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PDBsum entry 1v0d

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protein metals links
Hydrolase PDB id
1v0d
Jmol
Contents
Protein chain
245 a.a. *
Metals
_PB
_ZN
_MG
Waters ×16
* Residue conservation analysis
PDB id:
1v0d
Name: Hydrolase
Title: Crystal structure of caspase-activated dnase (cad)
Structure: DNA fragmentation factor 40 kda subunit. Chain: a. Fragment: residues 1-329. Synonym: dff-40, caspase-activated deoxyribonuclease, caspase-activated dnasecad. Engineered: yes
Source: Mus musculus. Mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
2.60Å     R-factor:   0.218     R-free:   0.246
Authors: E.-J.Woo,Y.-G.Kim,M.-S.Kim,W.-D.Han,S.Shin,B.-H.Oh
Key ref:
E.J.Woo et al. (2004). Structural mechanism for inactivation and activation of CAD/DFF40 in the apoptotic pathway. Mol Cell, 14, 531-539. PubMed id: 15149602 DOI: 10.1016/S1097-2765(04)00258-8
Date:
26-Mar-04     Release date:   21-May-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O54788  (DFFB_MOUSE) -  DNA fragmentation factor subunit beta
Seq:
Struc:
344 a.a.
245 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   5 terms 
  Biological process     apoptotic process   4 terms 
  Biochemical function     protein binding     6 terms  

 

 
DOI no: 10.1016/S1097-2765(04)00258-8 Mol Cell 14:531-539 (2004)
PubMed id: 15149602  
 
 
Structural mechanism for inactivation and activation of CAD/DFF40 in the apoptotic pathway.
E.J.Woo, Y.G.Kim, M.S.Kim, W.D.Han, S.Shin, H.Robinson, S.Y.Park, B.H.Oh.
 
  ABSTRACT  
 
CAD/DFF40 is responsible for the degradation of chromosomal DNA into nucleosomal fragments and subsequent chromatin condensation during apoptosis. It exists as an inactive complex with its inhibitor ICAD/DFF45 in proliferating cells but becomes activated upon cleavage of ICAD/DFF45 into three domains by caspases in dying cells. The molecular mechanism underlying the control and activation of CAD/DFF40 was unknown. Here, the crystal structure of activated CAD/DFF40 reveals that it is a pair of molecular scissors with a deep active-site crevice that appears ideal for distinguishing internucleosomal DNA from nucleosomal DNA. Ensuing studies show that ICAD/DFF45 sequesters the nonfunctional CAD/DFF40 monomer and is also able to disassemble the functional CAD/DFF40 dimer. This capacity requires the involvement of the middle domain of ICAD/DFF45, which by itself cannot remain bound to CAD/DFF40 due to low binding affinity for the enzyme. Thus, the consequence of the caspase-cleavage of ICAD/DFF45 is a self-assembly of CAD/DFF40 into the active dimer.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structural Aspects of CAD(A) The monomeric structure. The secondary structures in Domains C2 and C3 are numbered in the order of appearance in the primary sequence. The invisible Domain C1 is represented as a sphere. The catalytically important histidine and lysine residues are shown in ball-and-sticks. The Zn^2+ binding site is shown with the Zn^2+ in orange and the cysteinyl sulfur in yellow. The inset shows the detailed interactions of the catalytic residues together with the final 2F[o] − F[c] electron density map (2.6 Å, 1.0 σ). The putative Mg^2+ is represented as a yellow sphere. Asp262, His308, and two loosely bound water molecules provide the metal coordination arms. Asn260 and a water molecule are on the hydrogen-bonded network with a metal-coordinating water.(B) The dimeric structure. In the side view (top), one subunit in blue is oriented similar to that in (A). The catalytic residues and the Zn^2+ binding site are shown. A DNA strand shows CAD on the same scale. The top view (bottom) is looking down along the molecular 2-fold axis. The crevice between the C3 domains spans 14 base pairs of the modeled DNA. Of note, the longest helix α4 fits into the major groove of the DNA.
Figure 4.
Figure 4. Estimation of Molecular WeightThe apparent molecular weight of each indicated complex was analyzed with a HiLoad 26/60 Superdex 75 column. The proteins were eluted at a rate of 1.5 ml/min with 30 mM TrisHCl buffer (pH 8.0) containing 100 mM NaCl and 3 mM dithiothreitol. For clarity, the elution profiles for only CAD:ICAD and CAD are shown. The size marker proteins were the TRAIL:DR5 complex (99 kDa), albumin (66 kDa), ovalbumin (45 kDa), chymotrypsinogen (25 kDa), and ribonuclease A (14 kDa). The calculated molecular weights of CAD, ICAD-L, ICAD-S, I1, I1-I2, and I2-I3 that we generated are 37.53, 34.42, 28.77, 12.87, 24.76, and 21.56 kDa, respectively.
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2004, 14, 531-539) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21322759 C.Andrady, S.K.Sharma, and K.A.Chester (2011).
Antibody-enzyme fusion proteins for cancer therapy.
  Immunotherapy, 3, 193-211.  
21182594 I.Kitazumi, and M.Tsukahara (2011).
Regulation of DNA fragmentation: the role of caspases and phosphorylation.
  FEBS J, 278, 427-441.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
20309017 S.J.McBryant, X.Lu, and J.C.Hansen (2010).
Multifunctionality of the linker histones: an emerging role for protein-protein interactions.
  Cell Res, 20, 519-528.  
19781927 B.He, N.Lu, and Z.Zhou (2009).
Cellular and nuclear degradation during apoptosis.
  Curr Opin Cell Biol, 21, 900-912.  
19958504 L.J.Wee, J.C.Tong, T.W.Tan, and S.Ranganathan (2009).
A multi-factor model for caspase degradome prediction.
  BMC Genomics, 10, S6.  
19459847 M.Mathew, and R.S.Verma (2009).
Humanized immunotoxins: a new generation of immunotoxins for targeted cancer therapy.
  Cancer Sci, 100, 1359-1365.  
18775303 C.E.Johnson, and S.Kornbluth (2008).
Caspase cleavage is not for everyone.
  Cell, 134, 720-721.  
18500987 C.Wu, Y.Zhang, Z.Sun, and P.Li (2008).
Molecular evolution of Cide family proteins: novel domain formation in early vertebrates and the subsequent divergence.
  BMC Evol Biol, 8, 159.  
18283539 J.Hanus, M.Kalinowska-Herok, and P.Widlak (2008).
The major apoptotic endonuclease DFF40/CAD is a deoxyribose-specific and double-strand-specific enzyme.
  Apoptosis, 13, 377-382.  
18514017 S.Nagata (2008).
Rheumatoid polyarthritis caused by a defect in DNA degradation.
  Cytokine Growth Factor Rev, 19, 295-302.  
18953336 W.Yang (2008).
An equivalent metal ion in one- and two-metal-ion catalysis.
  Nat Struct Mol Biol, 15, 1228-1231.  
17616520 A.V.Ageichik, K.Samejima, S.H.Kaufmann, and W.C.Earnshaw (2007).
Genetic analysis of the short splice variant of the inhibitor of caspase-activated DNase (ICAD-S) in chicken DT40 cells.
  J Biol Chem, 282, 27374-27382.  
17626049 F.Xiao, P.Widlak, and W.T.Garrard (2007).
Engineered apoptotic nucleases for chromatin research.
  Nucleic Acids Res, 35, e93.  
17082814 J.C.Timmer, and G.S.Salvesen (2007).
Caspase substrates.
  Cell Death Differ, 14, 66-72.  
17979851 S.Nagata (2007).
Autoimmune diseases caused by defects in clearing dead cells and nuclei expelled from erythroid precursors.
  Immunol Rev, 220, 237-250.  
17925275 S.R.Dunn, C.E.Schnitzler, and V.M.Weis (2007).
Apoptosis and autophagy as mechanisms of dinoflagellate symbiont release during cnidarian bleaching: every which way you lose.
  Proc Biol Sci, 274, 3079-3085.  
16470805 C.H.Lu, Y.S.Lin, Y.C.Chen, C.S.Yu, S.Y.Chang, and J.K.Hwang (2006).
The fragment transformation method to detect the protein structural motifs.
  Proteins, 63, 636-643.  
16699957 P.Widlak, and W.T.Garrard (2006).
The apoptotic endonuclease DFF40/CAD is inhibited by RNA, heparin and other polyanions.
  Apoptosis, 11, 1331-1337.  
16936813 P.Widlak, and W.T.Garrard (2006).
Unique features of the apoptotic endonuclease DFF40/CAD relative to micrococcal nuclease as a structural probe for chromatin.
  Biochem Cell Biol, 84, 405-410.  
16770683 S.R.Dunn, W.S.Phillips, J.W.Spatafora, D.R.Green, and V.M.Weis (2006).
Highly conserved caspase and Bcl-2 homologues from the sea anemone Aiptasia pallida: lower metazoans as models for the study of apoptosis evolution.
  J Mol Evol, 63, 95.  
15572351 C.Korn, S.R.Scholz, O.Gimadutdinow, R.Lurz, A.Pingoud, and G.Meiss (2005).
Interaction of DNA fragmentation factor (DFF) with DNA reveals an unprecedented mechanism for nuclease inhibition and suggests that DFF can be activated in a DNA-bound state.
  J Biol Chem, 280, 6005-6015.  
16204257 D.Lechardeur, S.Dougaparsad, C.Nemes, and G.L.Lukacs (2005).
Oligomerization state of the DNA fragmentation factor in normal and apoptotic cells.
  J Biol Chem, 280, 40216-40225.  
15909124 G.Banfalvi, M.Gacsi, G.Nagy, Z.B.Kiss, and A.G.Basnakian (2005).
Cadmium induced apoptotic changes in chromatin structure and subphases of nuclear growth during the cell cycle in CHO cells.
  Apoptosis, 10, 631-642.  
16150810 I.A.Cymerman, G.Meiss, and J.M.Bujnicki (2005).
DNase II is a member of the phospholipase D superfamily.
  Bioinformatics, 21, 3959-3962.  
15703174 J.D.West, C.Ji, and L.J.Marnett (2005).
Modulation of DNA fragmentation factor 40 nuclease activity by poly(ADP-ribose) polymerase-1.
  J Biol Chem, 280, 15141-15147.  
16103871 K.Samejima, and W.C.Earnshaw (2005).
Trashing the genome: the role of nucleases during apoptosis.
  Nat Rev Mol Cell Biol, 6, 677-688.  
15897201 M.Ghosh, G.Meiss, A.Pingoud, R.E.London, and L.C.Pedersen (2005).
Structural insights into the mechanism of nuclease A, a betabeta alpha metal nuclease from Anabaena.
  J Biol Chem, 280, 27990-27997.
PDB code: 1zm8
16133872 M.Kalinowska, W.Garncarz, M.Pietrowska, W.T.Garrard, and P.Widlak (2005).
Regulation of the human apoptotic DNase/RNase endonuclease G: involvement of Hsp70 and ATP.
  Apoptosis, 10, 821-830.  
16212486 N.Yan, and Y.Shi (2005).
Mechanisms of apoptosis through structural biology.
  Annu Rev Cell Dev Biol, 21, 35-56.  
15723341 P.Widlak, and W.T.Garrard (2005).
Discovery, regulation, and action of the major apoptotic nucleases DFF40/CAD and endonuclease G.
  J Cell Biochem, 94, 1078-1087.  
15771588 S.Nagata (2005).
DNA degradation in development and programmed cell death.
  Annu Rev Immunol, 23, 853-875.  
16236713 S.Reh, C.Korn, O.Gimadutdinow, and G.Meiss (2005).
Structural basis for stable DNA complex formation by the caspase-activated DNase.
  J Biol Chem, 280, 41707-41715.  
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.