PDBsum entry 3spd

Hydrolase/DNA

PDB id: 3spd

Contents

Protein chains

200 a.a.

DNA/RNA

Ligands

SO4 ×16

Metals

_ZN ×4

Waters ×1105

PDB id:

3spd

Name:

Hydrolase/DNA

Title:

Crystal structure of aprataxin ortholog hnt3 in complex with DNA

Structure:

Aprataxin-like protein. Chain: a, b, c, d. Fragment: unp residues 33-232. Synonym: hnt3 protein, hit family protein 3. Engineered: yes. Mutation: yes. DNA (5'-d( Tp Ap Tp Tp Cp Cp Gp Ap Tp Ap Gp Tp Gp Ap C)- 3'). Chain: e, g.

Source:

Schizosaccharomyces pombe. Fission yeast. Organism_taxid: 284812. Strain: atcc 38366 / 972. Gene: hnt3, spcc18.09c. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: DNA oligonucleotides were synthesized from shanghai

Resolution:

1.91Å R-factor: 0.177 R-free: 0.212

Authors:

Y.Gong,D.Zhu,J.Ding,C.Dou,X.Ren,T.Jiang,D.Wang

Key ref:

Y.Gong et al. (2011). Crystal structures of aprataxin ortholog Hnt3 reveal the mechanism for reversal of 5'-adenylated DNA. Nat Struct Biol, 18, 1297-1299. PubMed id: 21984208

Date:

01-Jul-11 Release date: 12-Oct-11

Protein chains

O74859  (APTX_SCHPO) -  Aprataxin-like protein from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 232 a.a.

Struc: 200 a.a.*

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

DNA/RNA chains

T-A-T-T-C-C-G-A-T-A-G-T-G-A 14 bases

G-T-C-A-C-T-A-T-C-G-G-A-A-T 14 bases

T-A-T-T-C-C-G-A-T-A-G-T-G-A 14 bases

G-T-C-A-C-T-A-T-C-G-G-A-A-T 14 bases

Enzyme reactions

• Enzyme class 2: 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⁺
• Enzyme class 3: 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⁺

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

Nat Struct Biol 18:1297-1299 (2011)

PubMed id: 21984208

Crystal structures of aprataxin ortholog Hnt3 reveal the mechanism for reversal of 5'-adenylated DNA.

Y.Gong, D.Zhu, J.Ding, C.N.Dou, X.Ren, L.Gu, T.Jiang, D.C.Wang.

ABSTRACT

Aprataxin is a DNA deadenylase that resolves DNA 5'-AMP termini and reverses abortive DNA ligation. The crystal structures of Schizosaccharomyces pombe aprataxin Hnt3 in its apo form and in complex to dsDNA and dsDNA-AMP reveal how Hnt3 recognizes and processes 5'-adenylated DNA in a structure-specific manner. The bound DNA adopts a 5'-flap conformation that facilitates 5'-AMP access to the active site, where AMP cleavage occurs by a canonical catalytic mechanism.