PDBsum entry 2nol

Hydrolase, lyase/DNA

PDB id: 2nol

Contents

Protein chain

314 a.a. *

DNA/RNA

Metals

_CA ×2

Waters ×153

* Residue conservation analysis

PDB id:

2nol

Name:

Hydrolase, lyase/DNA

Title:

Structure of catalytically inactive human 8-oxoguanine glycosylase distal crosslink to oxog DNA

Structure:

5'-d( Gp Gp Tp Ap Gp Ap Cp Cp Tp Gp Gp Ap Cp Gp C)-3'. Chain: b. Engineered: yes. 5'-d( Gp Cp Gp Tp Cp Cp Ap (G42)p Gp Tp Cp Tp Ap Cp C)-3'. Chain: c. Engineered: yes. N-glycosylase/DNA lyase. Chain: a. Fragment: 8-oxoguanine DNA glycosylase, DNA-(apurinic or apyrimidinic

Source:

Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Gene: ogg1, mmh, mutm, ogh1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Trimer (from PQS)

Resolution:

2.57Å R-factor: 0.206 R-free: 0.250

Authors:

A.Banerjee,C.T.Radom,G.L.Verdine

Key ref:

C.T.Radom et al. (2007). Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations. J Biol Chem, 282, 9182-9194. PubMed id: 17114185 DOI: 10.1074/jbc.M608989200

Date:

25-Oct-06 Release date: 21-Nov-06

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 5 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-8OG-G-T-C-T-A-C-C 15 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: 10.1074/jbc.M608989200

J Biol Chem 282:9182-9194 (2007)

PubMed id: 17114185

Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations.

C.T.Radom, A.Banerjee, G.L.Verdine.

ABSTRACT

The human 8-oxoguanine DNA glycosylase (hOGG1) protein is responsible for initiating base excision DNA repair of the endogenous mutagen 8-oxoguanine. Like nearly all DNA glycosylases, hOGG1 extrudes its substrate from the DNA helix and inserts it into an extrahelical enzyme active site pocket lined with residues that participate in lesion recognition and catalysis. Structural analysis has been performed on mutant versions of hOGG1 having changes in catalytic residues but not on variants having altered 7,8-dihydro-8-oxoguanine (oxoG) contact residues. Here we report high resolution structural analysis of such recognition variants. We found that Ala substitution at residues that contact the phosphate 5' to the lesion (H270A mutation) and its Watson-Crick face (Q315A mutation) simply removed key functionality from the contact interface but otherwise had no effect on structure. Ala substitution at the only residue making an oxoG-specific contact (G42A mutation) introduced torsional stress into the DNA contact surface of hOGG1, but this was overcome by local interactions within the folded protein, indicating that this oxoG recognition motif is "hardwired." Introduction of a side chain intended to sterically obstruct the active site pocket (Q315F mutation) led to two different structures, one of which (Q315F(*149)) has the oxoG lesion in an exosite flanking the active site and the other of which (Q315F(*292)) has the oxoG inserted nearly completely into the lesion recognition pocket. The latter structure offers a view of the latest stage in the base extrusion pathway yet observed, and its lack of catalytic activity demonstrates that the transition state for displacement of the lesion base is geometrically demanding.

Selected figure(s)

Figure 2.
FIGURE 2. Effect of the H270A mutation. A, view of the active site region of the H270A structure (side chains in teal and DNA backbone in gold) showing four water molecules (green spheres) that coordinate the 5'-phosphate of oxoG to the protein with dashed lines denoting hydrogen bonds. B, least squares superposition showing the active site region of the H270A structure (colored as in A) with that of the proximally cross-linked recognition complex (LRC^*149; Protein Data Bank code 1YQR (28)) (white side chains and DNA backbone).

Figure 3.
FIGURE 3. Role of Gly-42 and consequences of the G42A mutation. A, stereoview of the G42A complex (protein chain in teal except for Ala-42, which is shown in magenta; DNA backbone in gold; and waters as green spheres) showing extensive hydrogen bonding interactions among residues of the Gly-42 loop and surrounding residues. B, schematic detailing the interactions from A. C, superposition of the G42A complex (colored as in A) with the LRC (protein and DNA in white and waters in gray). Inset, close-up view of the G42A complex showing the near eclipsing interaction of Ala-42 and the hydrogen bond formed between N7-H of oxoG and the carbonyl oxygen of Ala-42.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 9182-9194) copyright 2007.

Figures were selected by an automated process.