PDBsum entry 1l2c

Hydrolase/DNA

PDB id: 1l2c

Contents

Protein chain

259 a.a. *

DNA/RNA

Metals

_ZN

Waters ×141

* Residue conservation analysis

PDB id:

1l2c

Name:

Hydrolase/DNA

Title:

Mutm (fpg)-DNA estranged thymine mismatch recognition complex

Structure:

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

Source:

Synthetic: yes. Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: mutm. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Trimer (from PQS)

Resolution:

2.20Å R-factor: 0.213 R-free: 0.247

Authors:

J.C.Fromme,G.L.Verdine

Key ref:

J.C.Fromme and G.L.Verdine (2002). Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM. Nat Struct Biol, 9, 544-552. PubMed id: 12055620 DOI: 10.1038/nsb809

Date:

20-Feb-02 Release date: 14-Jun-02

Protein chain

P84131  (P84131_GEOSE) -  Formamidopyrimidine-DNA glycosylase from Geobacillus stearothermophilus

Seq: 274 a.a.

Struc: 259 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

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

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

Enzyme reactions

• Enzyme class 1: E.C.3.2.2.23 - DNA-formamidopyrimidine glycosylase.
• Reaction: Hydrolysis of DNA containing ring-opened N(7)-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimide.
• 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: 10.1038/nsb809

Nat Struct Biol 9:544-552 (2002)

PubMed id: 12055620

Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM.

J.C.Fromme, G.L.Verdine.

ABSTRACT

MutM is a bacterial 8-oxoguanine glycosylase responsible for initiating base-excision repair of oxidized guanine residues in DNA. Here we report five different crystal structures of MutM-DNA complexes that represent different steps of the repair reaction cascade catalyzed by the protein and also differ in the identity of the base opposite the lesion (the 'estranged' base). These structures reveal that the MutM active site performs the multiple steps of base-excision and 3' and 5' nicking with minimal rearrangement of the DNA backbone.

Selected figure(s)

Figure 3.
Figure 3. Comparison of active sites from three different stages of catalysis. a, Active site structure of the rAb C recognition complex 6. The density corresponding to the C1' atom and its hydroxyl is weak, presumably owing to several rotamers about the C2'-C3' bond.

Figure 4.
Figure 4. Recognition of the estranged base by MutM. a, Recognition in the rAb C complex. b, Recognition in the rAb G complex. c, Recognition in the rAb T complex. Dashes indicate hydrogen bonds, and red circles denote a van der Waals interaction. d−f, Structural formulae schematics of the mode of recognition seen in (a−c), respectively.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 544-552) copyright 2002.

Figures were selected by an automated process.