PDBsum entry 1m3h

Hydrolase/DNA

PDB id: 1m3h

Contents

Protein chain

314 a.a. *

DNA/RNA

Metals

_CA

Waters ×92

* Residue conservation analysis

PDB id:

1m3h

Name:

Hydrolase/DNA

Title:

Crystal structure of hogg1 d268e mutant with product oligonucleotide

Structure:

5'-d(p Gp Gp Tp Ap Gp Ap Cp Cp Tp Gp Gp Ap Cp Gp C)-3'. Chain: b. Engineered: yes. 5'-d(p Gp Cp Gp Tp Cp Cp Ap (Ddx))-3'. Chain: c. Engineered: yes. 5'-d(p Gp Tp Cp Tp Ap Cp C)-3'. Chain: d. Engineered: yes.

Source:

Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Gene: ogg1. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Tetramer (from PQS)

Resolution:

2.05Å R-factor: 0.239 R-free: 0.282

Authors:

S.J.Chung,G.L.Verdine

Key ref:

S.J.Chung and G.L.Verdine (2004). Structures of end products resulting from lesion processing by a DNA glycosylase/lyase. Chem Biol, 11, 1643-1649. PubMed id: 15610848 DOI: 10.1016/j.chembiol.2004.09.014

Date:

27-Jun-02 Release date: 20-Apr-04

Protein chain

O15527  (OGG1_HUMAN) -  N-glycosylase/DNA lyase from Homo sapiens

Seq: 345 a.a.

Struc: 314 a.a.*

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

DNA/RNA chains

G-G-T-A-G-A-C-C-T-G-G-A-C-G-C 15 bases

G-C-G-T-C-C-A-DDX 8 bases

G-T-C-T-A-C-C 7 bases

Enzyme reactions

• Enzyme class 1: E.C.3.2.2.- - ?????
• Enzyme class 2: 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.

DOI no: 10.1016/j.chembiol.2004.09.014

Chem Biol 11:1643-1649 (2004)

PubMed id: 15610848

Structures of end products resulting from lesion processing by a DNA glycosylase/lyase.

S.J.Chung, G.L.Verdine.

ABSTRACT

DNA glycosylase/lyases initiate the repair of damaged nucleobases in the genome by catalyzing excision of aberrant nucleobases and nicking of the lesion-containing DNA strand. Nearly all of these proteins have the unusual property of remaining tightly bound in vitro to the end products of the reaction cascade. We have taken advantage of this property to crystallize and structurally characterize the end product resulting from complete DNA processing by a catalytically active mutant form of human 8-oxoguanine DNA glycosylase (D268E hOgg1). The resulting structure is consistent with the currently accepted catalytic mechanism for the protein. Unexpectedly, however, soaking of a nucleobase analog into the crystals results in religation of the DNA backbone in situ.

Selected figure(s)

Figure 1.
Figure 1. Proposed Mechanism for hOgg1-Catalyzed Excision of 8-Oxoguanine (oxoG) and Cleavage of the DNA Strand

Figure 2.
Figure 2. Active Site Structure of the End-Product Complex

The above figures are reprinted by permission from Cell Press: Chem Biol (2004, 11, 1643-1649) copyright 2004.

Figures were selected by an automated process.