PDBsum entry: 1yql

Hydrolase/DNA

PDB id: 1yql

Contents

Protein chain

314 a.a. *

DNA/RNA

Metals

_CA ×2

Waters ×117

* Residue conservation analysis

PDB id:

1yql

Name:

Hydrolase/DNA

Title:

Catalytically inactive hogg1 crosslinked with 7-deaza-8- azaguanine containing DNA

Structure:

5'-d(p Gp Gp Tp Ap Gp Ap Cp Cp Tp Gp Gp Ap C)-3'. Chain: b. Engineered: yes. 5'-d(p Gp Tp Cp Cp Ap (Ppw)p Gp Tp Cp Tp Ap C)- 3'. Chain: c. Engineered: yes. N-glycosylase/DNA lyase. Chain: a.

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:

2.60Å R-factor: 0.213 R-free: 0.260

Authors:

A.Banerjee,W.Yang,M.Karplus,G.L.Verdine

Key ref:

A.Banerjee et al. (2005). Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA. Nature, 434, 612-618. PubMed id: 15800616 DOI: 10.1038/nature03458

Date:

02-Feb-05 Release date: 05-Apr-05

Protein chain

O15527  (OGG1_HUMAN) -  N-glycosylase/DNA lyase

Seq: 345 a.a.

Struc: 314 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.2.99.18 - DNA-(apurinic or apyrimidinic site) lyase.
• Reaction: The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.

 Gene Ontology (GO) functional annotation 

• Cellular component: nucleus (5 terms)
• Biological process: metabolic process (10 terms)
• Biochemical function: catalytic activity (10 terms)

DOI no: 10.1038/nature03458

Nature 434:612-618 (2005)

PubMed id: 15800616

Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA.

A.Banerjee, W.Yang, M.Karplus, G.L.Verdine.

ABSTRACT

How DNA repair proteins distinguish between the rare sites of damage and the vast expanse of normal DNA is poorly understood. Recognizing the mutagenic lesion 8-oxoguanine (oxoG) represents an especially formidable challenge, because this oxidized nucleobase differs by only two atoms from its normal counterpart, guanine (G). Here we report the use of a covalent trapping strategy to capture a human oxoG repair protein, 8-oxoguanine DNA glycosylase I (hOGG1), in the act of interrogating normal DNA. The X-ray structure of the trapped complex features a target G nucleobase extruded from the DNA helix but denied insertion into the lesion recognition pocket of the enzyme. Free energy difference calculations show that both attractive and repulsive interactions have an important role in the preferential binding of oxoG compared with G to the active site. The structure reveals a remarkably effective gate-keeping strategy for lesion discrimination and suggests a mechanism for oxoG insertion into the hOGG1 active site.

Selected figure(s)

Figure 1.
Figure 1: Generation of 8-oxoguanine (oxoG), its recognition by human 8-oxoguanine DNA glycosylase (hOGG1) and overview of the structure-based trapping strategy used here to obtain a complex of hOGG1 bound to undamaged DNA. a, Structural differences between G and oxoG. Inset: close-up view of the lesion recognition pocket of hOGG1 showing residues involved in recognition of oxoG and catalysis, highlighting the direct contact between N7 H and Gly 42, and the catalytic nucleophile Lys 249. b, Schematic overview of the crosslinking and validation strategy. c, Details of the trapping chemistry. Attachment of a tether at the N4 position of cytosine is known to preserve Watson -Crick pairing in protein-unbound DNA, with the tether protruding into the major groove^31. d, Sequence of the DNA duplex used in this work.

Figure 5.
Figure 5: Superposition of the oxoG complex with the G complex in the region around the protein -DNA interface. a, Overlay using the protein backbone only (grey) for superposition, with the DNA backbone of the oxoG complex in green and G complex in gold. Spheres indicate Ca^2+ ions. Residues that interact with DNA through backbone amide nitrogen atoms are denoted in magenta, whereas those that interact through side chains are in black. Dotted lines indicate hydrogen bonds. b, Ribbon diagram in the same orientation as a, but showing the whole DNA duplex. c, Comparison of the DNA in the two complexes, using the left flank for superposition. Arrows labelled a, b and c indicate bonds that have undergone significant rotations: +110° for a (C4' -C5' bond of the residue 3' to oxoG/G), +119° for b (C4' -C5' bond of oxoG/G) and -151° for c (P -O5' bond of oxoG/G).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2005, 434, 612-618) copyright 2005.

Figures were selected by the author.