PDBsum entry 1sdz

Apoptosis

PDB id: 1sdz

Contents

Protein chain

97 a.a. *

Ligands

ALA-VAL-ALA-PHE-TYR-ILE-PRO

Metals

_ZN

Waters ×154

* Residue conservation analysis

PDB id:

1sdz

Name:

Apoptosis

Title:

Crystal structure of diap1 bir1 bound to a reaper peptide

Structure:

Apoptosis 1 inhibitor. Chain: a. Fragment: diap1 bir1 domain. Synonym: inhibitor of apoptosis 1, diap1, thread protein. Engineered: yes. Reaper. Chain: b. Fragment: reaper n-terminal peptide. Engineered: yes

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: iap1, th. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the sequence of this peptide occurs naturally in drosophila (fruit flies).

Biol. unit:

Hexamer (from PQS)

Resolution:

1.78Å R-factor: 0.232 R-free: 0.267

Authors:

N.Yan,J.W.Wu,Y.Shi

Key ref:

N.Yan et al. (2004). Molecular mechanisms of DrICE inhibition by DIAP1 and removal of inhibition by Reaper, Hid and Grim. Nat Struct Mol Biol, 11, 420-428. PubMed id: 15107838 DOI: 10.1038/nsmb764

Date:

15-Feb-04 Release date: 27-Apr-04

Protein chain

Q24306  (DIAP1_DROME) -  Death-associated inhibitor of apoptosis 1 from Drosophila melanogaster

Seq: 438 a.a.

Struc: 97 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine

DOI no: 10.1038/nsmb764

Nat Struct Mol Biol 11:420-428 (2004)

PubMed id: 15107838

Molecular mechanisms of DrICE inhibition by DIAP1 and removal of inhibition by Reaper, Hid and Grim.

N.Yan, J.W.Wu, J.Chai, W.Li, Y.Shi.

ABSTRACT

The Drosophila melanogaster inhibitor of apoptosis protein DIAP1 suppresses apoptosis in part through inhibition of the effector caspase DrICE. The pro-death proteins Reaper, Hid and Grim (RHG) induce apoptosis by antagonizing DIAP1 function. However, the underlying molecular mechanisms remain unknown. Here we demonstrate that DIAP1 directly inhibits the catalytic activity of DrICE through its BIR1 domain and this inhibition is countered effectively by the RHG proteins. Inhibition of DrICE by DIAP1 occurs only after the cleavage of its N-terminal 20 amino acids and involves a conserved surface groove on BIR1. Crystal structures of BIR1 bound to the RHG peptides show that the RHG proteins use their N-terminal IAP-binding motifs to bind to the same surface groove, hence relieving DIAP1-mediated inhibition of DrICE. These studies define novel molecular mechanisms for the inhibition and activation of a representative D. melanogaster effector caspase.

Selected figure(s)

Figure 2.
Figure 2. The conserved pocket of DIAP1-BIR1 is involved in DrICE interaction and inhibition. (a) Identification of mutations on BIR1 that result in loss of DrICE inhibition. Various BIR1 proteins were examined for their ability to inhibit DrICE activity. The double mutants K77D K79D and D94K E99K did not inhibit DrICE activity. (b) Inhibition of DrICE correlates with its interaction with DIAP1-BIR1. In this gel filtration assay, various BIR1 proteins were individually incubated with the active DrICE protein. The mixture was applied to a gel filtration analysis from which contiguous fractions were visualized on SDS-PAGE by Coomassie blue staining. (c) The structure of DIAP1-BIR2 (ref. 32) showing the predicted surface location of the mutated residues in BIR1. The residues whose corresponding mutation in BIR1 resulted in loss of interaction with DrICE are red. The corresponding BIR1 residues are indicated in parentheses. The conserved surface pocket among most BIR domains is indicated by a purple oval circle. This panel was generated using MolScript41.

Figure 4.
Figure 4. A mechanistic explanation for developmental GOF mutations in the BIR1 domain. (a) The GOF mutations retain DrICE inhibition and can no longer be regulated by the Hid peptide. Wild-type BIR1 inhibited DrICE (lane 4), and this inhibition was removed by the presence of the Hid peptide (lane 5). In contrast, the mutant proteins G88S and G88D inhibited DrICE (lanes 6 and 8), but this inhibition was not removed by Hid (lanes 7 and 9). (b) Interaction between DrICE and the mutant BIR1 proteins can no longer be weakened or disrupted by the Hid peptide. The developmental GOF mutations in the BIR1 domain (G88S and G88D) retained a stable interaction with DrICE as shown by gel filtration. The presence of Hid peptide did not affect this interaction.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2004, 11, 420-428) copyright 2004.

Figures were selected by an automated process.