PDBsum entry 4ndh

DNA binding protein/DNA

PDB id: 4ndh

Contents

Protein chains

180 a.a.

DNA/RNA

Ligands

AMP ×2

Metals

_ZN ×2

Waters ×516

PDB id:

4ndh

Name:

DNA binding protein/DNA

Title:

Human aprataxin (aptx) bound to DNA, amp, and zn - product complex

Structure:

Aprataxin. Chain: a, b. Synonym: forkhead-associated domain histidine triad-like protein, fha-hit. Engineered: yes. 5'-d(p Gp Tp Tp Cp Tp Ap Gp Ap Ap C)-3'. Chain: d, e, g, h. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: aptx, axa1. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes

Resolution:

1.85Å R-factor: 0.164 R-free: 0.196

Authors:

M.J.Schellenberg,P.S.Tumbale,R.S.Williams

Key ref:

P.Tumbale et al. (2014). Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity. Nature, 506, 111-115. PubMed id: 24362567 DOI: 10.1038/nature12824

Date:

26-Oct-13 Release date: 18-Dec-13

Protein chains

Q7Z2E3  (APTX_HUMAN) -  Aprataxin from Homo sapiens

Seq: 356 a.a.

Struc: 180 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

DNA/RNA chains

G-T-T-C-T-A-G-A-A-C 10 bases

G-T-T-C-T-A-G-A-A-C 10 bases

G-T-T-C-T-A-G-A-A-C 10 bases

G-T-T-C-T-A-G-A-A-C 10 bases

Enzyme reactions

• Enzyme class 1: E.C.3.6.1.71 - adenosine-5'-diphospho-5'-[DNA] diphosphatase.
• Reaction:
  1. a 5'-end adenosine-5'-diphospho-5'-2'-deoxyribonucleoside-DNA + H2O = a 5'-end 5'-phospho-2'-deoxyribonucleoside-DNA + AMP + 2 H⁺
  2. a 5'-end adenosine-5'-diphospho-5'-ribonucleoside- 2'-deoxyribonucleotide-DNA + H2O = a 5'-end 5'-phospho-ribonucleoside- 2'-deoxyribonucleotide-DNA + AMP + 2 H⁺

5'-end adenosine-5'-diphospho-5'-2'-deoxyribonucleoside-DNA + H2O = 5'-end 5'-phospho-2'-deoxyribonucleoside-DNA + AMP (Bound ligand (Het Group name = AMP) corresponds exactly) + 2 × H(+)

5'-end adenosine-5'-diphospho-5'-ribonucleoside- 2'-deoxyribonucleotide-DNA + H2O = 5'-end 5'-phospho-ribonucleoside- 2'-deoxyribonucleotide-DNA + AMP (Bound ligand (Het Group name = AMP) corresponds exactly) + 2 × H(+)

• Enzyme class 2: E.C.3.6.1.72 - DNA-3'-diphospho-5'-guanosine diphosphatase.
• Reaction: a 3'-end 2'-deoxyribonucleotide-3'-diphospho-5'-guanosine-DNA + H2O = a 3'-end 2'-deoxyribonucleotide 3'-phosphate-DNA + GMP + 2 H⁺

3'-end 2'-deoxyribonucleotide-3'-diphospho-5'-guanosine-DNA + H2O = 3'-end 2'-deoxyribonucleotide 3'-phosphate-DNA + GMP (Bound ligand (Het Group name = AMP) matches with 95.83% similarity) + 2 × H(+)

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.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/nature12824

Nature 506:111-115 (2014)

PubMed id: 24362567

Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity.

P.Tumbale, J.S.Williams, M.J.Schellenberg, T.A.Kunkel, R.S.Williams.

ABSTRACT

Faithful maintenance and propagation of eukaryotic genomes is ensured by three-step DNA ligation reactions used by ATP-dependent DNA ligases. Paradoxically, when DNA ligases encounter nicked DNA structures with abnormal DNA termini, DNA ligase catalytic activity can generate and/or exacerbate DNA damage through abortive ligation that produces chemically adducted, toxic 5'-adenylated (5'-AMP) DNA lesions. Aprataxin (APTX) reverses DNA adenylation but the context for deadenylation repair is unclear. Here we examine the importance of APTX to RNase-H2-dependent excision repair (RER) of a lesion that is very frequently introduced into DNA, a ribonucleotide. We show that ligases generate adenylated 5' ends containing a ribose characteristic of RNase H2 incision. APTX efficiently repairs adenylated RNA-DNA, and acting in an RNA-DNA damage response (RDDR), promotes cellular survival and prevents S-phase checkpoint activation in budding yeast undergoing RER. Structure-function studies of human APTX-RNA-DNA-AMP-Zn complexes define a mechanism for detecting and reversing adenylation at RNA-DNA junctions. This involves A-form RNA binding, proper protein folding and conformational changes, all of which are affected by heritable APTX mutations in ataxia with oculomotor apraxia 1. Together, these results indicate that accumulation of adenylated RNA-DNA may contribute to neurological disease.