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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1k82
Original Entry
Title:
Hydrolase/dna
Compound:
5'-d(*cp*cp*ap*gp*gp*ap*(ped)p*gp*ap*ap*gp*cp*c)- 3'
Mutant:
No
UniProt/Swiss-Prot:
P05523-FPG_ECOLI
EC Class:
3.2.2.23
Other CSA Entries:
Overview of all sites for 1k82
Homologues of 1k82
Entries for UniProt/Swiss-Prot: P05523
Entries for EC: 3.2.2.23
Other Databases:
PDB entry: 1k82
PDBsum entry: 1k82
UniProt/Swiss-Prot: P05523
IntEnz entry: 3.2.2.23
Literature Report:
Introduction:
Formamidopyrimidine-DNA glycosylase is a bifunctional base excision repair enzyme - it has both DNA glycosylase and AP lyase activities - and is involved in removal of oxidised purines from oxidatively-damaged DNA in initiation of the base excision repair pathway.
Mechanism:
Formamidopyrimidine-DNA glycosylase catalyses the hydrolysis of DNA. 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.

Nucelophilic attack at C1' of the deoxyribose sugar by Pro 1 and protonation of O4' by Glu 2 leads to base displacement and the opening of the deoxyribose ring. A Schiff base involving Pro 1 is formed with O4' stabilised by hydrogen bonding to Glu 2 and Arg 258. Lys 56 as a general base deprotonates C2', and then protonates the 3' phosphate leading to beta-elimination. Deprotonation of C4' is followed by protonation of the 5' phosphate by Arg 258 and the second beta-elimination.
Sites:

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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
PROA 1 2Sidechain
NucleophileSubstrate
Nucleophilically attacks the deoxyribose ring to cause ring cleavage.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12065399 Current protein Mutagenesis of residue
PubMed ID 10921868 Current protein Structural similarity to homologue of known mechanism
PubMed ID 11912217 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 10921868 Current protein Residue is positioned appropriately (ligand position hypothetical)
PubMed ID 12065399 Current protein Conservation of residue
PubMed ID 10921868 Current protein Computer modelling
PubMed ID 9030608 Current protein Residue is covalently bound to intermediate, based on structural data

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLUA 2 3Sidechain
Acid/baseSubstrate
Acts as a general acid catalyst and also stabilises the transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11912217 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 10921868 Current protein Residue is positioned appropriately (ligand position hypothetical)
PubMed ID 11106507 Current protein Mutagenesis of residue
PubMed ID 12065399 Current protein Conservation of residue
PubMed ID 11106507 Current protein Conservation of residue
PubMed ID 10921868 Current protein Computer modelling
PubMed ID 10921868 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
LYSA 56 57Sidechain
Acid/baseSubstrate
Acts as a general acid/base catalyst.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12065399 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 10921868 Current protein Residue is positioned appropriately (ligand position hypothetical)
PubMed ID 9826758 Current protein Conservation of residue
PubMed ID 10921868 Current protein Computer modelling
PubMed ID 11912217 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 9826758 Current protein Mutagenesis of residue
PubMed ID 12065399 Current protein Conservation of residue
PubMed ID 10921868 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ARGA 258 259Sidechain
Acid/baseSubstrate
Acts as a general acid/base catalyst, and stabilises the transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11912217 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 10921868 Current protein Structural similarity to homologue of known mechanism
PubMed ID 12065399 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 12065399 Current protein Conservation of residue
PubMed ID 10921868 Current protein Computer modelling
References:
1
Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8.
M. Sugahara and T. Mikawa and T. Kumasaka and M. Yamamoto and R. Kato and K. Fukuyama and Y. Inoue and S. Kuramitsu
EMBO J 19, (15) 3857-69, (2000).
10921868
2
Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA.
R. Gilboa and D. O. Zharkov and G. Golan and A. S. Fernandes and S. E. Gerchman and E. Matz and J. H. Kycia and A. P. Grollman and G. Shoham
J Biol Chem 277, (22) 19811-6, (2002).
11912217
3
NH2-terminal proline acts as a nucleophile in the glycosylase/AP-lyase reaction catalyzed by Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg) protein.
D. O. Zharkov and R. A. Rieger and C. R. Iden and A. P. Grollman
J Biol Chem 272, (8) 5335-41, (1997).
9030608
4
Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA.
L. Serre and K. Pereira de J├ęsus and S. Boiteux and C. Zelwer and B. Castaing
EMBO J 21, (12) 2854-65, (2002).
12065399
5
Involvement of phylogenetically conserved acidic amino acid residues in catalysis by an oxidative DNA damage enzyme formamidopyrimidine glycosylase.
O. V. Lavrukhin and R. S. Lloyd
Biochemistry 39, (49) 15266-71, (2000).
11106507
6
Role of lysine-57 in the catalytic activities of Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg protein).
O. M. Sidorkina and J. Laval
Nucleic Acids Res 26, (23) 5351-7, (1998).
9826758
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