PDBsum entry 6fbx

Apoptosis

PDB id: 6fbx

Contents

Protein chains

148 a.a.

22 a.a.

Waters ×105

PDB id:

6fbx

Name:

Apoptosis

Title:

Crystal structure of a zebra-fish pro-survival protein nrz:bad bh3 complex

Structure:

Bcl2-like 10. Chain: a. Synonym: bcl2-like 10 (apoptosis facilitator),nr13,pro-survival protein nrz. Engineered: yes. Bcl2-antagonist of cell death. Chain: b. Synonym: bcl2-associated agonist of cell death b,bad protein. Engineered: yes

Source:

Danio rerio. Zebrafish. Organism_taxid: 7955. Gene: bcl2l10, mcl1l, nr13. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_cell_line: codon plus. Synthetic: yes. Organism_taxid: 7955

Resolution:

1.64Å R-factor: 0.189 R-free: 0.207

Authors:

C.D.Suraweera,M.G.Hinds,M.Kvansakul

Key ref:

C.D.Suraweera et al. (2018). A structural investigation of NRZ mediated apoptosis regulation in zebrafish. Cell Death Dis, 9, 967. PubMed id: 30237469

Date:

20-Dec-17 Release date: 27-Mar-19

Protein chain

Q8UWD5  (Q8UWD5_DANRE) -  BCL2-like 10 from Danio rerio

Seq: 176 a.a.

Struc: 148 a.a.

Protein chain

Q4V925  (Q4V925_DANRE) -  BCL2-antagonist of cell death from Danio rerio

Seq: 147 a.a.

Struc: 22 a.a.

Cell Death Dis 9:967 (2018)

PubMed id: 30237469

A structural investigation of NRZ mediated apoptosis regulation in zebrafish.

C.D.Suraweera, S.Caria, M.Järvå, M.G.Hinds, M.Kvansakul.

ABSTRACT

Bcl-2 family proteins play a crucial role in regulating apoptosis, a process critical for development, eliminating damaged or infected cells, host-pathogen interactions and in disease. Dysregulation of Bcl-2 proteins elicits an expansive cell survival mechanism promoting cell migration, invasion and metastasis. Through a network of intra-family protein-protein interactions Bcl-2 family members regulate the release of cell death factors from mitochondria. NRZ is a novel zebrafish pro-survival Bcl-2 orthologue resident on mitochondria and the endoplasmic reticulum (ER). However, the mechanism of NRZ apoptosis inhibition has not yet been clarified. Here we examined the interactions of NRZ with pro-apoptotic members of the Bcl-2 family using a combination of isothermal calorimetry and mutational analysis of NRZ. We show that NRZ binds almost all zebrafish pro-apoptotic proteins and displays a broad range of affinities. Furthermore, we define the structural basis for apoptosis inhibition of NRZ by solving the crystal structure of both apo-NRZ and a holo form bound to a peptide spanning the binding motif of the pro-apoptotic zBad, a BH3-only protein orthologous to mammalian Bad. The crystal structure of NRZ revealed that it adopts the conserved Bcl-2 like fold observed for other cellular pro-survival Bcl-2 proteins and employs the canonical ligand binding groove to bind Bad BH3 peptide. NRZ engagement of Bad BH3 involves the canonical ionic interaction between NRZ R86 and Bad D104 and an additional ionic interaction between NRZ D79 and Bad R100, and substitution of either NRZ R86 or D79 to Ala reduces the binding to Bad BH3 tenfold or more. Our findings provide a detailed mechanistic understanding for NRZ mediated anti-apoptotic activity in zebrafish by revealing binding to both Bad and Noxa, suggesting that NRZ is likely to occupy a unique mechanistic role in zebrafish apoptosis regulation by acting as a highly promiscuous pro-apoptotic Bcl-2 binder.