1XB1

The Structure of the BIR domain of IAP-like protein 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The BIR domain of IAP-like protein 2 is conformationally unstable: implications for caspase inhibition

Shin, H.Renatus, M.Eckelman, B.P.Nunes, V.A.Sampaio, C.A.M.Salvesen, G.S.

(2005) Biochem.J. 385: 1-10

  • DOI: 10.1042/BJ20041107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Several IAP (inhibitor of apoptosis) proteins regulate cell fate decisions, and the X-linked IAP (XIAP) does so in part by inhibiting caspases, proteases that execute the apoptotic pathway. A tissue-specific homologue of XIAP, known as ILP2 (IAP-like ...

    Several IAP (inhibitor of apoptosis) proteins regulate cell fate decisions, and the X-linked IAP (XIAP) does so in part by inhibiting caspases, proteases that execute the apoptotic pathway. A tissue-specific homologue of XIAP, known as ILP2 (IAP-like protein 2), has previously been implicated in the control of apoptosis in the testis by direct inhibition of caspase 9. In examining this protein we found that the putative caspase 9 interaction domain is a surprisingly weak inhibitor and is also conformationally unstable. Comparison with the equivalent domain in XIAP demonstrated that the instability is due to the lack of a linker segment N-terminal to the inhibitory BIR (baculovirus IAP repeat) domain. Fusion of a 9-residue linker from XIAP to the N-terminus of ILP2 restored tight caspase 9 inhibition, dramatically increased conformational stability and allowed crystallization of the ILP2 BIR domain in a form strikingly similar to the XIAP third BIR domain. We conclude that ILP2 is an unstable protein, and cannot inhibit caspase 9 in a physiological way on its own. We speculate that ILP2 requires assistance from unidentified cellular factors to be an effective inhibitor of apoptosis in vivo.


    Organizational Affiliation

    Program in Apoptosis and Cell Death Research, The Burnham Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Baculoviral IAP repeat-containing protein 8
A, B, C, D, E, F
108Homo sapiensMutation(s): 0 
Gene Names: BIRC8 (ILP2)
Find proteins for Q96P09 (Homo sapiens)
Go to Gene View: BIRC8
Go to UniProtKB:  Q96P09
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Diablo homolog, mitochondrial
G, H, I, J, K, L
7Homo sapiensMutation(s): 0 
Gene Names: DIABLO (SMAC)
Find proteins for Q9NR28 (Homo sapiens)
Go to Gene View: DIABLO
Go to UniProtKB:  Q9NR28
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.232 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.689α = 90.00
b = 88.689β = 90.00
c = 191.355γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance