PDBsum entry 2msd

Lipid binding protein

PDB id: 2msd

Contents

Protein chains

198 a.a.

185 a.a.

Ligands

PCW ×64

17F ×16

GNP

Metals

_MG

PDB id:

2msd

Name:

Lipid binding protein

Title:

Nmr data-driven model of gtpase kras-gnp tethered to a lipid-bilayer nanodisc

Structure:

Apolipoprotein a-i. Chain: a, c. Fragment: unp residues 68-265. Synonym: apoa-i,apolipoprotein a1. Engineered: yes. Gtpase kras. Chain: b. Fragment: unp residues 1-185. Synonym: k-ras 2,ki-ras,c-k-ras,c-ki-ras.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: apoa1. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: kras, kras2, rask2.

NMR struc:

10 models

Authors:

M.Mazhab-Jafari,P.Stathopoulos,C.Marshall,M.Ikura

Key ref:

M.T.Mazhab-Jafari et al. (2015). Oncogenic and RASopathy-associated K-RAS mutations relieve membrane-dependent occlusion of the effector-binding site. Proc Natl Acad Sci U S A, 112, 6625-6630. PubMed id: 25941399 DOI: 10.1073/pnas.1419895112

Date:

29-Jul-14 Release date: 03-Jun-15

Protein chains

P02647  (APOA1_HUMAN) -  Apolipoprotein A-I from Homo sapiens

Seq: 267 a.a.

Struc: 198 a.a.

Protein chain

P01116  (RASK_HUMAN) -  GTPase KRas from Homo sapiens

Seq: 189 a.a.

Struc: 185 a.a.*

* PDB and UniProt seqs differ at 17 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, C: E.C.?
• Enzyme class 3: Chain B: 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(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1073/pnas.1419895112

Proc Natl Acad Sci U S A 112:6625-6630 (2015)

PubMed id: 25941399

Oncogenic and RASopathy-associated K-RAS mutations relieve membrane-dependent occlusion of the effector-binding site.

M.T.Mazhab-Jafari, C.B.Marshall, M.J.Smith, G.M.Gasmi-Seabrook, P.B.Stathopulos, F.Inagaki, L.E.Kay, B.G.Neel, M.Ikura.

ABSTRACT

K-RAS4B (Kirsten rat sarcoma viral oncogene homolog 4B) is a prenylated, membrane-associated GTPase protein that is a critical switch for the propagation of growth factor signaling pathways to diverse effector proteins, including rapidly accelerated fibrosarcoma (RAF) kinases and RAS-related protein guanine nucleotide dissociation stimulator (RALGDS) proteins. Gain-of-function KRAS mutations occur frequently in human cancers and predict poor clinical outcome, whereas germ-line mutations are associated with developmental syndromes. However, it is not known how these mutations affect K-RAS association with biological membranes or whether this impacts signal transduction. Here, we used solution NMR studies of K-RAS4B tethered to nanodiscs to investigate lipid bilayer-anchored K-RAS4B and its interactions with effector protein RAS-binding domains (RBDs). Unexpectedly, we found that the effector-binding region of activated K-RAS4B is occluded by interaction with the membrane in one of the NMR-observable, and thus highly populated, conformational states. Binding of the RAF isoform ARAF and RALGDS RBDs induced marked reorientation of K-RAS4B from the occluded state to RBD-specific effector-bound states. Importantly, we found that two Noonan syndrome-associated mutations, K5N and D153V, which do not affect the GTPase cycle, relieve the occluded orientation by directly altering the electrostatics of two membrane interaction surfaces. Similarly, the most frequent KRAS oncogenic mutation G12D also drives K-RAS4B toward an exposed configuration. Further, the D153V and G12D mutations increase the rate of association of ARAF-RBD with lipid bilayer-tethered K-RAS4B. We revealed a mechanism of K-RAS4B autoinhibition by membrane sequestration of its effector-binding site, which can be disrupted by disease-associated mutations. Stabilizing the autoinhibitory interactions between K-RAS4B and the membrane could be an attractive target for anticancer drug discovery.