The 2.2 Å crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with RaplA and a GTP analogue

@article{Nassar1995The2,
  title={The 2.2 {\AA} crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with RaplA and a GTP analogue},
  author={Nicolas N. Nassar and Gudrun Horn and Christian Herrmann and Anna Scherer and Frank McCormick and Alfred Wittinghofer},
  journal={Nature},
  year={1995},
  volume={375},
  pages={554-560}
}
The X-ray crystal structure of the complex between the Ras-related protein RaplA in the GTP-analogue (GppNHp) form and the Ras-binding domain (RBD) of the Ras effector molecule c-Raf1, a Ser/Thr-specific protein kinase, has been solved to a resolution of 2.2 Å. It shows that RBD has the ubiquitin superfold and that the structure of RaplA is very similar to that of Ras. The interaction between the two proteins is mediated by an apparent central antiparallel β-sheet formed by strands B1–B2 from… 
Molecular Dynamics on Complexes of ras-p21 and Its Inhibitor Protein, rap-1A, Bound to the ras-Binding Domain of the raf-p74 Protein: Identification of Effector Domains in the raf Protein
TLDR
It is found that despite the similarities of the starting structures for both complexes, the average structures differ considerably, indicating that these two proteins do not interact in the same way with this vital target protein.
Identification, Using Molecular Dynamics, of an Effector Domain of the ras-Binding Domain of the raf-p74 Protein That Is Uniquely Involved in Oncogenic ras-p21 Signaling
TLDR
Molecular dynamics on the Val 12-ras-p21-RBD complex is performed and it is found that there is a large displacement of a loop involving these residues when the structures of the two complexes are compared and suggests that oncogenic p21 uses this loop to interact with raf in a unique manner.
Crystal structure of the GTPase-activating domain of human p120GAP and implications for the interaction with Ras
TLDR
A model for the interaction between Ras and GAP is proposed that satisfies numerous biochemical and genetic data on this important regulatory process.
Crystal Structure of M-Ras Reveals a GTP-bound “Off” State Conformation of Ras Family Small GTPases*
TLDR
31P NMR analysis shows that free M-Ras-Gpp(NH)p predominantly assumes the state 1 conformation, which undergoes conformational transition to state 2 upon association with c-Raf-1.
The solution structure of the Raf-1 cysteine-rich domain: a novel ras and phospholipid binding site.
TLDR
The characterization of a second Ras-binding site in the cysteine-rich domain (CRD) and the involvement of both Ras- binding sites in effective Raf-1-mediated transformation provides insight into the molecular aspects and consequences of Ras-Raf interactions.
Molecular Dissection of the Interaction between the Small G Proteins Rac1 and RhoA and Protein Kinase C-related Kinase 1 (PRK1)*
TLDR
It is demonstrated thatPRK1 binds with a similar affinity to RhoA and Rac1, two members of the Rho family, and the solution structure of the second HR1 domain from the regulatory N-terminal region of PRK1 is presented and it is shown that it forms an anti-parallel coiled-coil.
Oncogenic amino acid substitutions in the inhibitory rap-1A protein cause it to adopt a ras-p21-like conformation as computed using molecular dynamics.
TLDR
The average low energy structures for each of the three proteins, ras-p21, rap-1A and mutant rap1A, called rap-M, are computed and Pro 34 is identified as a critical residue which may determine if the protein transforms cells or inhibits cell transformation.
Crystal Structure of the RUN Domain of the RAP2-interacting Protein x*
TLDR
Using cell-free synthesis and NMR, it is determined that the region encompassing residues 83-255 of mouse RPIPx, which is 40-residues larger than the predicted RUN domain, is the minimum fragment that forms a correctly folded protein.
Structural basis for the interaction of Ras with RaIGDS
TLDR
The 2.1 Å crystal structure of the complex between Ras and the Ras-interacting domain (RID) of RalGDS reveals that the β-sheet of the RID joins the switch I region of Ras to form an extended β- sheet with a topology similar to that found in the Rap–Raf complex.
...
...

References

SHOWING 1-10 OF 50 REFERENCES
Crystal structure of the nuclear Ras-related protein Ran in its GDP-bound form
TLDR
This structure reveals a similarity with the Ras core (G-domain) but with significant variations in regions involved in GDP and Mg2+ coordination (switch I and switch II regions in Ras)9,10, suggesting that there could be major conformational changes upon GTP binding.
Direct interaction of Ras and the amino-terminal region of Raf-1 in vitro
TLDR
It is reported that the amino-terminal cysteine-rich regulatory region of p74c-raf-1 expressed as a glutathione-S-transferase (GST) fusion protein binds directly to Ras with relatively high affinity (50 nM).
Chemical shift assignments and folding topology of the Ras-binding domain of human Raf-1 as determined by heteronuclear three-dimensional NMR spectroscopy.
TLDR
This work has expressed a corresponding segment of the human Raf sequence (Raf55-132) in Escherichia coli as a fusion with maltose binding protein and observed its structure resembles that of ubiquitin, even though there is no more than 11% sequence homology between the two proteins.
Identification of the guanine nucleotide dissociation stimulator for Ral as a putative effector molecule of R-ras, H-ras, K-ras, and Rap.
TLDR
Using the two-hybrid system, it is shown that RalGDS-RBD interacts with H-ra, K-ras, and Rap, and with active but not with inactive point mutants of these Ras-like GTPases, and is a putative effector molecule for R-ras.
Refined crystal structure of the triphosphate conformation of H‐ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis.
TLDR
A mechanism for GTP hydrolysis involving mainly Gln61 and Glu63 as activating species for in‐line attack of water as well as a mechanism for rate enhancement by GAP is proposed.
Critical binding and regulatory interactions between Ras and Raf occur through a small, stable N-terminal domain of Raf and specific Ras effector residues
TLDR
A novel competition assay is used to measure in vitro the relative affinity of the c-Raf-1 regulatory region for Ras-GTP, Ras- GDP, and 10 oncogenic and effector mutant Ras proteins, demonstrating that the mechanism of cyclic AMP downregulation results through structural changes occurring exclusively in this small Ras-binding domain.
A single amino acid change in Raf-1 inhibits Ras binding and alters Raf-1 function.
TLDR
It is shown that a single amino acid mutation in Raf-1 (Arg89 to Leu) disrupted the interaction with Ras in vitro and in the yeast two-hybrid system, and the finding that tyrosine kinases can stimulate the enzymatic activity of Raf- 1 proteins containing a mutation at the Ras-interaction site suggests that Raf-2 can be activated by Ras-independent pathways.
Identification of the sites of interaction between c-Raf-1 and Ras-GTP.
Specific sites of protein-protein interaction were identified in the 51-149 region of c-Raf-1 using contact epitope scanning and site-directed mutagenesis. Nineteen overlapping peptides based upon
Complexes of Ras.GTP with Raf-1 and mitogen-activated protein kinase kinase.
TLDR
The forming of complexes containing MAPKK activity and Raf-1 protein are dependent upon the activity of Ras, and the specific interaction of activated Ras with active MAP kinase kinase (MAPKK) was confirmed by direct assays.
...
...