PDBsum entry 5ufe

Hydrolase/de novo protein

PDB id: 5ufe

Contents

Protein chains

166 a.a.

54 a.a.

Ligands

GNP

Metals

_CO ×3

_CA ×3

_CD ×4

_CL ×3

_MG

Waters ×95

PDB id:

5ufe

Name:

Hydrolase/de novo protein

Title:

Wild-type k-ras(gnp)/r11.1.6 complex

Structure:

Gtpase kras. Chain: a. Fragment: unp residues 1-166. Synonym: k-ras 2,ki-ras,c-k-ras,c-ki-ras. Engineered: yes. R11.1.6. Chain: b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: kras, kras2, rask2. Expressed in: escherichia coli. Expression_system_taxid: 562. Sulfolobus solfataricus. Organism_taxid: 2287. Expression_system_taxid: 562

Resolution:

2.30Å R-factor: 0.190 R-free: 0.241

Authors:

J.A.Parker,C.Mattos

Key ref:

M.J.Kauke et al. (2017). An engineered protein antagonist of K-Ras/B-Raf interaction. Sci Rep, 7, 5831. PubMed id: 28724936

Date:

04-Jan-17 Release date: 02-Aug-17

Protein chain

P01116  (RASK_HUMAN) -  GTPase KRas from Homo sapiens

Seq: 189 a.a.

Struc: 166 a.a.*

Protein chain

No UniProt id for this chain

Struc: 54 a.a.

* PDB and UniProt seqs differ at 4 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

Sci Rep 7:5831 (2017)

PubMed id: 28724936

An engineered protein antagonist of K-Ras/B-Raf interaction.

M.J.Kauke, M.W.Traxlmayr, J.A.Parker, J.D.Kiefer, R.Knihtila, J.McGee, G.Verdine, C.Mattos, K.D.Wittrup.

ABSTRACT

Ras is at the hub of signal transduction pathways controlling cell proliferation and survival. Its mutants, present in about 30% of human cancers, are major drivers of oncogenesis and render tumors unresponsive to standard therapies. Here we report the engineering of a protein scaffold for preferential binding to K-Ras G12D. This is the first reported inhibitor to achieve nanomolar affinity while exhibiting specificity for mutant over wild type (WT) K-Ras. Crystal structures of the protein R11.1.6 in complex with K-Ras WT and K-Ras G12D offer insight into the structural basis for specificity, highlighting differences in the switch I conformation as the major defining element in the higher affinity interaction. R11.1.6 directly blocks interaction with Raf and reduces signaling through the Raf/MEK/ERK pathway. Our results support greater consideration of the state of switch I and provide a novel tool to study Ras biology. Most importantly, this work makes an unprecedented contribution to Ras research in inhibitor development strategy by revealing details of a targetable binding surface. Unlike the polar interfaces found for Ras/effector interactions, the K-Ras/R11.1.6 complex reveals an extensive hydrophobic interface that can serve as a template to advance the development of high affinity, non-covalent inhibitors of K-Ras oncogenic mutants.