Structures of active conformations of Gi alpha 1 and the mechanism of GTP hydrolysis.
02 Sep 1994-Science (American Association for the Advancement of Science)-Vol. 265, Iss: 5177, pp 1405-1412
TL;DR: AlF4- complexes formed by the G protein Gi alpha 1 demonstrate specific roles in transition-state stabilization for two highly conserved residues, suggesting a mechanism that may promote release of the beta gamma subunit complex when the alpha subunit is activated by GTP.
Abstract: Mechanisms of guanosine triphosphate (GTP) hydrolysis by members of the G protein alpha subunit-p21ras superfamily of guanosine triphosphatases have been studied extensively but have not been well understood. High-resolution x-ray structures of the GTP gamma S and GDP.AlF4- complexes formed by the G protein Gi alpha 1 demonstrate specific roles in transition-state stabilization for two highly conserved residues. Glutamine204 (Gln61 in p21ras) stabilizes and orients the hydrolytic water in the trigonal-bipyramidal transition state. Arginine 178 stabilizes the negative charge at the equatorial oxygen atoms of the pentacoordinate phosphate intermediate. Conserved only in the G alpha family, this residue may account for the higher hydrolytic rate of G alpha proteins relative to those of the p21ras family members. The fold of Gi alpha 1 differs from that of the homologous Gt alpha subunit in the conformation of a helix-loop sequence located in the alpha-helical domain that is characteristic of these proteins; this site may participate in effector binding. The amino-terminal 33 residues are disordered in GTP gamma S-Gi alpha 1, suggesting a mechanism that may promote release of the beta gamma subunit complex when the alpha subunit is activated by GTP.
Citations
More filters
TL;DR: Some features of the structure and function of mammalian G protein subunits are summarized, then how the elements of the cellular language may be ordered and weighted to allow the cell to respond properly to the message is discussed.
1,448 citations
Cites background from "Structures of active conformations ..."
...The helical domain may also contribute to the effector-binding site (Coleman et al., 1994), along with other regions on the GTPase domain (see below)....
[...]
...A new era in understanding the structural basis for cz subunit function opened when the crystal structure of GTP-and GDP-liganded transducin and ml was solved (Noel et al., 1993; Lambright et al., 1994; Coleman et al., 1994)....
[...]
...The first 25 amino acids of the ~ subu nit are essential for 13y binding (Fung and Nash, 1983; Denker et al., 1992a), but their position is unknown because they are mobile and do not show in the crystal (Coleman et al., 1994)....
[...]
TL;DR: The structural arrangement in the active site is consistent with a mostly associative mechanism of phosphoryl transfer and provides an explanation for the activation of Ras by glycine-12 and glutamine-61 mutations.
Abstract: The three-dimensional structure of the complex between human H-Ras bound to guanosine diphosphate and the guanosine triphosphatase (GTPase)-activating domain of the human GTPase-activating protein p120GAP (GAP-334) in the presence of aluminum fluoride was solved at a resolution of 2.5 angstroms. The structure shows the partly hydrophilic and partly hydrophobic nature of the communication between the two molecules, which explains the sensitivity of the interaction toward both salts and lipids. An arginine side chain (arginine-789) of GAP-334 is supplied into the active site of Ras to neutralize developing charges in the transition state. The switch II region of Ras is stabilized by GAP-334, thus allowing glutamine-61 of Ras, mutation of which activates the oncogenic potential, to participate in catalysis. The structural arrangement in the active site is consistent with a mostly associative mechanism of phosphoryl transfer and provides an explanation for the activation of Ras by glycine-12 and glutamine-61 mutations. Glycine-12 in the transition state mimic is within van der Waals distance of both arginine-789 of GAP-334 and glutamine-61 of Ras, and even its mutation to alanine would disturb the arrangements of residues in the transition state.
1,440 citations
TL;DR: The crystal structure of a peptide complex with the substrate-binding unit of DnaK has been determined at 2.0 Å resolution, which suggests a model of conformation-dependent substrate binding that features a latch mechanism for maintaining long lifetime complexes.
Abstract: DnaK and other members of the 70-kilodalton heat-shock protein (hsp70) family promote protein folding, interaction, and translocation, both constitutively and in response to stress, by binding to unfolded polypeptide segments. These proteins have two functional units: a substrate-binding portion binds the polypeptide, and an adenosine triphosphatase portion facilitates substrate exchange. The crystal structure of a peptide complex with the substrate-binding unit of DnaK has now been determined at 2.0 angstroms resolution. The structure consists of a beta-sandwich subdomain followed by alpha-helical segments. The peptide is bound to DnaK in an extended conformation through a channel defined by loops from the beta sandwich. An alpha-helical domain stabilizes the complex, but does not contact the peptide directly. This domain is rotated in the molecules of a second crystal lattice, which suggests a model of conformation-dependent substrate binding that features a latch mechanism for maintaining long lifetime complexes.
1,243 citations
TL;DR: The recent resolution of crystal structures of heterotrimeric G proteins in inactive and active conformations provides a structural framework for understanding their role as conformational switches in signaling pathways.
1,163 citations
TL;DR: The structure of a heterotrimeric G protein reveals the mechanism of the nucleotide-dependent engagement of the α and βγ subunits that regulates their interaction with receptor and effector molecules.
Abstract: The structure of a heterotrimeric G protein reveals the mechanism of the nucleotide-dependent engagement of the alpha and beta gamma subunits that regulates their interaction with receptor and effector molecules. The interaction involves two distinct interfaces and dramatically alters the conformation of the alpha but not of the beta gamma subunits. The location of the known sites for post-translational modification and receptor coupling suggest a plausible orientation with respect to the membrane surface and an activated heptahelical receptor.
1,138 citations
References
More filters
TL;DR: The PROCHECK suite of programs as mentioned in this paper provides a detailed check on the stereochemistry of a protein structure and provides an assessment of the overall quality of the structure as compared with well refined structures of the same resolution.
Abstract: The PROCHECK suite of programs provides a detailed check on the stereochemistry of a protein structure Its outputs comprise a number of plots in PostScript format and a comprehensive residue-by-residue listing These give an assessment of the overall quality of the structure as compared with well refined structures of the same resolution and also highlight regions that may need further investigation The PROCHECK programs are useful for assessing the quality not only of protein structures in the process of being solved but also of existing structures and of those being modelled on known structures
22,829 citations
TL;DR: The MOLSCRIPT program as discussed by the authors produces plots of protein structures using several different kinds of representations, including simple wire models, ball-and-stick models, CPK models and text labels.
Abstract: The MOLSCRIPT program produces plots of protein structures using several different kinds of representations. Schematic drawings, simple wire models, ball-and-stick models, CPK models and text labels can be mixed freely. The schematic drawings are shaded to improve the illusion of three dimensionality. A number of parameters affecting various aspects of the objects drawn can be changed by the user. The output from the program is in PostScript format.
13,971 citations
TL;DR: This paper presents a meta-analysis of G Protein Interactions and its Foundations, which states that G Proteins are Law-Regulated and G Protein-Effector Interactions are Nonvolatile.
Abstract: PERSPECTIVES AND SUMMARY .............................................................. 615 HISTORY ............................................................................................... 616 INDIVIDUAL G PROTEINS: FUNCTIONS AND MOLECULAR ENTITIES .......... 617 Criteria .for Involvement of a G Protein ..................................................... 618 Functions Regulated by G Proteins ........................................................... 619 Molecular Entities and Structure .............................................................. 622 LIGAND-G PROTEIN TERACTIONS ........................................................ 631 LIGAND-REGULATED PROTEIN-PROTEIN TERACTIONS ........................... 634 Receptor-G Protein Interactions ............................................................... 634 G Protein-Effector Interactions ................................................................ 638 G PROTEII~I-MEMBRANE INTERACTIONS .................................................. 643 COVALENT MODIFICATION F G PROTEINS ............................................ 644
6,160 citations
TL;DR: In this article, a statistical quantity (RfreeT) is defined to measure the agreement between observed and computed structure factor amplitudes for a 'test' set of reflections that is omitted in the modelling and refinement process.
Abstract: THE determination of macromolecular structure by crystallography involves fitting atomic models to the observed diffraction data1. The traditional measure of the quality of this fit, and presumably the accuracy of the model, is theR value. Despite stereochemical restraints2, it is possible to overfit or 'misfit' the diffraction data: an incorrect model can be refined to fairly good R values as several recent examples have shown3. Here I propose a reliable and unbiased indicator of the accuracy of such models. By analogy with the cross-validation method4,5 of testing statistical models I define a statistical quantity (RfreeT) that measures the agreement between observed and computed structure factor amplitudes for a 'test' set of reflections that is omitted in the modelling and refinement process. As examples show, there is a high correlation between RfreeT and the accuracy of the atomic model phases. This is useful because experimental phase information is usually inaccurate, incomplete or unavailable. I expect that RfreeT will provide a measure of the information content of recently proposed models of thermal motion and disorder6–8, time-averaging9 and bulk solvent10.
3,714 citations
TL;DR: GTPases are conserved molecular switches, built according to a common structural design, and rapidly accruing knowledge of individual GTPases—crystal structures, biochemical properties, or results of molecular genetic experiments—support and generate hypotheses relating structure to function in other members of the diverse family of GTPase.
Abstract: GTPases are conserved molecular switches, built according to a common structural design. Rapidly accruing knowledge of individual GTPases--crystal structures, biochemical properties, or results of molecular genetic experiments--support and generate hypotheses relating structure to function in other members of the diverse family of GTPases.
3,236 citations