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Protein

Formamidopyrimidine-DNA glycosylase

Gene

FPG1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: 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. Can process efficiently 4,6-diamino-5-formamidopyrimidine (FapyA), 2,6-diamino-4- hydroxy-5-formamidopyrimidine (FapyG) and the further oxidation products of 8-oxoguanine (8-oxoG), such as guanidinohydantoin and spiroiminodihydantoin. Has marginal activity towards 8-oxoG. Has AP (apurinic/apyrimidinic) lyase activity. 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.3 Publications

Catalytic activityi

Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine.1 Publication
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.PROSITE-ProRule annotation1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei2 – 21Schiff-base intermediate with DNAPROSITE-ProRule annotation
Active sitei3 – 31Proton donorPROSITE-ProRule annotation
Active sitei60 – 601Proton donor; for beta-elimination activityPROSITE-ProRule annotation
Binding sitei107 – 1071DNA1 Publication
Binding sitei126 – 1261DNABy similarity
Binding sitei167 – 1671DNA1 Publication
Binding sitei186 – 1861DNA1 Publication

GO - Molecular functioni

GO - Biological processi

  • base-excision repair Source: InterPro
  • DNA repair Source: TAIR
  • nucleotide-excision repair Source: InterPro
  • response to oxidative stress Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase, Lyase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciARA:AT1G52500-MONOMER.
BRENDAi3.2.2.23. 399.

Names & Taxonomyi

Protein namesi
Recommended name:
Formamidopyrimidine-DNA glycosylase (EC:3.2.2.23, EC:4.2.99.18)
Short name:
Fapy-DNA glycosylase
Alternative name(s):
DNA-(apurinic or apyrimidinic site) lyase FPG1
Formamidopyrimidine-DNA glycosylase 1
Short name:
AtFPG-1
Formamidopyrimidine-DNA glycosylase 2
Short name:
AtFPG-2
Protein MutM homolog 1
Short name:
AtMMH-1
Protein MutM homolog 2
Short name:
AtMMH-2
Gene namesi
Name:FPG1
Synonyms:FPG2
Ordered Locus Names:At1g52500
ORF Names:F6D8.28
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G52500.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

No visible phenotype under normal growth conditions or UV-A irradiation stress.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 390389Formamidopyrimidine-DNA glycosylasePRO_0000421261Add
BLAST

Proteomic databases

PaxDbiO80358.
PRIDEiO80358.

PTM databases

iPTMnetiO80358.

Expressioni

Tissue specificityi

Expressed in leaves (at protein levels).1 Publication

Gene expression databases

GenevisibleiO80358. AT.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

STRINGi3702.AT1G52500.2.

Structurei

Secondary structure

1
390
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 1714Combined sources
Turni18 – 203Combined sources
Beta strandi22 – 287Combined sources
Turni32 – 343Combined sources
Helixi40 – 478Combined sources
Beta strandi51 – 588Combined sources
Beta strandi61 – 699Combined sources
Beta strandi71 – 755Combined sources
Turni77 – 793Combined sources
Beta strandi81 – 855Combined sources
Helixi93 – 953Combined sources
Beta strandi108 – 1147Combined sources
Helixi115 – 1173Combined sources
Beta strandi119 – 1235Combined sources
Beta strandi125 – 1273Combined sources
Beta strandi130 – 1356Combined sources
Helixi137 – 1393Combined sources
Helixi143 – 1453Combined sources
Turni150 – 1523Combined sources
Helixi157 – 1659Combined sources
Helixi171 – 1766Combined sources
Turni178 – 1803Combined sources
Beta strandi181 – 1833Combined sources
Helixi186 – 19510Combined sources
Helixi204 – 2063Combined sources
Helixi209 – 22820Combined sources
Turni229 – 2313Combined sources
Helixi233 – 2353Combined sources
Helixi241 – 2444Combined sources
Beta strandi260 – 2645Combined sources
Beta strandi267 – 2715Combined sources
Turni273 – 2753Combined sources
Helixi280 – 2867Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3TWKX-ray2.30A/B1-281[»]
3TWLX-ray1.70A1-304[»]
3TWMX-ray2.80A/B1-304[»]
ProteinModelPortaliO80358.
SMRiO80358. Positions 2-287.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the FPG family.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG410IKB3. Eukaryota.
COG0266. LUCA.
HOGENOMiHOG000191723.
InParanoidiO80358.
KOiK10563.
OMAiHAHVFFR.
PhylomeDBiO80358.

Family and domain databases

InterProiIPR015886. DNA_glyclase/AP_lyase_DNA-bd.
IPR020629. Formamido-pyr_DNA_Glyclase.
IPR012319. FPG_cat.
IPR010979. Ribosomal_S13-like_H2TH.
[Graphical view]
PfamiPF01149. Fapy_DNA_glyco. 1 hit.
PF06831. H2TH. 1 hit.
[Graphical view]
SMARTiSM00898. Fapy_DNA_glyco. 1 hit.
SM01232. H2TH. 1 hit.
[Graphical view]
SUPFAMiSSF46946. SSF46946. 1 hit.
SSF81624. SSF81624. 1 hit.
TIGRFAMsiTIGR00577. fpg. 1 hit.
PROSITEiPS51068. FPG_CAT. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: O80358-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MPELPEVEAA RRAIEENCLG KKIKRVIIAD DNKVIHGISP SDFQTSILGK
60 70 80 90 100
TIISARRKGK NLWLELDSPP FPSFQFGMAG AIYIKGVAVT KYKRSAVKDS
110 120 130 140 150
EEWPSKYSKF FVELDDGLEL SFTDKRRFAK VRLLANPTSV SPISELGPDA
160 170 180 190 200
LLEPMTVDEF AESLAKKKIT IKPLLLDQGY ISGIGNWIAD EVLYQARIHP
210 220 230 240 250
LQTASSLSKE QCEALHTSIK EVIEKAVEVD ADSSQFPSYW IFHNREKKPG
260 270 280 290 300
KAFVDGKKID FITAGGRTTA YVPELQKLYG KDAEKAAKVR PAKRGVKPKE
310 320 330 340 350
DDGDGEEDEQ ETEKEDESAK SKKGQKPRGG RGKKPASKTK TEESDDDGDD
360 370 380 390
SEAEEEVVKP KGRGTKPAIK RKSEEKATSQ AGKKPKGRKS
Length:390
Mass (Da):43,194
Last modified:November 1, 1998 - v1
Checksum:iF6B5E0DAFD6FD010
GO
Isoform 2 (identifier: O80358-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     224-274: EKAVEVDADS...GGRTTAYVPE → QHAVQVNADS...LMKQNLGFCR
     275-390: Missing.

Note: No experimental confirmation available.
Show »
Length:274
Mass (Da):30,762
Checksum:iE1C7829A15E0D360
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti239 – 2391Y → N in AAC97952 (PubMed:11535407).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei224 – 27451EKAVE…AYVPE → QHAVQVNADSKEFPVEWLFH FRWGKKAGKVNGKLSHHLSI NLMKQNLGFCR in isoform 2. 1 PublicationVSP_045377Add
BLAST
Alternative sequencei275 – 390116Missing in isoform 2. 1 PublicationVSP_045378Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB010690 Genomic DNA. Translation: BAA32702.1.
AB010690 Genomic DNA. Translation: BAA32703.1.
AF099970 mRNA. Translation: AAC97952.1.
AF099971 mRNA. Translation: AAC97953.1.
AC008016 Genomic DNA. Translation: AAD55612.1.
AC008016 Genomic DNA. Translation: AAD55613.1.
CP002684 Genomic DNA. Translation: AEE32814.1.
CP002684 Genomic DNA. Translation: AEE32815.1.
BT043496 mRNA. Translation: ACG58696.1.
PIRiE96565.
T51713.
T51714.
RefSeqiNP_564608.1. NM_104128.2. [O80358-1]
NP_849798.1. NM_179467.2. [O80358-2]
UniGeneiAt.11653.
At.46186.

Genome annotation databases

EnsemblPlantsiAT1G52500.2; AT1G52500.2; AT1G52500. [O80358-1]
GeneIDi841681.
KEGGiath:AT1G52500.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB010690 Genomic DNA. Translation: BAA32702.1.
AB010690 Genomic DNA. Translation: BAA32703.1.
AF099970 mRNA. Translation: AAC97952.1.
AF099971 mRNA. Translation: AAC97953.1.
AC008016 Genomic DNA. Translation: AAD55612.1.
AC008016 Genomic DNA. Translation: AAD55613.1.
CP002684 Genomic DNA. Translation: AEE32814.1.
CP002684 Genomic DNA. Translation: AEE32815.1.
BT043496 mRNA. Translation: ACG58696.1.
PIRiE96565.
T51713.
T51714.
RefSeqiNP_564608.1. NM_104128.2. [O80358-1]
NP_849798.1. NM_179467.2. [O80358-2]
UniGeneiAt.11653.
At.46186.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3TWKX-ray2.30A/B1-281[»]
3TWLX-ray1.70A1-304[»]
3TWMX-ray2.80A/B1-304[»]
ProteinModelPortaliO80358.
SMRiO80358. Positions 2-287.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT1G52500.2.

PTM databases

iPTMnetiO80358.

Proteomic databases

PaxDbiO80358.
PRIDEiO80358.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G52500.2; AT1G52500.2; AT1G52500. [O80358-1]
GeneIDi841681.
KEGGiath:AT1G52500.

Organism-specific databases

TAIRiAT1G52500.

Phylogenomic databases

eggNOGiENOG410IKB3. Eukaryota.
COG0266. LUCA.
HOGENOMiHOG000191723.
InParanoidiO80358.
KOiK10563.
OMAiHAHVFFR.
PhylomeDBiO80358.

Enzyme and pathway databases

BioCyciARA:AT1G52500-MONOMER.
BRENDAi3.2.2.23. 399.

Miscellaneous databases

PROiO80358.

Gene expression databases

GenevisibleiO80358. AT.

Family and domain databases

InterProiIPR015886. DNA_glyclase/AP_lyase_DNA-bd.
IPR020629. Formamido-pyr_DNA_Glyclase.
IPR012319. FPG_cat.
IPR010979. Ribosomal_S13-like_H2TH.
[Graphical view]
PfamiPF01149. Fapy_DNA_glyco. 1 hit.
PF06831. H2TH. 1 hit.
[Graphical view]
SMARTiSM00898. Fapy_DNA_glyco. 1 hit.
SM01232. H2TH. 1 hit.
[Graphical view]
SUPFAMiSSF46946. SSF46946. 1 hit.
SSF81624. SSF81624. 1 hit.
TIGRFAMsiTIGR00577. fpg. 1 hit.
PROSITEiPS51068. FPG_CAT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular cloning of AtMMH, an Arabidopsis thaliana ortholog of the Escherichia coli mutM gene, and analysis of functional domains of its product."
    Ohtsubo T., Matsuda O., Iba K., Terashima I., Sekiguchi M., Nakabeppu Y.
    Mol. Gen. Genet. 259:577-590(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, TISSUE SPECIFICITY.
    Strain: cv. Columbia.
  2. "Multiple forms of formamidopyrimidine-DNA glycosylase produced by alternative splicing in Arabidopsis thaliana."
    Murphy T.M., Gao M.J.
    J. Photochem. Photobiol. B 61:87-93(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    Strain: cv. Landsberg erecta.
  3. "Alternative forms of formamidopyrimidine-DNA glycosylase from Arabidopsis thaliana."
    Gao M.J., Murphy T.M.
    Photochem. Photobiol. 73:128-134(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), FUNCTION.
    Strain: cv. Landsberg erecta.
  4. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
    Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
    , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
    Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  5. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  6. "Arabidopsis ORF clones."
    De Los Reyes C., Quan R., Chen H., Bautista V., Kim C.J., Ecker J.R.
    Submitted (AUG-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
  7. "What is base excision repair good for?: knockout mutants for FPG and OGG glycosylase genes in Arabidopsis."
    Murphy T.M.
    Physiol. Plantarum 123:227-233(2005)
    Cited for: DISRUPTION PHENOTYPE.
  8. "Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks."
    Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A., Grossmann J., Gruissem W., Baginsky S.
    Plant Physiol. 150:889-903(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "Structural and biochemical studies of a plant formamidopyrimidine-DNA glycosylase reveal why eukaryotic Fpg glycosylases do not excise 8-oxoguanine."
    Duclos S., Aller P., Jaruga P., Dizdaroglu M., Wallace S.S., Doublie S.
    DNA Repair 11:714-725(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 1-304 IN COMPLEX WITH DNA, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT.

Entry informationi

Entry nameiFPG_ARATH
AccessioniPrimary (citable) accession number: O80358
Secondary accession number(s): O80359, Q9SBB4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 6, 2013
Last sequence update: November 1, 1998
Last modified: May 11, 2016
This is version 110 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.