PDBsum entry 2ea0

Hydrolase/DNA

PDB id: 2ea0

Contents

Protein chain

254 a.a. *

DNA/RNA

Ligands

SO4 ×5

GOL

Metals

_ZN

Waters ×412

* Residue conservation analysis

PDB id:

2ea0

Name:

Hydrolase/DNA

Title:

Crystal structure of the DNA repair enzyme endonuclease-viii (nei) from e. Coli in complex with ap-site containing DNA substrate

Structure:

5'-d(p Gp Gp Cp Tp Tp Cp Ap Tp Cp Cp Tp G)-3'. Chain: b. Engineered: yes. 5'-d(p Cp Ap Gp Gp Ap (Ped)p Gp Ap Ap Gp Cp C)-3'. Chain: c. Engineered: yes. Endonuclease viii. Chain: a. Synonym: DNA glycosylase/ap lyase nei, DNA-apurinic or apyrimidinic

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Gene: nei. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.40Å R-factor: 0.160 R-free: 0.204

Authors:

G.Golan,D.O.Zharov,A.P.Grollman,G.Shoham

Key ref:

G.Golan et al. Active site plasticity of endonuclease VIII: conformational changes compensating for different substrate and mutations of critical residues. To be published, .

Date:

29-Jan-07 Release date: 26-Feb-08

Protein chain

P50465  (END8_ECOLI) -  Endonuclease 8 from Escherichia coli (strain K12)

Seq: 263 a.a.

Struc: 254 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

G-G-C-T-T-C-A-T-C-C-T-G 12 bases

C-A-G-G-A-PED-G-A-A-G-C-C 12 bases

Enzyme reactions

• Enzyme class 2: E.C.3.2.2.- - ?????
• Enzyme class 3: E.C.4.2.99.18 - DNA-(apurinic or apyrimidinic site) lyase.
• Reaction: 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)- 2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho- 2'-deoxyribonucleoside-DNA + 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.