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Kottayil I Varughese

Publications and source records attributed to Kottayil I Varughese.

14 recordsLinked to original sources
PubMed2006

The crystal structure of YycH involved in the regulation of the essential YycFG two-component system in Bacillus subtilis reveals a novel tertiary structure.

The Bacillus subtilis YycFG two-component signal transduction system is essential for cell viability, and the YycH protein is part of the regulatory circuit that controls its activity. The crystal structure of YycH was solved by two-wavelength selenium anomalous dispersion data, and was refined using 2.3 A data to an R-factor of 25.2%. The molecule is made up of three domains, and has a novel three-dimensional structure. The N-terminal domain features a calcium binding site and the central domain contains two conserved loop regions.

Amino Acid Sequence↗
PubMed2006

Interactions between the YycFG and PhoPR two-component systems in Bacillus subtilis: the PhoR kinase phosphorylates the non-cognate YycF response regulator upon phosphate limitation.

Two-component signal transduction systems (TCS) are an important mechanism by which bacteria sense and respond to their environment. Although each two-component system appears to detect and respond to a specific signal(s), it is now evident that they do not always act independently of each other. In this paper we present data indicating regulatory links between the PhoPR two-component system that participates in the cellular response to phosphate limitation, and the essential YycFG two-component system in Bacillus subtilis. We show that the PhoR sensor kinase can activate the YycF response regulator during a phosphate limitation-induced stationary phase, and that this reaction occurs in the presence of the cognate YycG sensor kinase. Phosphorylation of YycF by PhoR also occurs in vitro, albeit at a reduced level. However, the reciprocal cross-phosphorylation does not occur. A second level of interaction between PhoPR and YycFG is indicated by the fact that cells depleted for YycFG have a severely deficient PhoPR-dependent phosphate limitation response and that YycF can bind directly to the promoter of the phoPR operon. YycFG-depleted cells neither activate expression of phoA and phoPR nor repress expression of the essential tagAB and tagDEF operons upon phosphate limitation. This effect is specific to the PhoPR-dependent phosphate limitation response because PhoPR-independent phosphate limitation responses can be initiated in YycFG-depleted cells.

Alkaline Phosphatase↗
PubMed2006

The crystal structure of beryllofluoride Spo0F in complex with the phosphotransferase Spo0B represents a phosphotransfer pretransition state.

A number of regulatory circuits in biological systems function through the exchange of phosphoryl groups from one protein to another. Spo0F and Spo0B are components of a phosphorelay that control sporulation in the bacterium Bacillus subtilis through the exchange of a phosphoryl group. Using beryllofluoride as a mimic for phosphorylation, we trapped the interaction of the phosphorylated Spo0F with Spo0B in the crystal lattice. The transition state of phosphoryl transfer continues to be a highly debated issue, as to whether it is associative or dissociative in nature. The geometry of Spo0F binding to Spo0B favors an associative mechanism for phosphoryl transfer. In order to visualize the autophosphorylation of the histidine kinase, KinA, and the subsequent phosphoryl transfer to Spo0F, we generated in silico models representing these reaction steps.

Bacillus subtilis↗
PubMed2005

A computational analysis on the specificity of interactions between histidine kinases and response regulators.

Bacteria process and transmit signals simultaneously through several two-component/phosphorelay networks using closely related proteins. Therefore discrimination against mismatches and discrete recognition between protein partners is an absolute requirement for producing the correct responses. We tried to address this issue by comparing and analyzing sequences from the helix-bundle regions of histidine kinases of Bacillus subtilis. Our analysis shows how conservation and variability in the sequences give rise to selective association and unique recognition. The observed pattern suggests that the chances for cross talk between non-partner proteins are extremely low, but cross talk could take place in special cases.

Amino Acid Sequence↗
PubMed2005

Conformational changes of Spo0F along the phosphotransfer pathway.

Spo0F is a secondary messenger in the sporulation phosphorelay, and its structure has been characterized crystallographically in the apo-state, in the metal-bound state, and in an interacting state with a phosphotransferase. Additionally, the solution structure of the molecule has been characterized by nuclear magnetic resonance techniques in the unliganded state and in complex with beryllofluoride. Spo0F is a single-domain protein with a well-defined three-dimensional structure, but it is capable of adapting to specific conformations for catching and releasing the phosphoryl moiety. This commentary deals with the conformational fluctuations of the molecule as it moves from an apo-state to a metal-coordinated state, to a phosphorylated state, and then to a phosphoryl-transferring state.

Bacterial Proteins↗
PubMed2004

Metals in the sporulation phosphorelay: manganese binding by the response regulator Spo0F.

As a part of studies on the structural characterization of the components of the sporulation phosphorelay in Bacillus subtilis, the crystal structure of the manganese derivative of an intermediate signal transducer, Spo0F, has been elucidated at 2.25 A resolution. The calcium complex and the apo structures have been analyzed previously. In apo Spo0F, the active-site cation cavity is only partially formed and it only becomes completed upon metal coordination. The carbonyl of Lys56 is coordinated to the metal and interestingly the side chain of Lys56 exists in a variety of conformations in the three crystal structures of Spo0F. The affinity of the magnesium ion for Spo0F is in fact low; however, it binds Spo0F when it is in complex with Spo0B. It is proposed that the existence of a deep pocket which extends from the surface to the metal site could attract and direct the metal, thereby facilitating the metal binding of the complex.

Bacillus subtilis↗
PubMed2004

Platinum-induced space-group transformation in crystals of the platelet glycoprotein Ib alpha N-terminal domain.

The interaction between platelet glycoprotein (GP) Ib alpha and von Willebrand factor (VWF) is essential for thrombus formation, leading to the arrest of bleeding. The N-terminal domain of GP Ib alpha, which contains the binding sites for VWF and alpha-thrombin, crystallized in the tetragonal space group P4(3) with one molecule in the asymmetric unit. When the crystals were treated with platinum, the crystals changed their symmetry from tetragonal to monoclinic P2(1) with two molecules in the asymmetric unit. The structure of the monoclinic form was solved using two-wavelength platinum anomalous dispersion data. The tetragonal crystal structure was subsequently solved using molecular-replacement techniques using the monoclinic structure as the search model and was refined with 1.7 A resolution data.

Crystallography, X-Ray↗
PubMed2003

Structure of pteridine reductase (PTR1) from Leishmania tarentolae.

The protozoan parasites Leishmania utilize a pteridine-reducing enzyme, pteridine reductase (PTR1), to bypass antifolate inhibition. The crystal structure of PTR1 from L. tarentolae has been solved as a binary complex with NADPH at 2.8 A resolution. The structure was solved by molecular-replacement techniques using the recently reported L. major PTR1 structure as a search model. Comparisons of the present structure with the L. major PTR1 allowed us to identify regions of flexibility in the molecule. PTR1 is a member of the growing family of short-chain dehydrogenases (SDR) which share the characteristic Tyr(Xaa)(3)Lys motif in the vicinity of the active site. The functional enzyme is a tetramer and the crystallographic asymmetric unit contains a tetramer with 222 point-group symmetry.

Amino Acid Sequence↗
PubMed2003

Modulation of alpha-thrombin function by distinct interactions with platelet glycoprotein Ibalpha.

Thrombin bound to platelets contributes to stop bleeding and, in pathological conditions, may cause vascular thrombosis. We have determined the structure of platelet glycoprotein Ibalpha (GpIbalpha) bound to thrombin at 2.3 angstrom resolution and defined two sites in GpIbalpha that bind to exosite II and exosite I of two distinct alpha-thrombin molecules, respectively. GpIbalpha occupancy may be sequential, as the site binding to alpha-thrombin exosite I appears to be cryptic in the unoccupied receptor but exposed when a first thrombin molecule is bound through exosite II. These interactions may modulate alpha-thrombin function by mediating GpIbalpha clustering and cleavage of protease-activated receptors, which promote platelet activation, while limiting fibrinogen clotting through blockade of exosite I.

Binding Sites↗
PubMed2003

Red cell adenylate kinase deficiency: molecular study of 3 new mutations (118G>A, 190G>A, and GAC deletion) associated with hereditary nonspherocytic hemolytic anemia.

We report here 2 patients with chronic nonspherocytic hemolytic anemia (CNSHA) and severe red blood cell (RBC) adenylate kinase (AK) deficiency. One of these patients, a boy of Spanish origin, exhibited a neonatal icterus and splenomegaly and required blood transfusions until the age of 2 years. The other patient was a white, American infant born to parents who were first cousins; he also presented with neonatal icterus and anemia. In neither case was psychomotor impairment observed. The first patient was found to be a compound heterozygote for 2 different missense mutations, 118G>A(Gly40Arg) and 190G>A(Gly64Arg) (cDNA sequence first described by Matsuura et al, 1989). The second patient was homozygous for an in-frame deletion (GAC) from nucleotide (nt) 498 to 500 or nt 501 to 503 of the cDNA sequence, predicting deletion of either aspartic acid (Asp) 140 or 141. The crystal structure of porcine cytosolic AK was used as a molecular model to investigate how these mutations may affect enzyme structure and function.

Adenylate Kinase↗
PubMed2002

DNA complexed structure of the key transcription factor initiating development in sporulating bacteria.

Sporulation in Bacillus species, the ultimate bacterial adaptive response, requires the precisely coordinated expression of a complex genetic pathway, and is initiated through the accumulation of the phosphorylated form of Spo0A, a pleiotropic response regulator transcription factor. Spo0A controls the transcription of several hundred genes in all spore-forming Bacilli including genes for sporulation and toxin regulation in pathogens such as Bacillus anthracis. The crystal structure of the effector domain of Spo0A from Bacillus subtilis in complex with its DNA target was determined. In the crystal lattice, two molecules form a tandem dimer upon binding to adjacent sites on DNA. The protein:protein and protein:DNA interfaces revealed in the crystal provide a basis for interpreting the transcription activation process and for the design of drugs to counter infections by these bacteria.

Amino Acid Sequence↗
PubMed2002

Structure and function of the von Willebrand factor A1 domain.

The role of von Willebrand factor (VWF) in blocking hemorrhage is centered on its ability to act as a bridging adhesive molecule between platelets and components of the extracellular matrix or other platelets. In the course of chronic vascular diseases, moreover, the same properties of VWF may become the cause of pathological thrombus formation leading to arterial occlusion. There is convincing evidence that VWF functions involving interactions with platelets ultimately depend on binding to the membrane glycoprotein (GP) Ibalpha receptor mediated by the A1 domain. In this review, we present the current knowledge on the structural features of the VWF A1 domain that support its functions.

Amino Acid Sequence↗
PubMedDate not supplied

A single amino acid change in the binding pocket alters specificity of an anti-integrin antibody AP7.4 as revealed by its crystal structure.

Monoclonal antibody (mAb) AP7.4 is an anti-integrin antibody recombinantly expressed in Escherichia coli specific to alphavbeta3. It is known that in a variety of RGD-containing molecules, ligand specificity is regulated by structural determinants within the immediate vicinity of the RGD sequence. To better understand the role of the RGD sequence in integrin specificity, we report here the three-dimensional structure of Fab of mAb AP7.4 to a resolution of 2.25 A. The crystals belong to a triclinic space group P1 and the volume of the unit cell is consistent with the presence of two Fab molecules in it. The RGD sequence is located at the tip of a flexible loop in the complementary determining region (CDR-3) of the heavy chain. It has been shown that specific recognition of RGD ligands by their receptors is influenced mainly by the conformation of the tripeptide RGD and the amino acid residues flanking it on either side. Hence, the flexibility of the RGD-carrying loop observed in the crystal structure may stem from the fact that the antibody molecule mimics the function of these cell adhesion molecules.

Amino Acid Sequence↗