Determinants of BH3 binding specificity for Mcl-1 versus Bcl-xL.

Dutta, S.; Gulla, S.; Chen, T.S.; Fire, E.; Grant, R.A.; Keating, A.E.

doi:10.2210/pdb3kz0/pdb

Macromolecule Content

Total Structure Weight: 42020.77
Atom Count: 2683
Residue Count: 362
Unique protein chains: 2

3KZ0

MCL-1 complex with MCL-1-specific selected peptide

DOI: 10.2210/pdb3KZ0/pdb

Classification: APOPTOSIS
Organism(s): Homo sapiens
Expression System: Escherichia coli

Deposited: 2009-12-07 Released: 2010-05-05
Deposition Author(s): Dutta, S., Fire, E., Grant, R.A., Sauer, R.T., Keating, A.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.349 Å
R-Value Free: 0.270
R-Value Work: 0.222

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Determinants of BH3 binding specificity for Mcl-1 versus Bcl-xL.

Dutta, S., Gulla, S., Chen, T.S., Fire, E., Grant, R.A., Keating, A.E.

(2010) J.Mol.Biol. 398: 747-762

PubMed: 20363230 Search on PubMedSearch on PubMed Central
DOI: 10.1016/j.jmb.2010.03.058

PubMed Abstract:

Interactions among Bcl-2 family proteins are important for regulating apoptosis. Prosurvival members of the family interact with proapoptotic BH3 (Bcl-2-homology-3)-only members, inhibiting execution of cell death through the mitochondrial pathway. Structurally, this interaction is mediated by binding of the alpha-helical BH3 region of the proapoptotic proteins to a conserved hydrophobic groove on the prosurvival proteins. Native BH3-only proteins exhibit selectivity in binding prosurvival members, as do small molecules that block these interactions. Understanding the sequence and structural basis of interaction specificity in this family is important, as it may allow the prediction of new Bcl-2 family associations and/or the design of new classes of selective inhibitors to serve as reagents or therapeutics. In this work, we used two complementary techniques--yeast surface display screening from combinatorial peptide libraries and SPOT peptide array analysis--to elucidate specificity determinants for binding to Bcl-x(L)versus Mcl-1, two prominent prosurvival proteins. We screened a randomized library and identified BH3 peptides that bound to either Mcl-1 or Bcl-x(L) selectively or to both with high affinity. The peptides competed with native ligands for binding into the conserved hydrophobic groove, as illustrated in detail by a crystal structure of a specific peptide bound to Mcl-1. Mcl-1-selective peptides from the screen were highly specific for binding Mcl-1 in preference to Bcl-x(L), Bcl-2, Bcl-w, and Bfl-1, whereas Bcl-x(L)-selective peptides showed some cross-interaction with related proteins Bcl-2 and Bcl-w. Mutational analyses using SPOT arrays revealed the effects of 170 point mutations made in the background of a peptide derived from the BH3 region of Bim, and a simple predictive model constructed using these data explained much of the specificity observed in our Mcl-1 versus Bcl-x(L) binders.

Organizational Affiliation:

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Induced myeloid leukemia cell differentiation protein Mcl-1	A, B	158	Homo sapiens	Mutation(s): 0 Gene Names: MCL1 (BCL2L3)
Find proteins for Q07820 (Homo sapiens) Go to Gene View: MCL1 Go to UniProtKB: Q07820
Protein Feature View Full Protein Feature View for Q07820

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Mcl-1 specific peptide MB7	C, D	23	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
ZN Query on ZN Download SDF File Download CCD File	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
SO4 Query on SO4 Download SDF File Download CCD File	A	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction