6DCO

Bcl-xL complex with Beclin 1 BH3 domain T108D

DOI: 10.2210/pdb6DCO/pdb
Entry: 6DCO supersedes: 5VB4

Classification: APOPTOSIS
Organism(s): Homo sapiens
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2018-05-07 Released: 2018-05-30
Deposition Author(s): Lee, E.F., Smith, B.J., Smith, N.A., Yao, S., Fairlie, W.D.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.231
R-Value Work: 0.203
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural insights into BCL2 pro-survival protein interactions with the key autophagy regulator BECN1 following phosphorylation by STK4/MST1.

Lee, E.F., Smith, N.A., Soares da Costa, T.P., Meftahi, N., Yao, S., Harris, T.J., Tran, S., Pettikiriarachchi, A., Perugini, M.A., Keizer, D.W., Evangelista, M., Smith, B.J., Fairlie, W.D.

(2019) Autophagy 15: 785-795

PubMed: 30626284 Search on PubMedSearch on PubMed Central
DOI: 10.1080/15548627.2018.1564557
Primary Citation of Related Structures:
6DCN, 6DCO

PubMed Abstract:

BECN1/Beclin 1 is a critical protein in the initiation of autophagosome formation. Recent studies have shown that phosphorylation of BECN1 by STK4/MST1 at threonine 108 (T108) within its BH3 domain blocks macroautophagy/autophagy by increasing BECN1 affinity for its negative regulators, the anti-apoptotic proteins BCL2/Bcl-2 and BCL2L1/Bcl-x _L. It was proposed that this increased binding is due to formation of an electrostatic interaction with a conserved histidine residue on the anti-apoptotic molecules. Here, we performed biophysical studies which demonstrated that a peptide corresponding to the BECN1 BH3 domain in which T108 is phosphorylated (p-T108) does show increased affinity for anti-apoptotic proteins that is significant, though only minor (<2-fold). We also determined X-ray crystal structures of BCL2 and BCL2L1 with T108-modified BECN1 BH3 peptides, but only showed evidence of an interaction between the BH3 peptide and the conserved histidine residue when the histidine flexibility was restrained due to crystal contacts. These data, together with molecular dynamics studies, indicate that the histidine is highly flexible, even when complexed with BECN1 BH3. Binding studies also showed that detergent can increase the affinity of the interaction. Although this increase was similar for both the phosphorylated and non-phosphorylated peptides, it suggests factors such as membranes could impact on the interaction between BECN1 and BCL2 proteins, and therefore, on the regulation of autophagy. Hence, we propose that phosphorylation of BECN1 by STK4/MST1 can increase the affinity of the interaction between BECN1 and anti-apoptotic proteins and this interaction can be stabilized by local environmental factors. Abbreviations: asu: asymmetric unit; BH3: BCL2/Bcl-2 homology 3; DAPK: death associated protein kinase; MD: molecular dynamics; MST: microscale thermophoresis; NMR: nuclear magnetic resonance; PDB: protein data bank; p-T: phosphothreonine; SPR: surface plasmon resonance; STK4/MST1: serine/threonine kinase 4.

Organizational Affiliation:

c School of Cancer Medicine , La Trobe University , Melbourne , Australia.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bcl-2-like protein 1,Bcl-2-like protein 1	A, B	156	Homo sapiens	Mutation(s): 0 Gene Names: BCL2L1, BCL2L, BCLX
Find proteins for Q07817 (Homo sapiens) Explore Q07817 Go to UniProtKB: Q07817
NIH Common Fund Data Resources
PHAROS Q07817 GTEx ENSG00000171552
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beclin-1	C, D	26	Homo sapiens	Mutation(s): 1 Gene Names: BECN1, GT197
Find proteins for Q14457 (Homo sapiens) Explore Q14457 Go to UniProtKB: Q14457
NIH Common Fund Data Resources
PHAROS Q14457 GTEx ENSG00000126581
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [A] SDF format, chain F [A] SDF format, chain G [A] MOL2 format, chain E [A] MOL2 format, chain F [A] MOL2 format, chain G [A]	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction