PDBsum entry 5wpm

Signaling protein

PDB id: 5wpm

Contents

Protein chains

153 a.a.

30 a.a.

31 a.a.

Ligands

GNP

SO4

Metals

_MG ×2

Waters ×69

PDB id:

5wpm

Name:

Signaling protein

Title:

Kras g12v, bound to gppnhp and miniprotein 225-11(a30r)

Structure:

Gtpase kras. Chain: a. Fragment: residues 1-166. Synonym: k-ras 2,ki-ras,c-k-ras,c-ki-ras. Engineered: yes. Ras binding peptide. Chain: b, c. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: kras, kras2, rask2. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Saccharomyces cerevisiae. Baker's yeast.

Resolution:

1.72Å R-factor: 0.237 R-free: 0.285

Authors:

S.-J.Lee,S.Y.Shim,J.H.Mcgee,G.L.Verdine

Key ref:

J.H.McGee et al. (2018). Exceptionally high-affinity Ras binders that remodel its effector domain. J Biol Chem, 293, 3265-3280. PubMed id: 29282294 DOI: 10.1074/jbc.M117.816348

Date:

05-Aug-17 Release date: 03-Jan-18

Protein chain

P01116  (RASK_HUMAN) -  GTPase KRas from Homo sapiens

Seq: 189 a.a.

Struc: 153 a.a.*

Protein chain

No UniProt id for this chain

Struc: 30 a.a.

Protein chain

No UniProt id for this chain

Struc: 31 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chain A: E.C.3.6.5.2 - small monomeric GTPase.
• Reaction: GTP + H2O = GDP + phosphate + H⁺

GTP + H2O = GDP (Bound ligand (Het Group name = GNP) matches with 81.82% similarity) + phosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M117.816348

J Biol Chem 293:3265-3280 (2018)

PubMed id: 29282294

Exceptionally high-affinity Ras binders that remodel its effector domain.

J.H.McGee, S.Y.Shim, S.J.Lee, P.K.Swanson, S.Y.Jiang, M.A.Durney, G.L.Verdine.

ABSTRACT

The Ras proteins are aberrantly activated in a wide range of human cancers, often endowing tumors with aggressive properties and resistance to therapy. Decades of effort to develop direct Ras inhibitors for clinical use have thus far failed, largely because of a lack of adequate small-molecule-binding pockets on the Ras surface. Here, we report the discovery of Ras-binding miniproteins from a naïve library and their evolution to afford versions with midpicomolar affinity to Ras. A series of biochemical experiments indicated that these miniproteins bind to the Ras effector domain as dimers, and high-resolution crystal structures revealed that these miniprotein dimers bind Ras in an unprecedented mode in which the Ras effector domain is remodeled to expose an extended pocket that connects two isolated pockets previously found to engage small-molecule ligands. We also report a Ras point mutant that stabilizes the protein in the open conformation trapped by these miniproteins. These findings provide new tools for studying Ras structure and function and present opportunities for the development of both miniprotein and small-molecule inhibitors that directly target the Ras proteins.