1TW6

Structure of an ML-IAP/XIAP chimera bound to a 9mer peptide derived from Smac


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Engineering ML-IAP to produce an extraordinarily potent caspase 9 inhibitor: implications for Smac-dependent anti-apoptotic activity of ML-IAP

Vucic, D.Franklin, M.C.Wallweber, H.J.A.Das, K.Eckelman, B.P.Shin, H.Elliott, L.O.Kadkhodayan, S.Deshayes, K.Salvesen, G.S.Fairbrother, W.J.

(2005) Biochem J 385: 11-20

  • DOI: 10.1042/BJ20041108
  • Primary Citation of Related Structures:  
    1TW6

  • PubMed Abstract: 
  • ML-IAP (melanoma inhibitor of apoptosis) is a potent anti-apoptotic protein that is strongly up-regulated in melanoma and confers protection against a variety of pro-apoptotic stimuli. The mechanism by which ML-IAP regulates apoptosis is unclear, alt ...

    ML-IAP (melanoma inhibitor of apoptosis) is a potent anti-apoptotic protein that is strongly up-regulated in melanoma and confers protection against a variety of pro-apoptotic stimuli. The mechanism by which ML-IAP regulates apoptosis is unclear, although weak inhibition of caspases 3 and 9 has been reported. Here, the binding to and inhibition of caspase 9 by the single BIR (baculovirus IAP repeat) domain of ML-IAP has been investigated and found to be significantly less potent than the ubiquitously expressed XIAP (X-linked IAP). Engineering of the ML-IAP-BIR domain, based on comparisons with the third BIR domain of XIAP, resulted in a chimeric BIR domain that binds to and inhibits caspase 9 significantly better than either ML-IAP-BIR or XIAP-BIR3. Mutational analysis of the ML-IAP-BIR domain demonstrated that similar enhancements in caspase 9 affinity can be achieved with only three amino acid substitutions. However, none of these modifications affected binding of the ML-IAP-BIR domain to the IAP antagonist Smac (second mitochondrial activator of caspases). ML-IAP-BIR was found to bind mature Smac with low nanomolar affinity, similar to that of XIAP-BIR2-BIR3. Correspondingly, increased expression of ML-IAP results in formation of a ML-IAP-Smac complex and disruption of the endogenous interaction between XIAP and mature Smac. These results suggest that ML-IAP might regulate apoptosis by sequestering Smac and preventing it from antagonizing XIAP-mediated inhibition of caspases, rather than by direct inhibition of caspases.


    Related Citations: 
    • Structure and Function Analysis of Peptide Antagonists of Melanoma Inhibitor of Apoptosis (ML-IAP)
      Franklin, M.C., Kadkhodayan, S., Ackerly, H., Alexandru, D., Distefano, M.D., Elliott, L.O., Flygare, J.A., Vucic, D., Deshayes, K., Fairbrother, W.J.
      (2003) Biochemistry 42: 8223
    • Mechanism of XIAP-mediated inhibition of caspase-9
      Shizoaki, E.N., Chai, J., Rigotti, D.J., Riedl, S.J., Li, P., Srinivasula, S.M., Alnemri, E.S., Fairman, R., Shi, Y.
      (2003) Mol Cell 11: 519

    Organizational Affiliation

    Department of Molecular Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Diablo homolog, mitochondrialC, D9Homo sapiensMutation(s): 0 
Gene Names: DIABLOSMAC
Find proteins for Q9NR28 (Homo sapiens)
Explore Q9NR28 
Go to UniProtKB:  Q9NR28
NIH Common Fund Data Resources
PHAROS  Q9NR28
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Baculoviral IAP repeat-containing protein 7A, B133Homo sapiensMutation(s): 0 
Gene Names: BIRC7KIAPLIVINMLIAPRNF50UNQ5800/PRO19607/PRO21344
EC: 2.3.2.27
Find proteins for Q96CA5 (Homo sapiens)
Explore Q96CA5 
Go to UniProtKB:  Q96CA5
NIH Common Fund Data Resources
PHAROS  Q96CA5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BTB
Query on BTB

Download CCD File 
B
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
LI
Query on LI

Download CCD File 
B
LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.856α = 90
b = 87.856β = 90
c = 74.634γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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