PDBsum entry 6cvs

Hydrolase/DNA

PDB id: 6cvs

Contents

Protein chains

180 a.a.

DNA/RNA

Ligands

AMP ×2

BME ×2

Metals

_ZN ×2

Waters ×498

PDB id:

6cvs

Name:

Hydrolase/DNA

Title:

Human aprataxin (aptx) l248m bound to DNA, amp and zn product

Structure:

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

Source:

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

Resolution:

2.11Å R-factor: 0.175 R-free: 0.196

Authors:

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

Key ref:

P.Tumbale et al. Mechanism of aptx nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease.. Embo j, . PubMed id: 29934293

Date:

28-Mar-18 Release date: 04-Jul-18

Protein chains

Q7Z2E3  (APTX_HUMAN) -  Aprataxin from Homo sapiens

Seq: 356 a.a.

Struc: 180 a.a.*

* PDB and UniProt seqs differ at 5 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