PDBsum entry 1g3f

Apoptosis

PDB id: 1g3f

Contents

Protein chain

117 a.a. *

Ligands

ALA-VAL-PRO-ILE-ALA-GLN-LYS-SER-GLU

Metals

_ZN

* Residue conservation analysis

PDB id:

1g3f

Name:

Apoptosis

Title:

Nmr structure of a 9 residue peptide from smac/diablo complexed to the bir3 domain of xiap

Structure:

Inhibitor of apoptosis protein 3. Chain: a. Fragment: residues 241-356. Synonym: x-linked inhibitor of apoptosis protein, xiap. Engineered: yes. Smac. Chain: b. Fragment: 9 residue peptide. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the 9 residue peptide was chemically synthesized.

NMR struc:

1 models

Authors:

Z.Liu,C.Sun,E.T.Olejniczak,R.P.Meadows,S.F.Betz,T.Oost,J.Herrmann, J.C.Wu,S.W.Fesik

Key ref:

Z.Liu et al. (2000). Structural basis for binding of Smac/DIABLO to the XIAP BIR3 domain. Nature, 408, 1004-1008. PubMed id: 11140637 DOI: 10.1038/35050006

Date:

24-Oct-00 Release date: 10-Jan-01

Protein chain

P98170  (XIAP_HUMAN) -  E3 ubiquitin-protein ligase XIAP from Homo sapiens

Seq: 497 a.a.

Struc: 117 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: 10.1038/35050006

Nature 408:1004-1008 (2000)

PubMed id: 11140637

Structural basis for binding of Smac/DIABLO to the XIAP BIR3 domain.

Z.Liu, C.Sun, E.T.Olejniczak, R.P.Meadows, S.F.Betz, T.Oost, J.Herrmann, J.C.Wu, S.W.Fesik.

ABSTRACT

The inhibitor-of-apoptosis proteins (IAPs) regulate programmed cell death by inhibiting members of the caspase family of enzymes. Recently, a mammalian protein called Smac (also named DIABLO) was identified that binds to the IAPs and promotes caspase activation. Although undefined in the X-ray structure, the amino-terminal residues of Smac are critical for its function. To understand the structural basis for molecular recognition between Smac and the IAPs, we determined the solution structure of the BIR3 domain of X-linked IAP (XIAP) complexed with a functionally active nine-residue peptide derived from the N terminus of Smac. The peptide binds across the third beta-strand of the BIR3 domain in an extended conformation with only the first four residues contacting the protein. The complex is stabilized by four intermolecular hydrogen bonds, an electrostatic interaction involving the N terminus of the peptide, and several hydrophobic interactions. This structural information, along with the binding data from BIR3 and Smac peptide mutants reported here, should aid in the design of small molecules that may be used for the treatment of cancers that overexpress IAPs.

Selected figure(s)

Figure 1.
Figure 1: Similarity of IAP BIR domains and N-terminal sequences of IAP binding proteins. a, Sequence alignment of the BIR domains and surrounding residues of IAPs that bind to Smac or to Reaper, Hid and Grim. Identical residues are highlighted in blue, and highly homologous residues are highlighted in green. Residues that have intermolecular NOEs to the Smac peptide are indicated with asterisks. The secondary structural elements in the NMR structure of BIR3 are shown above the sequence. Circles denote the residues that were mutated and tested for caspase-9 inhibition (blue) and Smac peptide binding (red). Filled circles indicate a >10-fold decrease in caspase-9 inhibition or Smac peptide binding, half-filled circles indicate >5-fold decrease, and open circles indicate mutants that have no significant effect. b, Sequence alignment of the N-terminal residues of mature Smac, Hid, Reaper and Grim. Residue 1 of mature Smac corresponds to residue 56 of unprocessed Smac.

Figure 2.
Figure 2: Structure of the XIAP BIR3 domain/Smac peptide complex.
Figure 2 : Structure of the XIAP BIR3 domain/Smac peptide complex. Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, or to obtain a text description, please contact npg@nature.com-
a, Stereo view of 30 superimposed NMR-derived structures of the BIR3 domain of XIAP (showing residues 258–346) complexed to the Smac peptide (showing residues 1'–4'). The Smac peptide is colour-coded by atom type. The root mean square deviation (r.m.s.d.) to the mean coordinate positions for residues 260–345 of the protein is 0.38 0.04 Å for the backbone atoms (N, C^ , C') and 0.78 0.05 Å for all heavy atoms. The distance restraint force constant was 50 kcal mol^-1 Å ^-2, and no NOE was violated by more than 0.4 Å. The final energy of the NOE constraints (ENOE) was 24 13 kcal mol^-1. The torsion restraint force constant was 200 kcal mol^-1 rad^-2, and no torsion restraint was violated by more than 5°. Only the covalent geometry terms, NOE, torsion, and repulsive van der Waals terms were employed in the refinement. Even so, a large, negative Lennard–Jones potential energy was observed (-399 13 kcal mol^-1), indicating good non-bonded geometry. Procheck^25 analysis indicated that 97% of the residues are in allowed regions of the Ramachandran map. b, Ribbons^27 representation of the averaged minimized NMR structure of the XIAP BIR3/Smac peptide complex. c, Close-up of the binding site. The carbon atoms of the Smac peptide (A1'–I4') are shown in white. d, Surface representation of the binding site of the BIR3 domain bound to the Smac peptide.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2000, 408, 1004-1008) copyright 2000.