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P05523

- FPG_ECOLI

UniProt

P05523 - FPG_ECOLI

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Protein
Formamidopyrimidine-DNA glycosylase
Gene
mutM, fpg, b3635, JW3610
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG) and its derivatives such as guanidinohydantoin:C and spiroiminodihydantoin:C, however it also acts on thymine glycol:G, 5,6-dihydrouracil:G and 5-hydroxyuracil:G. Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Cleaves ssDNA containing an AP site.2 Publications

Catalytic activityi

Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine.UniRule annotation
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.UniRule annotation

Cofactori

Binds 1 zinc ion per subunit.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei2 – 21Schiff-base intermediate with DNA
Active sitei3 – 31Proton donor Inferred
Active sitei57 – 571Proton donor; for beta-elimination activity Inferred
Binding sitei90 – 901DNA
Binding sitei109 – 1091DNA
Binding sitei150 – 1501DNA
Active sitei259 – 2591Proton donor; for delta-elimination activity Inferred

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri235 – 26935FPG-typeUniRule annotation
Add
BLAST

GO - Molecular functioni

  1. DNA N-glycosylase activity Source: EcoliWiki
  2. DNA-(apurinic or apyrimidinic site) lyase activity Source: EcoliWiki
  3. damaged DNA binding Source: EcoCyc
  4. endonuclease activity Source: EcoliWiki
  5. metal ion binding Source: EcoliWiki
  6. oxidized purine nucleobase lesion DNA N-glycosylase activity Source: EcoCyc
  7. oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity Source: EcoCyc
  8. zinc ion binding Source: EcoliWiki
Complete GO annotation...

GO - Biological processi

  1. DNA catabolic process, endonucleolytic Source: GOC
  2. base-excision repair, AP site formation Source: EcoCyc
  3. cellular response to DNA damage stimulus Source: EcoliWiki
  4. nucleic acid phosphodiester bond hydrolysis Source: GOC
  5. nucleotide-excision repair Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase, Lyase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG10329-MONOMER.
ECOL316407:JW3610-MONOMER.
MetaCyc:EG10329-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Formamidopyrimidine-DNA glycosylase (EC:3.2.2.23)
Short name:
Fapy-DNA glycosylase
Alternative name(s):
DNA-(apurinic or apyrimidinic site) lyase MutM (EC:4.2.99.18)
Short name:
AP lyase MutM
Gene namesi
Name:mutM
Synonyms:fpg
Ordered Locus Names:b3635, JW3610
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10329. mutM.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi3 – 31E → Q: Strong decrease of glycosylase activity; slight decrease of AP lyase activity. 1 Publication
Mutagenesisi6 – 61E → Q: Decrease of glycosylase activity; no effect on AP lyase activity. 1 Publication
Mutagenesisi90 – 901H → A: Increase of substrate affinity and decrease of activity. 1 Publication
Mutagenesisi107 – 1071D → N: No effect on glycosylase and AP lyase activity. 1 Publication
Mutagenesisi109 – 1091R → A: Over 100-fold decrease of activity. 1 Publication
Mutagenesisi110 – 1101R → A: Over 100-fold increase of substrate affinity and decrease of activity. 1 Publication
Mutagenesisi132 – 1321E → Q: Decrease of glycosylase activity; slight decrease of AP lyase activity. 1 Publication
Mutagenesisi160 – 1601D → N: No effect on glycosylase and AP lyase activity. 1 Publication
Mutagenesisi174 – 1741E → Q: Strong decrease of glycosylase activity; slight decrease of AP lyase activity. 1 Publication
Mutagenesisi218 – 2181K → T: Slight increase of substrate affinity and decrease of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 269268Formamidopyrimidine-DNA glycosylaseUniRule annotation
PRO_0000170822Add
BLAST

Proteomic databases

PaxDbiP05523.
PRIDEiP05523.

Expressioni

Gene expression databases

GenevestigatoriP05523.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

DIPiDIP-10286N.
IntActiP05523. 12 interactions.
STRINGi511145.b3635.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 1815
Beta strandi22 – 298
Beta strandi32 – 365
Helixi39 – 435
Beta strandi46 – 494
Beta strandi51 – 555
Beta strandi58 – 625
Beta strandi67 – 715
Turni73 – 753
Beta strandi77 – 848
Beta strandi93 – 975
Beta strandi102 – 1065
Beta strandi113 – 1186
Beta strandi120 – 1234
Helixi124 – 1263
Helixi140 – 1478
Helixi154 – 1585
Turni161 – 1633
Helixi169 – 17911
Helixi187 – 1893
Helixi192 – 21120
Helixi231 – 2333
Turni245 – 2473
Beta strandi252 – 2565
Beta strandi259 – 2635
Turni265 – 2673

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K82X-ray2.10A/B/C/D2-269[»]
ProteinModelPortaliP05523.
SMRiP05523. Positions 2-269.

Miscellaneous databases

EvolutionaryTraceiP05523.

Family & Domainsi

Domaini

The zinc-finger is necessary for DNA binding.UniRule annotation

Sequence similaritiesi

Belongs to the FPG family.

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG0266.
HOGENOMiHOG000020881.
KOiK10563.
OMAiDHVDLKL.
OrthoDBiEOG6QP131.
PhylomeDBiP05523.

Family and domain databases

HAMAPiMF_00103. Fapy_DNA_glycosyl.
InterProiIPR015886. DNA_glyclase/AP_lyase_DNA-bd.
IPR015887. DNA_glyclase_Znf_dom_DNA_BS.
IPR000191. DNA_glycosylase/AP_lyase.
IPR012319. DNA_glycosylase/AP_lyase_cat.
IPR020629. Formamido-pyr_DNA_Glyclase.
IPR010979. Ribosomal_S13-like_H2TH.
IPR000214. Znf_DNA_glyclase/AP_lyase.
IPR010663. Znf_DNA_glyclase/IsotRNA_synth.
[Graphical view]
PfamiPF01149. Fapy_DNA_glyco. 1 hit.
PF06831. H2TH. 1 hit.
PF06827. zf-FPG_IleRS. 1 hit.
[Graphical view]
SMARTiSM00898. Fapy_DNA_glyco. 1 hit.
[Graphical view]
SUPFAMiSSF46946. SSF46946. 1 hit.
SSF81624. SSF81624. 1 hit.
TIGRFAMsiTIGR00577. fpg. 1 hit.
PROSITEiPS51068. FPG_CAT. 1 hit.
PS01242. ZF_FPG_1. 1 hit.
PS51066. ZF_FPG_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P05523-1 [UniParc]FASTAAdd to Basket

« Hide

MPELPEVETS RRGIEPHLVG ATILHAVVRN GRLRWPVSEE IYRLSDQPVL    50
SVQRRAKYLL LELPEGWIII HLGMSGSLRI LPEELPPEKH DHVDLVMSNG 100
KVLRYTDPRR FGAWLWTKEL EGHNVLTHLG PEPLSDDFNG EYLHQKCAKK 150
KTAIKPWLMD NKLVVGVGNI YASESLFAAG IHPDRLASSL SLAECELLAR 200
VIKAVLLRSI EQGGTTLKDF LQSDGKPGYF AQELQVYGRK GEPCRVCGTP 250
IVATKHAQRA TFYCRQCQK 269
Length:269
Mass (Da):30,290
Last modified:January 23, 2007 - v3
Checksum:i01826F7E0E4686EC
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M86305 Genomic DNA. Translation: AAA03747.1.
X06036 Genomic DNA. Translation: CAA29431.1.
L10328 Genomic DNA. Translation: AAA61988.1.
U00039 Genomic DNA. Translation: AAB18612.1.
U00096 Genomic DNA. Translation: AAC76659.1.
AP009048 Genomic DNA. Translation: BAE77657.1.
M60670 Genomic DNA. Translation: AAA24045.1.
PIRiA30254. DGECFP.
RefSeqiNP_418092.1. NC_000913.3.
YP_491798.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC76659; AAC76659; b3635.
BAE77657; BAE77657; BAE77657.
GeneIDi12933569.
946765.
KEGGiecj:Y75_p3539.
eco:b3635.
PATRICi32122757. VBIEscCol129921_3755.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M86305 Genomic DNA. Translation: AAA03747.1 .
X06036 Genomic DNA. Translation: CAA29431.1 .
L10328 Genomic DNA. Translation: AAA61988.1 .
U00039 Genomic DNA. Translation: AAB18612.1 .
U00096 Genomic DNA. Translation: AAC76659.1 .
AP009048 Genomic DNA. Translation: BAE77657.1 .
M60670 Genomic DNA. Translation: AAA24045.1 .
PIRi A30254. DGECFP.
RefSeqi NP_418092.1. NC_000913.3.
YP_491798.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1K82 X-ray 2.10 A/B/C/D 2-269 [» ]
ProteinModelPortali P05523.
SMRi P05523. Positions 2-269.
ModBasei Search...

Protein-protein interaction databases

DIPi DIP-10286N.
IntActi P05523. 12 interactions.
STRINGi 511145.b3635.

Proteomic databases

PaxDbi P05523.
PRIDEi P05523.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC76659 ; AAC76659 ; b3635 .
BAE77657 ; BAE77657 ; BAE77657 .
GeneIDi 12933569.
946765.
KEGGi ecj:Y75_p3539.
eco:b3635.
PATRICi 32122757. VBIEscCol129921_3755.

Organism-specific databases

EchoBASEi EB0325.
EcoGenei EG10329. mutM.

Phylogenomic databases

eggNOGi COG0266.
HOGENOMi HOG000020881.
KOi K10563.
OMAi DHVDLKL.
OrthoDBi EOG6QP131.
PhylomeDBi P05523.

Enzyme and pathway databases

BioCyci EcoCyc:EG10329-MONOMER.
ECOL316407:JW3610-MONOMER.
MetaCyc:EG10329-MONOMER.

Miscellaneous databases

EvolutionaryTracei P05523.
PROi P05523.

Gene expression databases

Genevestigatori P05523.

Family and domain databases

HAMAPi MF_00103. Fapy_DNA_glycosyl.
InterProi IPR015886. DNA_glyclase/AP_lyase_DNA-bd.
IPR015887. DNA_glyclase_Znf_dom_DNA_BS.
IPR000191. DNA_glycosylase/AP_lyase.
IPR012319. DNA_glycosylase/AP_lyase_cat.
IPR020629. Formamido-pyr_DNA_Glyclase.
IPR010979. Ribosomal_S13-like_H2TH.
IPR000214. Znf_DNA_glyclase/AP_lyase.
IPR010663. Znf_DNA_glyclase/IsotRNA_synth.
[Graphical view ]
Pfami PF01149. Fapy_DNA_glyco. 1 hit.
PF06831. H2TH. 1 hit.
PF06827. zf-FPG_IleRS. 1 hit.
[Graphical view ]
SMARTi SM00898. Fapy_DNA_glyco. 1 hit.
[Graphical view ]
SUPFAMi SSF46946. SSF46946. 1 hit.
SSF81624. SSF81624. 1 hit.
TIGRFAMsi TIGR00577. fpg. 1 hit.
PROSITEi PS51068. FPG_CAT. 1 hit.
PS01242. ZF_FPG_1. 1 hit.
PS51066. ZF_FPG_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Formamidopyrimidine-DNA glycosylase of Escherichia coli: cloning and sequencing of the fpg structural gene and overproduction of the protein."
    Boiteux S., O'Connor T.R., Laval J.
    EMBO J. 6:3177-3183(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes."
    Sofia H.J., Burland V., Daniels D.L., Plunkett G. III, Blattner F.R.
    Nucleic Acids Res. 22:2576-2586(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication."
    Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.
    Genomics 16:551-561(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] OF 1-182.
    Strain: K12 / MG1655 / ATCC 47076.
  6. "A gene coding for 3-deoxy-D-manno-octulosonic-acid transferase in Escherichia coli. Identification, mapping, cloning, and sequencing."
    Clementz T., Raetz C.R.H.
    J. Biol. Chem. 266:9687-9696(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 181-269.
    Strain: K12.
  7. "Homogeneous Escherichia coli FPG protein. A DNA glycosylase which excises imidazole ring-opened purines and nicks DNA at apurinic/apyrimidinic sites."
    Boiteux S., O'Connor T.R., Lederer F., Gouyette A., Laval J.
    J. Biol. Chem. 265:3916-3922(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-24, FUNCTION, SUBUNIT, COFACTOR.
  8. "Fpg protein of Escherichia coli is a zinc finger protein whose cysteine residues have a structural and/or functional role."
    O'Connor T.E., Graves R.J., de Murcia G., Castaing B., Laval J.
    J. Biol. Chem. 268:9063-9070(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  9. "Involvement of phylogenetically conserved acidic amino acid residues in catalysis by an oxidative DNA damage enzyme formamidopyrimidine glycosylase."
    Lavrukhin O.V., Lloyd R.S.
    Biochemistry 39:15266-15271(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF GLU-3; GLU-6; ASP-107; GLU-132; ASP-160 AND GLU-174.
  10. "The oxidative DNA glycosylases of Mycobacterium tuberculosis exhibit different substrate preferences from their Escherichia coli counterparts."
    Guo Y., Bandaru V., Jaruga P., Zhao X., Burrows C.J., Iwai S., Dizdaroglu M., Bond J.P., Wallace S.S.
    DNA Repair 9:177-190(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBSTRATES.
  11. "Substrate discrimination by formamidopyrimidine-DNA glycosylase: a mutational analysis."
    Zaika E.I., Perlow R.A., Matz E., Broyde S., Gilboa R., Grollman A.P., Zharkov D.O.
    J. Biol. Chem. 279:4849-4861(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF HIS-90; ARG-109; ARG-110 AND LYS-218.
  12. "Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA."
    Gilboa R., Zharkov D.O., Golan G., Fernandes A.S., Gerchman S.E., Matz E., Kycia J.H., Grollman A.P., Shoham G.
    J. Biol. Chem. 277:19811-19816(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 1-269 IN COMPLEX WITH DNA.

Entry informationi

Entry nameiFPG_ECOLI
AccessioniPrimary (citable) accession number: P05523
Secondary accession number(s): Q2M7U9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: January 23, 2007
Last modified: May 14, 2014
This is version 148 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Multifunctional enzyme, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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