PDBsum entry 2kqb

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protein metals links
Lyase PDB id
Protein chain
55 a.a. *
* Residue conservation analysis
PDB id:
Name: Lyase
Title: First pbz domain of human aplf protein
Structure: Aprataxin and pnk-like factor. Chain: a. Fragment: sequence database residues 363-451, pbz-type 1 domain. Synonym: apurinic-apyrimidinic endonuclease aplf, pnk and aptx-like fha domain-containing protein, xrcc1-interacting protein 1. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: aplf, c2orf13, palf, xip1. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 25 models
Authors: D.Neuhaus,S.Eustermann,C.Brockmann,J.Yang
Key ref:
S.Eustermann et al. (2010). Solution structures of the two PBZ domains from human APLF and their interaction with poly(ADP-ribose). Nat Struct Biol, 17, 241-243. PubMed id: 20098424 DOI: 10.1038/nsmb.1747
04-Nov-09     Release date:   19-Jan-10    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q8IW19  (APLF_HUMAN) -  Aprataxin and PNK-like factor
511 a.a.
55 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - DNA-(apurinic or apyrimidinic site) lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.


DOI no: 10.1038/nsmb.1747 Nat Struct Biol 17:241-243 (2010)
PubMed id: 20098424  
Solution structures of the two PBZ domains from human APLF and their interaction with poly(ADP-ribose).
S.Eustermann, C.Brockmann, P.V.Mehrotra, J.C.Yang, D.Loakes, S.C.West, I.Ahel, D.Neuhaus.
Addition of poly(ADP-ribose) (PAR) is an important post-translational modification in higher eukaryotes. Several DNA repair and checkpoint proteins possess specific PAR-binding zinc-finger (PBZ) modules critical for function. Here, we present solution structures of the two PBZ modules of aprataxin and PNK-like factor (APLF), revealing a novel type of zinc finger. By combining in vivo PAR-binding data with NMR interaction data using PAR fragments, we propose a structural basis for PBZ-PAR recognition.
  Selected figure(s)  
Figure 1.
(a) Domain architecture and partial sequence of human APLF. The PBZ modules (F1 and F2) are boxed, metal-binding residues are pink, key PAR-binding residues are violet and the additional loop of F1 is orange. Highly conserved residues are bold (Supplementary Fig. 11), and asterisks indicate residues mutated in our study. (b) Solution structures of APLF F1 and F2, colored as in a with zinc ions as blue spheres and helices dark red; the ten lowest-energy structures are shown. Structural statistics appear in Supplementary Table 1 and Supplementary Figure 2.
Figure 2.
(a) Structure of PAR and fragments; ADPR is the fragment within the gray area and RFA is that within the blue area (the darker blue area being common to both). The labels "protein" and "distal" are purely to indicate chain direction. (b,c) Structures of RFA bound to APLF F1 (b) and APLF F2 (c). In b, the RFA molecule is schematically extended to show how PAR may bind; c shows a close-up of key interactions (including H-bond adenosyl NH[2]–S426 O, dotted line).
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2010, 17, 241-243) copyright 2010.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20853319 A.Mangerich, and A.Bürkle (2011).
How to kill tumor cells with inhibitors of poly(ADP-ribosyl)ation.
  Int J Cancer, 128, 251-265.  
20830433 J.L.Furman, P.W.Mok, S.Shen, C.I.Stains, and I.Ghosh (2011).
A turn-on split-luciferase sensor for the direct detection of poly(ADP-ribose) as a marker for DNA repair and cell death.
  Chem Commun (Camb), 47, 397-399.  
20439749 G.Y.Li, R.D.McCulloch, A.L.Fenton, M.Cheung, L.Meng, M.Ikura, and C.A.Koch (2010).
Structure and identification of ADP-ribose recognition motifs of APLF and role in the DNA damage response.
  Proc Natl Acad Sci U S A, 107, 9129-9134.  
20603072 R.Krishnakumar, and W.L.Kraus (2010).
The PARP side of the nucleus: molecular actions, physiological outcomes, and clinical targets.
  Mol Cell, 39, 8.  
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