PDBsum entry 4b5h

Hydrolase/DNA

PDB id: 4b5h

Contents

Protein chain

259 a.a.

DNA/RNA

Metals

_MN

PDB id:

4b5h

Name:

Hydrolase/DNA

Title:

Substate bound inactive mutant of neisseria ap endonuclease in presence of metal ions

Structure:

Putative exodeoxyribonuclease. Chain: a. Synonym: neisseria ap endonuclease. Engineered: yes. Mutation: yes. 5'-d( Gp Cp Tp Ap Cp 3Drp Cp Ap Tp Cp Gp)-3'. Chain: u. Synonym: DNA 11mer containing abasic residue. Engineered: yes.

Source:

Neisseria meningitidis. Organism_taxid: 487. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 487

Resolution:

3.05Å R-factor: 0.196 R-free: 0.295

Authors:

D.Lu,J.Silhan,J.T.Macdonald,E.P.Carpenter,K.Jensen,C.M.Tang, G.S.Baldwin,P.S.Freemont

Key ref:

D.Lu et al. (2012). Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis. Proc Natl Acad Sci U S A, 109, 16852-16857. PubMed id: 23035246

Date:

03-Aug-12 Release date: 17-Oct-12

Protein chain

Q7DD47  (Q7DD47_NEIMB) -  Exodeoxyribonuclease from Neisseria meningitidis serogroup B (strain MC58)

Seq: 259 a.a.

Struc: 259 a.a.*

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

DNA/RNA chains

G-C-T-A-C-3DR-C-A-T-C-G 11 bases

C-G-A-T-G-G-G-T-A-G-C 11 bases

Enzyme reactions

• Enzyme class: E.C.3.1.11.2 - exodeoxyribonuclease Iii.
• Reaction: Degradation of double-stranded DNA. It acts progressively in a 3'- to 5'-direction, releasing nucleoside 5'-phosphates.

Proc Natl Acad Sci U S A 109:16852-16857 (2012)

PubMed id: 23035246

Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis.

D.Lu, J.Silhan, J.T.MacDonald, E.P.Carpenter, K.Jensen, C.M.Tang, G.S.Baldwin, P.S.Freemont.

ABSTRACT

Base excision repair (BER) is a highly conserved DNA repair pathway throughout all kingdoms from bacteria to humans. Whereas several enzymes are required to complete the multistep repair process of damaged bases, apurinic-apyrimidic (AP) endonucleases play an essential role in enabling the repair process by recognizing intermediary abasic sites cleaving the phosphodiester backbone 5' to the abasic site. Despite extensive study, there is no structure of a bacterial AP endonuclease bound to substrate DNA. Furthermore, the structural mechanism for AP-site cleavage is incomplete. Here we report a detailed structural and biochemical study of the AP endonuclease from Neisseria meningitidis that has allowed us to capture structural intermediates providing more complete snapshots of the catalytic mechanism. Our data reveal subtle differences in AP-site recognition and kinetics between the human and bacterial enzymes that may reflect different evolutionary pressures.