PDBsum entry 2kqc

Lyase

PDB id: 2kqc

Contents

Protein chain

47 a.a. *

Metals

_ZN

* Residue conservation analysis

PDB id:

2kqc

Name:

Lyase

Title:

Second pbz domain of human aplf protein

Structure:

Aprataxin and pnk-like factor. Chain: a. Fragment: sequence database residues 368-451, pbz-type 2 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

Date:

04-Nov-09 Release date: 19-Jan-10

Protein chain

Q8IW19  (APLF_HUMAN) -  Aprataxin and PNK-like factor from Homo sapiens

Seq: 511 a.a.

Struc: 47 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.-.-

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.

ABSTRACT

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.