1OXN

Structure and Function Analysis of Peptide Antagonists of Melanoma Inhibitor of Apoptosis (ML-IAP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.Mausisa, G.Okawa, D.C.Ong, D.Vucic, D.Deshayes, K.Fairbrother, W.J.

(2003) Biochemistry 42: 8223-8231

  • DOI: 10.1021/bi034227t
  • Primary Citation of Related Structures:  1OXQ, 1OY7
  • Also Cited By: 1TW6, 2I3H, 2I3I

  • PubMed Abstract: 
  • Melanoma inhibitor of apoptosis (ML-IAP) is a potent anti-apoptotic protein that is upregulated in a number of melanoma cell lines but not expressed in most normal adult tissues. Overexpression of IAP proteins, such as ML-IAP or the ubiquitously expr ...

    Melanoma inhibitor of apoptosis (ML-IAP) is a potent anti-apoptotic protein that is upregulated in a number of melanoma cell lines but not expressed in most normal adult tissues. Overexpression of IAP proteins, such as ML-IAP or the ubiquitously expressed X-chromosome-linked IAP (XIAP), in human cancers has been shown to suppress apoptosis induced by a variety of stimuli. Peptides based on the processed N-terminus of Smac/DIABLO can negate the ability of overexpressed ML-IAP or XIAP to suppress drug-induced apoptosis. Such peptides have been demonstrated to bind to the single baculovirus IAP repeat (BIR) of ML-IAP and the third BIR of XIAP with similar high affinities (approximately 0.5 microM). Herein, we use phage-display of naïve peptide libraries and synthetic peptides to investigate the peptide-binding properties of ML-IAP-BIR and XIAP-BIR3. X-ray crystal structures of ML-IAP-BIR in complex with Smac- and phage-derived peptides, together with peptide structure-activity-relationship data, indicate that the peptides can be modified to provide increased binding affinity and selectivity for ML-IAP-BIR relative to XIAP-BIR3. For instance, substitution of Pro3' in the Smac-based peptide (AVPIAQKSE) with (2S,3S)-3-methylpyrrolidine-2-carboxylic acid [(3S)-methyl-proline] results in a peptide with 7-fold greater affinity for ML-IAP-BIR and about 100-fold specificity for ML-IAP-BIR relative to XIAP-BIR3.


    Related Citations: 
    • SMAC negatively regulates the anti-apoptotic activity of melanoma inhibitor of apoptosis (ML-IAP)
      Vucic, D.,Deshayes, K.,Ackerly, H.,Pisabarro, M.T.,Kadkhodayan, S.,Fairbrother, W.J.,Dixit, V.M.
      (2002) J.Biol.Chem. 277: 12275
    • ML-IAP, a novel inhibitor of apoptosis that is preferentially expressed in human melanomas
      Vucic, D.,Stennicke, H.R.,Pisabarro, M.T.,Salvesen, G.S.,Dixit, V.M.
      (2000) Curr.Biol. 10: 1359


    Organizational Affiliation

    Department of Protein Engineering, Genentech, Inc., One DNA Way, South San Francisco, California 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Baculoviral IAP repeat-containing protein 7
A, B, C, D, E
140Homo sapiensGene Names: BIRC7 (KIAP, LIVIN, MLIAP, RNF50)
EC: 6.3.2.-
Find proteins for Q96CA5 (Homo sapiens)
Go to Gene View: BIRC7
Go to UniProtKB:  Q96CA5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
AEAVPWKSE peptide
F
9N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
P33
Query on P33

Download SDF File 
Download CCD File 
D
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
HEPTAETHYLENE GLYCOL, PEG330
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.169 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 82.770α = 90.00
b = 82.770β = 90.00
c = 93.170γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSphasing
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-26
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance