cornillez-Ty ◽  
David W. Lazinski
Keyword(s):  
Crystal Structure ◽  
Hepatitis Delta Virus ◽  
Coiled Coil ◽  
Proper Function ◽  
Hepatitis Delta ◽  
Amino Terminal ◽  
Delta Antigen ◽  
Antiparallel Coiled Coil ◽  
Delta Virus

ABSTRACT Hepatitis delta virus expresses two essential proteins, the small and large delta antigens, and both are required for viral propagation. Proper function of each protein depends on the presence of a common amino-terminal multimerization domain. A crystal structure, solved using a peptide fragment that contained residues 12 to 60, depicts the formation of an octameric ring composed of antiparallel coiled-coil dimers. Because this crystal structure was solved for only a fragment of the delta antigens, it is unknown whether octamers actually form in vivo at physiological protein concentrations and in the context of either intact delta antigen. To test the relevance of the octameric structure, we developed a new method to probe coiled-coil structures in vivo. We generated a panel of mutants containing cysteine substitutions at strategic locations within the predicted monomer-monomer interface and the dimer-dimer interface. Since the small delta antigen contains no cysteine residues, treatment of cell extracts with a mild oxidizing reagent was expected to induce disulfide bond formation only when the appropriate pairs of cysteine substitution mutants were coexpressed. We indeed found that, in vivo, both the small and large delta antigens assembled as antiparallel coiled-coil dimers. Likewise, we found that both proteins could assume an octameric quaternary structure in vivo. Finally, during the course of these experiments, we found that unprenylated large delta antigen molecules could be disulfide cross-linked via the sole cysteine residue located within the carboxy terminus. Therefore, in vivo, the C terminus likely provides an additional site of protein-protein interaction for the large delta antigen.

scholarly journals Platelet thrombospondin mediates attachment and spreading of human melanoma cells.

1987 ◽  
Vol 104 (1) ◽  
pp. 131-139 ◽  
Author(s):  
D D Roberts ◽  
J A Sherwood ◽  
V Ginsburg
Keyword(s):  
Monoclonal Antibodies ◽  
Cell Attachment ◽  
Melanoma Cells ◽  
Binding Domain ◽  
Heparin Binding ◽  
Amino Terminal ◽  
Sulfated Fucan ◽  
Heparin Binding Domain ◽  
Carboxyl Terminal ◽  
Inhibition Studies

Human platelet thrombospondin adsorbed on plastic promotes attachment and spreading of human G361 melanoma cells. Attachment is rapid, and spreading is maximal by 90 min with 60-90% of the attached cells spread. In contrast, thrombospondin promotes attachment but not spreading of human C32 melanoma cells, which attach and spread only on laminin substrates. The specificity of these interactions and the regions of the thrombospondin molecule involved in attachment and spreading were examined using proteolytic fragments of thrombospondin and by inhibition studies. The sulfated fucan, fucoidan, and monoclonal antibody A2.5, which is directed against the heparin-binding domain of thrombospondin, selectively inhibit spreading but only weakly inhibit attachment. Monoclonal antibodies against some other domains of thrombospondin, however, are potent inhibitors of attachment. The amino-terminal heparin-binding domain of thrombospondin does not promote attachment. Large fragments lacking the heparin-binding domain support attachment but not spreading of G361 cells. Attachment activity is lost following removal of the 18-kD carboxyl-terminal domain. These results suggest that at least two melanoma ligands are involved in cell attachment and spreading on thrombospondin. The carboxyl-terminal region and perhaps other regions of the molecule bind to receptor(s) on the melanoma surface that promote initial attachment but not cell spreading. Interaction of the heparin-binding domain with sulfated glycoconjugates on melanoma surface proteoglycans and/or sulfated glycolipids mediates spreading. Monoclonal antibodies A2.5 and C6.7 also reverse spreading of G361 cells growing on glass culture substrates, suggesting that binding to thrombospondin mediates attachment of these melanoma cells in culture.

scholarly journals Sequence of Events Underlying the Allosteric Transition of Rod Cyclic Nucleotide–gated Channels

1999 ◽  
Vol 113 (5) ◽  
pp. 621-640 ◽  
Author(s):  
Elizabeth R. Sunderman ◽  
William N. Zagotta
Keyword(s):  
Amino Acid ◽  
Cyclic Nucleotide ◽  
Binding Domain ◽  
Terminal Region ◽  
Allosteric Transition ◽  
Amino Terminal ◽  
Sequence Of Events ◽  
Carboxyl Terminal ◽  
Purine Ring ◽  
Closing Rate

Activation of cyclic nucleotide–gated (CNG) ion channels involves a conformational change in the channel protein referred to as the allosteric transition. The amino terminal region and the carboxyl terminal cyclic nucleotide–binding domain of CNG channels have been shown to be involved in the allosteric transition, but the sequence of molecular events occurring during the allosteric transition is unknown. We recorded single-channel currents from bovine rod CNG channels in which mutations had been introduced in the binding domain at position 604 and/or the rat olfactory CNG channel amino terminal region had been substituted for the bovine rod amino terminal region. Using a hidden Markov modeling approach, we analyzed the kinetics of these channels activated by saturating concentrations of cGMP, cIMP, and cAMP. We used thermodynamic mutant cycles to reveal an interaction during the allosteric transition between the purine ring of the cyclic nucleotides and the amino acid at position 604 in the binding site. We found that mutations at position 604 in the binding domain alter both the opening and closing rate constants for the allosteric transition, indicating that the interactions between the cyclic nucleotide and this amino acid are partially formed at the time of the transition state. In contrast, the amino terminal region affects primarily the closing rate constant for the allosteric transition, suggesting that the state-dependent stabilizing interactions between amino and carboxyl terminal regions are not formed at the time of the transition state for the allosteric transition. We propose that the sequence of events that occurs during the allosteric transition involves the formation of stabilizing interactions between the purine ring of the cyclic nucleotide and the amino acid at position 604 in the binding domain followed by the formation of stabilizing interdomain interactions.

scholarly journals Independent and Interchangeable Multimerization Domains of the AbrB, Abh, and SpoVT Global Regulatory Proteins

2005 ◽  
Vol 187 (18) ◽  
pp. 6354-6362 ◽  
Author(s):  
Fude Yao ◽  
Mark A. Strauch
Keyword(s):  
Dna Binding ◽  
Binding Domain ◽  
Chimeric Proteins ◽  
Dna Binding Domain ◽  
Global Regulators ◽  
Amino Terminal ◽  
Sequence Homologies ◽  
Carboxyl Terminal ◽  
Paralogous Proteins

ABSTRACT The global regulators AbrB, Abh, and SpoVT are paralogous proteins showing their most extensive sequence homologies in the DNA-binding amino-terminal regions (about 50 residues). The carboxyl-terminal portion of AbrB has been hypothesized to be a multimerization domain with little if any role in DNA-binding recognition or specificity. To investigate the multimerization potentials of the carboxyl-terminal portions of AbrB, Abh, and SpoVT we utilized an in vivo multimerization assay system based upon fusion of the domains to the DNA binding domain of the λ cI repressor protein. The results indicate that the N and C domains of all three paralogues are independent dimerization modules and that the intact Abh and SpoVT proteins are most probably tetramers. Chimeric proteins consisting of the AbrB N-terminal DNA-binding domain fused to the C domain of either Abh or SpoVT are indistinguishable from wild-type AbrB in their ability to regulate an AbrB target promoter in vivo.

scholarly journals Control of Recombination Directionality by the Listeria Phage A118 Protein Gp44 and the Coiled-Coil Motif of Its Serine Integrase

2017 ◽  
Vol 199 (11) ◽  
Author(s):  
Sridhar Mandali ◽  
Kushol Gupta ◽  
Anthony R. Dawson ◽  
Gregory D. Van Duyne ◽  
Reid C. Johnson
Keyword(s):  
Listeria Monocytogenes ◽  
Dna Binding ◽  
Coiled Coil ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Content Type ◽  
Bacterial Chromosomes ◽  
Carboxyl Terminal ◽  
Recombination Reactions ◽  
Serine Integrase

ABSTRACT The serine integrase of phage A118 catalyzes integrative recombination between attP on the phage and a specific attB locus on the chromosome of Listeria monocytogenes, but it is unable to promote excisive recombination between the hybrid attL and attR sites found on the integrated prophage without assistance by a recombination directionality factor (RDF). We have identified and characterized the phage-encoded RDF Gp44, which activates the A118 integrase for excision and inhibits integration. Gp44 binds to the C-terminal DNA binding domain of integrase, and we have localized the primary binding site to be within the mobile coiled-coil (CC) motif but distinct from the distal tip of the CC that is required for recombination. This interaction is sufficient to inhibit integration, but a second interaction involving the N-terminal end of Gp44 is also required to activate excision. We provide evidence that these two contacts modulate the trajectory of the CC motifs as they extend out from the integrase core in a manner dependent upon the identities of the four att sites. Our results support a model whereby Gp44 shapes the Int-bound complexes to control which att sites can synapse and recombine. IMPORTANCE Serine integrases mediate directional recombination between bacteriophage and bacterial chromosomes. These highly regulated site-specific recombination reactions are integral to the life cycle of temperate phage and, in the case of Listeria monocytogenes lysogenized by A118 family phage, are an essential virulence determinant. Serine integrases are also utilized as tools for genetic engineering and synthetic biology because of their exquisite unidirectional control of the DNA exchange reaction. Here, we identify and characterize the recombination directionality factor (RDF) that activates excision and inhibits integration reactions by the phage A118 integrase. We provide evidence that the A118 RDF binds to and modulates the trajectory of the long coiled-coil motif that extends from the large carboxyl-terminal DNA binding domain and is postulated to control the early steps of recombination site synapsis.

scholarly journals Centrosomal Proteins CG-NAP and Kendrin Provide Microtubule Nucleation Sites by Anchoring γ-Tubulin Ring Complex

2002 ◽  
Vol 13 (9) ◽  
pp. 3235-3245 ◽  
Author(s):  
Mikiko Takahashi ◽  
Akiko Yamagiwa ◽  
Tamako Nishimura ◽  
Hideyuki Mukai ◽  
Yoshitaka Ono
Keyword(s):  
Spindle Pole Body ◽  
Coiled Coil ◽  
Spindle Pole ◽  
Terminal Region ◽  
Microtubule Assembly ◽  
Microtubule Nucleation ◽  
Amino Terminal ◽  
Ring Complex ◽  
Carboxyl Terminal

Microtubule assembly is initiated by the γ-tubulin ring complex (γ-TuRC). In yeast, the microtubule is nucleated from γ-TuRC anchored to the amino-terminus of the spindle pole body component Spc110p, which interacts with calmodulin (Cmd1p) at the carboxy-terminus. However, mammalian protein that anchors γ-TuRC remains to be elucidated. A giant coiled-coil protein, CG-NAP (centrosome and Golgi localized PKN-associated protein), was localized to the centrosome via the carboxyl-terminal region. This region was found to interact with calmodulin by yeast two-hybrid screening, and it shares high homology with the carboxyl-terminal region of another centrosomal coiled-coil protein, kendrin. The amino-terminal region of either CG-NAP or kendrin indirectly associated with γ-tubulin through binding with γ-tubulin complex protein 2 (GCP2) and/or GCP3. Furthermore, endogenous CG-NAP and kendrin were coimmunoprecipitated with each other and with endogenous GCP2 and γ-tubulin, suggesting that CG-NAP and kendrin form complexes and interact with γ-TuRC in vivo. These proteins were localized to the center of microtubule asters nucleated from isolated centrosomes. Pretreatment of the centrosomes by antibody to CG-NAP or kendrin moderately inhibited the microtubule nucleation; moreover, the combination of these antibodies resulted in stronger inhibition. These results imply that CG-NAP and kendrin provide sites for microtubule nucleation in the mammalian centrosome by anchoring γ-TuRC.

scholarly journals Crystal structure of the Rab-binding domain of Rab11 family-interacting protein 2

2020 ◽  
Vol 76 (8) ◽  
pp. 357-363
Author(s):  
Aoife Mairead Kearney ◽  
Amir Rafiq Khan
Keyword(s):  
Crystal Structure ◽  
Membrane Trafficking ◽  
Coiled Coil ◽  
Small Gtpases ◽  
Binding Domain ◽  
Effector Proteins ◽  
Interacting Protein ◽  
Arginine Residues ◽  
Polar Interactions ◽  
Endocytic Compartments

The small GTPases Rab11, Rab14 and Rab25 regulate membrane trafficking through the recruitment of Rab11 family-interacting proteins (FIPs) to endocytic compartments. FIPs are multi-domain effector proteins that have a highly conserved Rab-binding domain (RBD) at their C-termini. Several structures of complexes of Rab11 with RBDs have previously been determined, including those of Rab11–FIP2 and Rab11–FIP3. In addition, the structures of the Rab14–FIP1 and Rab25–FIP2 complexes have been determined. All of the RBD structures contain a central parallel coiled coil in the RBD that binds to the switch 1 and switch 2 regions of the Rab. Here, the crystal structure of the uncomplexed RBD of FIP2 is presented at 2.3 Å resolution. The structure reveals antiparallel α-helices that associate through polar interactions. These include a remarkable stack of arginine residues within a four-helix bundle in the crystal lattice.

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