PDBsum entry 6erh

DNA binding protein

PDB id: 6erh

Contents

Protein chains

490 a.a.

534 a.a.

DNA/RNA

Ligands

LYS-PRO-ARG-GLY-LEU-PHE-SER

PRO-ARG-GLY-LEU-PHE-SER

SO4 ×2

Waters ×33

PDB id:

6erh

Name:

DNA binding protein

Title:

Complex of xlf and heterodimer ku bound to DNA

Structure:

X-ray repair cross-complementing protein 6. Chain: a, c. Synonym: 5'-deoxyribose-5-phosphate lyase ku70,5'-drp lyase ku70,70 kda subunit of ku antigen,atp-dependent DNA helicase 2 subunit 1,atp- dependent DNA helicase ii 70 kda subunit,ctc box-binding factor 75 kda subunit,ctcbf,DNA repair protein xrcc6,lupus ku autoantigen protein p70,ku70,thyroid-lupus autoantigen,tlaa,x-ray repair complementing defective repair in chinese hamster cells 6. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: xrcc6, g22p1. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf21. Gene: xrcc5, g22p2. Synthetic: yes.

Resolution:

2.80Å R-factor: 0.226 R-free: 0.252

Authors:

C.Nemoz,P.Legrand,V.Ropars,J.B.Charbonnier

Key ref:

C.Nemoz et al. (2018). XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining. Nat Struct Mol Biol, 25, 971-980. PubMed id: 30291363 DOI: 10.1038/s41594-018-0133-6

Date:

18-Oct-17 Release date: 17-Oct-18

Protein chains

P12956  (XRCC6_HUMAN) -  X-ray repair cross-complementing protein 6 from Homo sapiens

Seq: 609 a.a.

Struc: 490 a.a.

Protein chains

P13010  (XRCC5_HUMAN) -  X-ray repair cross-complementing protein 5 from Homo sapiens

Seq: 732 a.a.

Struc: 534 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

C-G-C-G-C-C-C-A-G-C-T-T-C-C-A-G-C-T-A-A-T-A-A-A-C-T-A-A-A-A-A-C 32 bases

G-T-T-T-T-T-A-G-T-T-T-A-T-T-G-G-G-C-G-C-G 21 bases

C-G-C-G-C-C-C-A-G-C-T-C-A-G-C-T-A-A-T-A-A-A-C-T-A-A-A-A-A-C 30 bases

G-T-T-T-T-T-A-G-T-T-T-A-T-T-G-G-G-C-G-C-G 21 bases

Enzyme reactions

• Enzyme class 2: Chains A, B, C, D: E.C.3.6.4.- - ?????
• Enzyme class 3: Chains A, C: E.C.4.2.99.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1038/s41594-018-0133-6

Nat Struct Mol Biol 25:971-980 (2018)

PubMed id: 30291363

XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining.

C.Nemoz, V.Ropars, P.Frit, A.Gontier, P.Drevet, J.Yu, R.Guerois, A.Pitois, A.Comte, C.Delteil, N.Barboule, P.Legrand, S.Baconnais, Y.Yin, S.Tadi, E.Barbet-Massin, I.Berger, E.Le Cam, M.Modesti, E.Rothenberg, P.Calsou, J.B.Charbonnier.

ABSTRACT

The Ku70-Ku80 (Ku) heterodimer binds rapidly and tightly to the ends of DNA double-strand breaks and recruits factors of the non-homologous end-joining (NHEJ) repair pathway through molecular interactions that remain unclear. We have determined crystal structures of the Ku-binding motifs (KBM) of the NHEJ proteins APLF (A-KBM) and XLF (X-KBM) bound to a Ku-DNA complex. The two KBM motifs bind remote sites of the Ku80 α/β domain. The X-KBM occupies an internal pocket formed by an unprecedented large outward rotation of the Ku80 α/β domain. We observe independent recruitment of the APLF-interacting protein XRCC4 and of XLF to laser-irradiated sites via binding of A- and X-KBMs, respectively, to Ku80. Finally, we show that mutation of the X-KBM and A-KBM binding sites in Ku80 compromises both the efficiency and accuracy of end joining and cellular radiosensitivity. A- and X-KBMs may represent two initial anchor points to build the intricate interaction network required for NHEJ.