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P84131

- P84131_GEOSE

UniProt

P84131 - P84131_GEOSE

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Protein
Formamidopyrimidine-DNA glycosylase
Gene
mutM, fpg
Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
Status
Unreviewed - Annotation score: 4 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). 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 By similarity.UniRule annotationSAAS annotations

Catalytic activityi

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

Cofactori

Binds 1 zinc ion per subunit By similarity.UniRule annotationSAAS annotations

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei2 – 21Schiff-base intermediate with DNA By similarityUniRule annotation
Active sitei60 – 601Proton donor; for beta-elimination activity By similarityUniRule annotation
Binding sitei93 – 931DNA By similarityUniRule annotation
Binding sitei112 – 1121DNA By similarityUniRule annotation
Metal bindingi249 – 2491ZincImported
Metal bindingi252 – 2521ZincImported
Active sitei264 – 2641Proton donor; for delta-elimination activity By similarityUniRule annotation
Metal bindingi269 – 2691ZincImported
Metal bindingi272 – 2721ZincImported

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri240 – 27435FPG-type By similarityUniRule annotation
Add
BLAST

GO - Molecular functioni

  1. damaged DNA binding Source: InterPro
  2. oxidized purine nucleobase lesion DNA N-glycosylase activity Source: UniProtKB-HAMAP
  3. zinc ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. base-excision repair Source: InterPro
  2. nucleotide-excision repair Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

GlycosidaseUniRule annotationSAAS annotations, Hydrolase, LyaseUniRule annotationSAAS annotations

Keywords - Biological processi

DNA damage, DNA repairUniRule annotationSAAS annotations

Keywords - Ligandi

DNA-bindingUniRule annotationSAAS annotations, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Formamidopyrimidine-DNA glycosylaseUniRule annotation (EC:3.2.2.23UniRule annotation)
Short name:
Fapy-DNA glycosylaseUniRule annotation
Alternative name(s):
DNA-(apurinic or apyrimidinic site) lyase MutM
Gene namesi
Name:mutMUniRule annotation
Synonyms:fpgUniRule annotation
OrganismiGeobacillus stearothermophilus (Bacillus stearothermophilus)Imported
Taxonomic identifieri1422 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

Interactioni

Subunit structurei

Monomer By similarity.UniRule annotationSAAS annotations

Structurei

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1L1TX-ray1.80A1-274[»]
1L1ZX-ray1.70A1-274[»]
1L2BX-ray2.40A1-274[»]
1L2CX-ray2.20A1-274[»]
1R2YX-ray2.34A1-274[»]
1R2ZX-ray1.63A1-274[»]
2F5NX-ray2.00A1-274[»]
2F5OX-ray2.05A1-274[»]
2F5PX-ray2.00A1-274[»]
2F5QX-ray2.35A1-274[»]
2F5SX-ray2.35A1-274[»]
3GO8X-ray1.89A2-274[»]
3GP1X-ray2.05A2-274[»]
3GPPX-ray2.15A2-274[»]
3GPUX-ray1.62A2-274[»]
3GPXX-ray1.78A2-274[»]
3GPYX-ray1.85A2-274[»]
3GQ3X-ray1.83A2-274[»]
3GQ4X-ray1.70A2-274[»]
3GQ5X-ray1.90A2-274[»]
3JR4X-ray2.60A2-274[»]
3JR5X-ray1.70A2-274[»]
3SARX-ray1.95A2-274[»]
3SASX-ray2.05A2-274[»]
3SATX-ray2.15A2-274[»]
3SAUX-ray1.65A2-274[»]
3SAVX-ray2.12A2-274[»]
3SAWX-ray2.35A2-274[»]
3SBJX-ray2.10A2-274[»]
3U6CX-ray1.80A2-274[»]
3U6DX-ray1.87A2-274[»]
3U6EX-ray1.70A2-274[»]
3U6LX-ray1.97A2-274[»]
3U6MX-ray2.10A2-274[»]
3U6OX-ray1.90A2-274[»]
3U6PX-ray1.60A2-274[»]
3U6QX-ray1.98A2-274[»]
3U6SX-ray1.77A2-274[»]
4G4NX-ray1.85A2-274[»]
4G4OX-ray1.95A2-274[»]
4G4QX-ray1.86A2-274[»]
4G4RX-ray1.95A2-274[»]
ProteinModelPortaliP84131.
SMRiP84131. Positions 2-274.

Miscellaneous databases

EvolutionaryTraceiP84131.

Family & Domainsi

Sequence similaritiesi

Belongs to the FPG family.UniRule annotation
Contains 1 FPG-type zinc finger.UniRule annotation
Contains FPG-type zinc finger.SAAS annotations

Keywords - Domaini

Zinc-fingerUniRule annotationSAAS annotations

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.

P84131-1 [UniParc]FASTAAdd to Basket

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MPQLPEVETI RRTLLPLIVG KTIEDVRIFW PNIIRHPRDS EAFAARMIGQ    50
TVRGLERRGK FLKFLLDRDA LISHLRMEGR YAVASALEPL EPHTHVVFCF 100
TDGSELRYRD VRKFGTMHVY AKEEADRRPP LAELGPEPLS PAFSPAVLAE 150
RAVKTKRSVK ALLLDQTVVA GFGNIYVDES LFRAGILPGR PAASLSSKEI 200
ERLHEEMVAT IGEAVMKGGS TVRTYVNTQG EAGTFQHHLY VYGRQGNPCK 250
RCGTPIEKTV VAGRGTHYCP RCQR 274
Length:274
Mass (Da):30,689
Last modified:September 13, 2004 - v1
Checksum:iC260712E9E1B7FD9
GO

Cross-referencesi

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1L1T X-ray 1.80 A 1-274 [» ]
1L1Z X-ray 1.70 A 1-274 [» ]
1L2B X-ray 2.40 A 1-274 [» ]
1L2C X-ray 2.20 A 1-274 [» ]
1R2Y X-ray 2.34 A 1-274 [» ]
1R2Z X-ray 1.63 A 1-274 [» ]
2F5N X-ray 2.00 A 1-274 [» ]
2F5O X-ray 2.05 A 1-274 [» ]
2F5P X-ray 2.00 A 1-274 [» ]
2F5Q X-ray 2.35 A 1-274 [» ]
2F5S X-ray 2.35 A 1-274 [» ]
3GO8 X-ray 1.89 A 2-274 [» ]
3GP1 X-ray 2.05 A 2-274 [» ]
3GPP X-ray 2.15 A 2-274 [» ]
3GPU X-ray 1.62 A 2-274 [» ]
3GPX X-ray 1.78 A 2-274 [» ]
3GPY X-ray 1.85 A 2-274 [» ]
3GQ3 X-ray 1.83 A 2-274 [» ]
3GQ4 X-ray 1.70 A 2-274 [» ]
3GQ5 X-ray 1.90 A 2-274 [» ]
3JR4 X-ray 2.60 A 2-274 [» ]
3JR5 X-ray 1.70 A 2-274 [» ]
3SAR X-ray 1.95 A 2-274 [» ]
3SAS X-ray 2.05 A 2-274 [» ]
3SAT X-ray 2.15 A 2-274 [» ]
3SAU X-ray 1.65 A 2-274 [» ]
3SAV X-ray 2.12 A 2-274 [» ]
3SAW X-ray 2.35 A 2-274 [» ]
3SBJ X-ray 2.10 A 2-274 [» ]
3U6C X-ray 1.80 A 2-274 [» ]
3U6D X-ray 1.87 A 2-274 [» ]
3U6E X-ray 1.70 A 2-274 [» ]
3U6L X-ray 1.97 A 2-274 [» ]
3U6M X-ray 2.10 A 2-274 [» ]
3U6O X-ray 1.90 A 2-274 [» ]
3U6P X-ray 1.60 A 2-274 [» ]
3U6Q X-ray 1.98 A 2-274 [» ]
3U6S X-ray 1.77 A 2-274 [» ]
4G4N X-ray 1.85 A 2-274 [» ]
4G4O X-ray 1.95 A 2-274 [» ]
4G4Q X-ray 1.86 A 2-274 [» ]
4G4R X-ray 1.95 A 2-274 [» ]
ProteinModelPortali P84131.
SMRi P84131. Positions 2-274.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei P84131.

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

  1. "Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM."
    Fromme J.C., Verdine G.L.
    Nat. Struct. Biol. 9:544-552(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEX WITH ZINC.
  2. "DNA lesion recognition by the bacterial repair enzyme MutM."
    Fromme J.C., Verdine G.L.
    J. Biol. Chem. 278:51543-51548(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.63 ANGSTROMS) IN COMPLEX WITH ZINC.
  3. "Structure of a DNA glycosylase searching for lesions."
    Banerjee A., Santos W.L., Verdine G.L.
    Science 311:1153-1157(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH ZINC.
  4. "Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme."
    Qi Y., Spong M.C., Nam K., Banerjee A., Jiralerspong S., Karplus M., Verdine G.L.
    Nature 462:762-766(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.62 ANGSTROMS) OF 2-274 IN COMPLEX WITH ZINC.
  5. "Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM."
    Qi Y., Spong M.C., Nam K., Karplus M., Verdine G.L.
    J. Biol. Chem. 285:1468-1478(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 2-274 IN COMPLEX WITH ZINC.
  6. "Sequence-dependent structural variation in DNA undergoing intrahelical inspection by the DNA glycosylase MutM."
    Sung R.J., Zhang M., Qi Y., Verdine G.L.
    J. Biol. Chem. 287:18044-18054(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 2-274 IN COMPLEX WITH ZINC.
  7. Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF 2-274 IN COMPLEX WITH ZINC.
  8. "Structural and biochemical analysis of DNA helix invasion by the bacterial 8-oxoguanine DNA glycosylase MutM."
    Sung R.J., Zhang M., Qi Y., Verdine G.L.
    J. Biol. Chem. 288:10012-10023(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 2-274 IN COMPLEX WITH ZINC.

Entry informationi

Entry nameiP84131_GEOSE
AccessioniPrimary (citable) accession number: P84131
Entry historyi
Integrated into UniProtKB/TrEMBL: September 13, 2004
Last sequence update: September 13, 2004
Last modified: July 9, 2014
This is version 76 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureImported, Multifunctional enzymeUniRule annotationSAAS annotations

External Data

Dasty 3

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