MG_498_MONOMER – formamidopyrimidine-DNA glycosylase

Name
WID	MG_498_MONOMER
Name	formamidopyrimidine-DNA glycosylase
Cross references	PDB: 1K82

Genetics
Gene	MG_498

Structure
Sequence	1 51 101 151 201 251 MPELPEVTTVINELKETVLNKPLDQVQVNLRKVLKNIDPQLLNKQLKNQF FTDIKRKGKYIIFLLSNGLYLVSHLRMEGKYFFEERGSKFNQKHVLVEFH FDDGSQLNYHDTRQFGTFHLYEKLEQAAQLNKLAFDPLEAGFDYRKIFQK AQNSKRKVKTFILDQTVISGIGNIYADEILFASKINPETMVDQLTIKEIE ILCKNATKILAKAIVMKGTTISSFSFKKDHTGGYQNFLKVHTKKDQPCSV CNQLIVKKKINGRGSYFCLNCQKITTKVSTKLNP* 50 100 150 200 250 285
Is N‑terminal methionine cleaved	Yes
Prosthetic groups	(1) ZN [c]
DNA footprint	Length: 9 (nt), Binding: dsDNA, Region: dsDNA
Empirical formula (pH 7.5)	H₂₃₈₇C₁₄₈₇N₃₉₅O₄₁₈S₉
Molecular weight (pH 7.5; Da)	32774.75
Extinction coefficient (260 nm, 25C, pH 7.0)	14035
Instability index	21.84
Is stable	True
Aliphatic index	90.60
GRAVY (25C, pH 7.0)	-0.380
Half life (OD (600 nm) = 0.3, M9 media, 36C; min)	1200

Synthesis
Localization	c

Function
Enzyme	3'-apurinic/apyrimidinic lyase [c]: dRibose5P_dRibose5P + H2O ⇒ (2) DR5P + H base excision (4,6-diamino-5-N-formamidopyrimidine) [c]: FAPydAMP + H2O ⇒ DR5P + FAPyAD base excision (2,6-diamino-4-hydroxy-5-formamidopyrimidine) [c]: FAPydGMP + H2O ⇒ DR5P + FAPyGN base excision (8-hydroxyadenine) [c]: H2O + oxo8dAMP ⇒ DR5P + oxo8AD base excision (8-Oxo-guanine; 8-hydroxyguanine) [c]: H2O + oxo8dGMP ⇒ DR5P + oxo8GN
Reaction participant	DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DNA gyrase) DNA_GYRASE[d] + MG_498_MONOMER[c] ⇒ DNA_GYRASE[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DNA topoisomerase I) MG_122_MONOMER[d] + MG_498_MONOMER[c] ⇒ MG_122_MONOMER[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DnaA 4mer-(3)ATP-(1)ADP) MG_469_4MER_3ATP_ADP[d] + MG_498_MONOMER[c] ⇒ MG_469_4MER_3ATP_ADP[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DNA polymerase core, β-clamp, and γ-complex) DNA_POLYMERASE_CORE_BETA_CLAMP_GAMMA_COMPLEX[d] + MG_498_MONOMER[c] ⇒ DNA_POLYMERASE_CORE_BETA_CLAMP_GAMMA_COMPLEX[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DNA ligase, NAD-dependent) MG_254_MONOMER[d] + MG_498_MONOMER[c] ⇒ MG_254_MONOMER[c] + MG_498_MONOMER[d] ... 30 more DNA bound protein release (formamidopyrimidine-DNA glycosylase releases putative DNA integrity scanning protein) MG_105_OCTAMER[d] + MG_498_MONOMER[c] ⇒ MG_105_OCTAMER[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DnaA 6mer-(5)ATP-(1)ADP) MG_469_6MER_5ATP_ADP[d] + MG_498_MONOMER[c] ⇒ MG_469_6MER_5ATP_ADP[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DnaA 3mer-(2)ATP-(1)ADP) MG_469_3MER_2ATP_ADP[d] + MG_498_MONOMER[c] ⇒ MG_469_3MER_2ATP_ADP[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DNA polymerase (2) core, β-clamp, γ-complex, and primase) DNA_POLYMERASE_2CORE_BETA_CLAMP_GAMMA_COMPLEX_PRIMASE[d] + MG_498_MONOMER[c] ⇒ DNA_POLYMERASE_2CORE_BETA_CLAMP_GAMMA_COMPLEX_PRIMASE[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases adenine-specific DNA modification methylase) MG_184_DIMER[d] + MG_498_MONOMER[c] ⇒ MG_184_DIMER[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases LuxR bacterial regulatory protein, putative) MG_428_DIMER[d] + MG_498_MONOMER[c] ⇒ MG_428_DIMER[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DnaA-ATP 7mer) MG_469_7MER_ATP[d] + MG_498_MONOMER[c] ⇒ MG_469_7MER_ATP[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DnaA-ADP) MG_469_1MER_ADP[d] + MG_498_MONOMER[c] ⇒ MG_469_1MER_ADP[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases single-strand binding protein family, octamer) MG_091_OCTAMER[d] + MG_498_MONOMER[c] ⇒ MG_091_OCTAMER[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DNA-directed RNA polymerase holoenzyme) MG_498_MONOMER[c] + RNA_POLYMERASE_HOLOENZYME[d] ⇒ MG_498_MONOMER[d] + RNA_POLYMERASE_HOLOENZYME[c] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DNA-directed RNA polymerase) MG_498_MONOMER[c] + RNA_POLYMERASE[d] ⇒ MG_498_MONOMER[d] + RNA_POLYMERASE[c] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DnaA 5mer-(4)ATP-(1)ADP) MG_469_5MER_4ATP_ADP[d] + MG_498_MONOMER[c] ⇒ MG_469_5MER_4ATP_ADP[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DnaA-ATP 6mer) MG_469_6MER_ATP[d] + MG_498_MONOMER[c] ⇒ MG_469_6MER_ATP[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases replicative DNA helicase) MG_094_HEXAMER[d] + MG_498_MONOMER[c] ⇒ MG_094_HEXAMER[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DnaA 2mer-(1)ATP-(1)ADP) MG_469_2MER_1ATP_ADP[d] + MG_498_MONOMER[c] ⇒ MG_469_2MER_1ATP_ADP[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases ferric uptake repressor) MG_236_MONOMER[d] + MG_498_MONOMER[c] ⇒ MG_236_MONOMER[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DnaA-ATP) MG_469_1MER_ATP[d] + MG_498_MONOMER[c] ⇒ MG_469_1MER_ATP[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases Spx subfamily protein) MG_127_MONOMER[d] + MG_498_MONOMER[c] ⇒ MG_127_MONOMER[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DNA polymerase III, beta clamp) MG_001_DIMER[d] + MG_498_MONOMER[c] ⇒ MG_001_DIMER[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DnaA-ATP 5mer) MG_469_5MER_ATP[d] + MG_498_MONOMER[c] ⇒ MG_469_5MER_ATP[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DnaA 7mer-(6)ATP-(1)ADP) MG_469_7MER_6ATP_ADP[d] + MG_498_MONOMER[c] ⇒ MG_469_7MER_6ATP_ADP[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases Uncharacterized HTH-type transcriptional regulator) MG_101_MONOMER[d] + MG_498_MONOMER[c] ⇒ MG_101_MONOMER[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DnaA-ATP 4mer) MG_469_4MER_ATP[d] + MG_498_MONOMER[c] ⇒ MG_469_4MER_ATP[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DNA polymerase core, β-clamp, and primase) DNA_POLYMERASE_CORE_BETA_CLAMP_PRIMASE[d] + MG_498_MONOMER[c] ⇒ DNA_POLYMERASE_CORE_BETA_CLAMP_PRIMASE[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases heat-inducible transcription repressor HrcA, putative) MG_205_DIMER[d] + MG_498_MONOMER[c] ⇒ MG_205_DIMER[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DnaA-ATP 2mer) MG_469_2MER_ATP[d] + MG_498_MONOMER[c] ⇒ MG_469_2MER_ATP[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases Chromosome Segregation Protein SMC with SCP Proteins-ADP) MG_213_214_298_6MER_ADP[d] + MG_498_MONOMER[c] ⇒ MG_213_214_298_6MER_ADP[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases type I restriction modification DNA specificity domain protein) MG_438_MONOMER[d] + MG_498_MONOMER[c] ⇒ MG_438_MONOMER[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases DnaA-ATP 3mer) MG_469_3MER_ATP[d] + MG_498_MONOMER[c] ⇒ MG_469_3MER_ATP[c] + MG_498_MONOMER[d] DNA bound protein release (formamidopyrimidine-DNA glycosylase releases topoisomerase IV) MG_203_204_TETRAMER[d] + MG_498_MONOMER[c] ⇒ MG_203_204_TETRAMER[c] + MG_498_MONOMER[d]

Comments
Comments	Functional Macromolecule Functional as monomer [PUB_0074]. Coenzymes Interacts with 1 ZN per monomer as prosthetic group [74]. N-terminal methionine cleavage Shewanella oneidensis MR-1 homolog undergoes N-terminal methionine cleavage [PUB_0280]. DNA-binding Fpg footprint is 9 nt [PUB_0719]. Ogg1 footprint is 10 nt [PUB_0719, PUB_0720, PUB_0721, PUB_0722]. Fpg footprint is 12 nt [PUB_0717].
References	Bruner SD, Norman DP, Verdine GL. Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA. Nature 403, 859-66 (2000). WholeCell: PUB_0721, PubMed: 10706276 Castaing B, Boiteux S, Zelwer C. DNA containing a chemically reduced apurinic site is a high affinity ligand for the E. coli formamidopyrimidine-DNA glycosylase. Nucleic Acids Res 20, 389-94 (1992). WholeCell: PUB_0074, PubMed: 1741272 Fromme JC, Bruner SD, Yang W, Karplus M, Verdine GL. Product-assisted catalysis in base-excision DNA repair. Nat Struct Biol 10, 204-11 (2003). WholeCell: PUB_0720, PubMed: 12592398 Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res 17, 1362-77 (2007). WholeCell: PUB_0280, PubMed: 17690205 Miao F, Bouziane M, O'Connor TR. Interaction of the recombinant human methylpurine-DNA glycosylase (MPG protein) with oligodeoxyribonucleotides containing xsDNA hypoxanthine or abasic sites. Nucleic Acids Res 26, 4034-41 (1998). WholeCell: PUB_0717, PubMed: 9705516 ... 2 more Norman DP, Bruner SD, Verdine GL. Coupling of substrate recognition and catalysis by a human base-excision DNA repair protein. J Am Chem Soc 123, 359-60 (2001). WholeCell: PUB_0722, PubMed: 11456534 Sidorenko VS, Zharkov DO. Correlated cleavage of damaged DNA by bacterial and human 8-oxoguanine-DNA glycosylases. Biochemistry 47, 8970-6 (2008). WholeCell: PUB_0719, PubMed: 18672903

Metadata
Created	2012-10-01 15:07:55
Last updated	2012-10-01 15:14:38