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PDBsum entry 1qbh

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protein metals links
Apoptosis PDB id
1qbh
Jmol
Contents
Protein chain
101 a.a. *
Metals
_ZN
* Residue conservation analysis
PDB id:
1qbh
Name: Apoptosis
Title: Solution structure of a baculoviral inhibitor of apoptosis (iap) repeat
Structure: Inhibitor of apoptosis protein (2mihb/c-iap-1). Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
NMR struc: 20 models
Authors: M.G.Hinds,R.S.Norton,D.L.Vaux,C.L.Day
Key ref:
M.G.Hinds et al. (1999). Solution structure of a baculoviral inhibitor of apoptosis (IAP) repeat. Nat Struct Biol, 6, 648-651. PubMed id: 10404221 DOI: 10.1038/10701
Date:
20-Apr-99     Release date:   20-Oct-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q13490  (BIRC2_HUMAN) -  Baculoviral IAP repeat-containing protein 2
Seq:
Struc:
 
Seq:
Struc:
618 a.a.
101 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of cell differentiation   8 terms 
  Biochemical function     transcription coactivator activity     2 terms  

 

 
DOI no: 10.1038/10701 Nat Struct Biol 6:648-651 (1999)
PubMed id: 10404221  
 
 
Solution structure of a baculoviral inhibitor of apoptosis (IAP) repeat.
M.G.Hinds, R.S.Norton, D.L.Vaux, C.L.Day.
 
  ABSTRACT  
 
Members of the inhibitor of apoptosis (IAP) family of proteins are able to inhibit cell death following viral infection, during development or in cell lines in vitro. All IAP proteins bear one or more baculoviral IAP repeats (BIRs). Here we describe the solution structure of the third BIR domain from the mammalian IAP homolog B (MIHB/c-IAP-1). The BIR domain has a novel fold that is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues. The structure consists of a series of short alpha-helices and turns with the zinc packed in an unusually hydrophobic environment created by residues that are highly conserved among all BIRs.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Structure of BIR3 from MIHB. a, Ribbon depiction of the NMR structure closest to the geometric average of BIR3 (residues 268−356 are shown). Helices are shown in blue, ligand side chains in pink and the zinc in green. b, Stereo view of the backbone (N, C , C) traces (blue) of the 20 superimposed lowest energy structures obtained from the NMR restraints for BIR3 (residues 268−356 are shown). The side chains of the ligands are colored pink, the zinc is colored green, the side chains of the buried residues are colored yellow and the conserved extension shown in cyan. c, Surface representation of the NMR structure closest to the geometric average of BIR3 (residues 268−356). The side chains of the conserved hydrophobic (Met, Leu, Ile, Val, Pro, Phe, Tyr, Trp), basic (Lys, Arg) and acidic (Asp, Glu) amino acids are colored yellow, blue and red, respectively. The right view is in a similar orientation to the ribbon diagram and the left view is rotated 180° about the vertical axis.
Figure 3.
Figure 3. Stereo view of the zinc site from the structure closest to the geometric average of BIR3. Ligands are colored pink, the zinc is colored green and side chains within 3.5 Å of the ligand side chains are colored yellow. The backbone trace of surrounding amino acids is shown in blue.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 648-651) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21264751 K.Miura, W.Fujibuchi, K.Ishida, T.Naitoh, H.Ogawa, T.Ando, N.Yazaki, K.Watanabe, S.Haneda, C.Shibata, and I.Sasaki (2011).
Inhibitor of apoptosis protein family as diagnostic markers and therapeutic targets of colorectal cancer.
  Surg Today, 41, 175-182.  
20660790 A.H.Filipovich, K.Zhang, A.L.Snow, and R.A.Marsh (2010).
X-linked lymphoproliferative syndromes: brothers or distant cousins?
  Blood, 116, 3398-3408.  
19844666 J.Liebmann, V.Kolb-Bachofen, C.Mahotka, and C.V.Suschek (2010).
Photolytically generated nitric oxide inhibits caspase activity and results in AIF-mediated cell death.
  J Mol Med, 88, 279-287.  
20392747 M.Bader, E.Arama, and H.Steller (2010).
A novel F-box protein is required for caspase activation during cellular remodeling in Drosophila.
  Development, 137, 1679-1688.  
20651737 M.Gyrd-Hansen, and P.Meier (2010).
IAPs: from caspase inhibitors to modulators of NF-kappaB, inflammation and cancer.
  Nat Rev Cancer, 10, 561-574.  
19373243 P.D.Mace, S.Shirley, and C.L.Day (2010).
Assembling the building blocks: structure and function of inhibitor of apoptosis proteins.
  Cell Death Differ, 17, 46-53.  
19590513 S.Galbán, and C.S.Duckett (2010).
XIAP as a ubiquitin ligase in cellular signaling.
  Cell Death Differ, 17, 54-60.  
19021159 M.Orzáez, A.Gortat, L.Mondragón, and E.Pérez-Payá (2009).
Peptides and peptide mimics as modulators of apoptotic pathways.
  ChemMedChem, 4, 146-160.  
19698783 M.Sun, G.Meares, L.Song, and R.S.Jope (2009).
XIAP associates with GSK3 and inhibits the promotion of intrinsic apoptotic signaling by GSK3.
  Cell Signal, 21, 1857-1865.  
18931692 E.C.LaCasse, D.J.Mahoney, H.H.Cheung, S.Plenchette, S.Baird, and R.G.Korneluk (2008).
IAP-targeted therapies for cancer.
  Oncogene, 27, 6252-6275.  
18239605 L.Chu, J.Gu, L.Sun, Q.Qian, C.Qian, and X.Liu (2008).
Oncolytic adenovirus-mediated shRNA against Apollon inhibits tumor cell growth and enhances antitumor effect of 5-fluorouracil.
  Gene Ther, 15, 484-494.  
18854135 M.X.O'Riordan, L.D.Bauler, F.L.Scott, and C.S.Duckett (2008).
Inhibitor of apoptosis proteins in eukaryotic evolution and development: a model of thematic conservation.
  Dev Cell, 15, 497-508.  
18729734 S.M.Best (2008).
Viral subversion of apoptotic enzymes: escape from death row.
  Annu Rev Microbiol, 62, 171-192.  
18439892 S.M.Srinivasula, and J.D.Ashwell (2008).
IAPs: what's in a name?
  Mol Cell, 30, 123-135.  
17573556 A.M.Hunter, E.C.LaCasse, and R.G.Korneluk (2007).
The inhibitors of apoptosis (IAPs) as cancer targets.
  Apoptosis, 12, 1543-1568.  
17382285 A.R.Mufti, E.Burstein, and C.S.Duckett (2007).
XIAP: cell death regulation meets copper homeostasis.
  Arch Biochem Biophys, 463, 168-174.  
16946729 B.A.Callus, and D.L.Vaux (2007).
Caspase inhibitors: viral, cellular and chemical.
  Cell Death Differ, 14, 73-78.  
16543147 A.R.Mufti, E.Burstein, R.A.Csomos, P.C.Graf, J.C.Wilkinson, R.D.Dick, M.Challa, J.K.Son, S.B.Bratton, G.L.Su, G.J.Brewer, U.Jakob, and C.S.Duckett (2006).
XIAP Is a copper binding protein deregulated in Wilson's disease and other copper toxicosis disorders.
  Mol Cell, 21, 775-785.  
16493416 G.Lettre, and M.O.Hengartner (2006).
Developmental apoptosis in C. elegans: a complex CEDnario.
  Nat Rev Mol Cell Biol, 7, 97.  
16575541 K.Mizukawa, A.Kawamura, T.Sasayama, K.Tanaka, M.Kamei, M.Sasaki, and E.Kohmura (2006).
Synthetic Smac peptide enhances the effect of etoposide-induced apoptosis in human glioblastoma cell lines.
  J Neurooncol, 77, 247-255.  
15803136 D.L.Vaux, and J.Silke (2005).
IAPs, RINGs and ubiquitylation.
  Nat Rev Mol Cell Biol, 6, 287-297.  
16212486 N.Yan, and Y.Shi (2005).
Mechanisms of apoptosis through structural biology.
  Annu Rev Cell Dev Biol, 21, 35-56.  
14701799 J.Lewis, E.Burstein, S.B.Reffey, S.B.Bratton, A.B.Roberts, and C.S.Duckett (2004).
Uncoupling of the signaling and caspase-inhibitory properties of X-linked inhibitor of apoptosis.
  J Biol Chem, 279, 9023-9029.  
14970392 M.E.Van Eden, M.P.Byrd, K.W.Sherrill, and R.E.Lloyd (2004).
Translation of cellular inhibitor of apoptosis protein 1 (c-IAP1) mRNA is IRES mediated and regulated during cell stress.
  RNA, 10, 469-481.  
15623349 M.H.Aziz, A.S.Ghotra, Y.Shukla, and N.Ahmad (2004).
Ultraviolet-B radiation causes an upregulation of survivin in human keratinocytes and mouse skin.
  Photochem Photobiol, 80, 602-608.  
15520809 S.J.Riedl, and Y.Shi (2004).
Molecular mechanisms of caspase regulation during apoptosis.
  Nat Rev Mol Cell Biol, 5, 897-907.  
12952938 J.Wilson-Annan, L.A.O'Reilly, S.A.Crawford, G.Hausmann, J.G.Beaumont, L.P.Parma, L.Chen, M.Lackmann, T.Lithgow, M.G.Hinds, C.L.Day, J.M.Adams, and D.C.Huang (2003).
Proapoptotic BH3-only proteins trigger membrane integration of prosurvival Bcl-w and neutralize its activity.
  J Cell Biol, 162, 877-887.  
12959752 T.E.Clarke, and R.J.Clem (2003).
Insect defenses against virus infection: the role of apoptosis.
  Int Rev Immunol, 22, 401-424.  
12218061 C.R.Arnt, M.V.Chiorean, M.P.Heldebrant, G.J.Gores, and S.H.Kaufmann (2002).
Synthetic Smac/DIABLO peptides enhance the effects of chemotherapeutic agents by binding XIAP and cIAP1 in situ.
  J Biol Chem, 277, 44236-44243.  
12032073 H.W.Wang, T.V.Sharp, A.Koumi, G.Koentges, and C.Boshoff (2002).
Characterization of an anti-apoptotic glycoprotein encoded by Kaposi's sarcoma-associated herpesvirus which resembles a spliced variant of human survivin.
  EMBO J, 21, 2602-2615.  
12427028 L.E.Luque, K.P.Grape, and M.Junker (2002).
A highly conserved arginine is critical for the functional folding of inhibitor of apoptosis (IAP) BIR domains.
  Biochemistry, 41, 13663-13671.  
  11516343 A.M.Verhagen, E.J.Coulson, and D.L.Vaux (2001).
Inhibitor of apoptosis proteins and their relatives: IAPs and other BIRPs.
  Genome Biol, 2, REVIEWS3009.  
11313486 H.Harlin, S.B.Reffey, C.S.Duckett, T.Lindsten, and C.B.Thompson (2001).
Characterization of XIAP-deficient mice.
  Mol Cell Biol, 21, 3604-3608.  
11179890 J.H.Laity, B.M.Lee, and P.E.Wright (2001).
Zinc finger proteins: new insights into structural and functional diversity.
  Curr Opin Struct Biol, 11, 39-46.  
11341966 Q.Huang, Q.L.Deveraux, S.Maeda, H.R.Stennicke, B.D.Hammock, and J.C.Reed (2001).
Cloning and characterization of an inhibitor of apoptosis protein (IAP) from Bombyx mori.
  Biochim Biophys Acta, 1499, 191-198.  
11257232 S.J.Riedl, M.Renatus, R.Schwarzenbacher, Q.Zhou, C.Sun, S.W.Fesik, R.C.Liddington, and G.S.Salvesen (2001).
Structural basis for the inhibition of caspase-3 by XIAP.
  Cell, 104, 791-800.
PDB code: 1i3o
  11257231 Y.Huang, Y.C.Park, R.L.Rich, D.Segal, D.G.Myszka, and H.Wu (2001).
Structural basis of caspase inhibition by XIAP: differential roles of the linker versus the BIR domain.
  Cell, 104, 781-790.
PDB code: 1i4o
11084331 A.G.Uren, L.Wong, M.Pakusch, K.J.Fowler, F.J.Burrows, D.L.Vaux, and K.H.Choo (2000).
Survivin and the inner centromere protein INCENP show similar cell-cycle localization and gene knockout phenotype.
  Curr Biol, 10, 1319-1328.  
11084335 D.Vucic, H.R.Stennicke, M.T.Pisabarro, G.S.Salvesen, and V.M.Dixit (2000).
ML-IAP, a novel inhibitor of apoptosis that is preferentially expressed in human melanomas.
  Curr Biol, 10, 1359-1366.  
10899114 E.A.Mercer, L.Korhonen, Y.Skoglösa, P.A.Olsson, J.P.Kukkonen, and D.Lindholm (2000).
NAIP interacts with hippocalcin and protects neurons against calcium-induced cell death through caspase-3-dependent and -independent pathways.
  EMBO J, 19, 3597-3607.  
10702224 F.Li, P.L.Flanary, D.C.Altieri, and H.G.Dohlman (2000).
Cell division regulation by BIR1, a member of the inhibitor of apoptosis family in yeast.
  J Biol Chem, 275, 6707-6711.  
  11073801 J.C.Reed (2000).
Mechanisms of apoptosis.
  Am J Pathol, 157, 1415-1430.  
10949039 L.Chantalat, D.A.Skoufias, J.P.Kleman, B.Jung, O.Dideberg, and R.L.Margolis (2000).
Crystal structure of human survivin reveals a bow tie-shaped dimer with two unusual alpha-helical extensions.
  Mol Cell, 6, 183-189.
PDB code: 1e31
10822260 P.Bangs, and K.White (2000).
Regulation and execution of apoptosis during Drosophila development.
  Dev Dyn, 218, 68-79.  
10669762 R.R.Hozak, G.A.Manji, and P.D.Friesen (2000).
The BIR motifs mediate dominant interference and oligomerization of inhibitor of apoptosis Op-IAP.
  Mol Cell Biol, 20, 1877-1885.  
  10655220 S.Lisi, I.Mazzon, and K.White (2000).
Diverse domains of THREAD/DIAP1 are required to inhibit apoptosis induced by REAPER and HID in Drosophila.
  Genetics, 154, 669-678.  
11057900 S.W.Fesik (2000).
Insights into programmed cell death through structural biology.
  Cell, 103, 273-282.  
10949038 S.W.Muchmore, J.Chen, C.Jakob, D.Zakula, E.D.Matayoshi, W.Wu, H.Zhang, F.Li, S.C.Ng, and D.C.Altieri (2000).
Crystal structure and mutagenic analysis of the inhibitor-of-apoptosis protein survivin.
  Mol Cell, 6, 173-182.
PDB code: 1m4m
11139813 J.S.Braun, E.I.Tuomanen, and J.L.Cleveland (1999).
Neuroprotection by caspase inhibitors.
  Expert Opin Investig Drugs, 8, 1599-1610.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.