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Protein

Formamidopyrimidine-DNA glycosylase

Gene

mutM

Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
Status
Unreviewed-Annotation score: Annotation score: 3 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.UniRule annotation
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).SAAS annotation

Catalytic activityi

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

Cofactori

Zn2+UniRule annotationNote: Binds 1 zinc ion per subunit.UniRule annotation

Sites

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

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri240 – 27435FPG-typeUniRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

GlycosidaseUniRule annotationSAAS annotation, Hydrolase, LyaseUniRule annotationSAAS annotation

Keywords - Biological processi

DNA damage, DNA repairUniRule annotationSAAS annotation

Keywords - Ligandi

DNA-bindingUniRule annotationSAAS annotation, Metal-binding, Zinc

Enzyme and pathway databases

BRENDAi3.2.2.23. 623.

Names & Taxonomyi

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

Interactioni

Subunit structurei

Monomer.UniRule annotationSAAS annotation

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP84131.

Family & Domainsi

Sequence similaritiesi

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

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri240 – 27435FPG-typeUniRule annotationAdd
BLAST

Keywords - Domaini

Zinc-fingerUniRule annotationSAAS annotation

Family and domain databases

HAMAPiMF_00103. Fapy_DNA_glycosyl.
InterProiIPR015886. DNA_glyclase/AP_lyase_DNA-bd.
IPR015887. DNA_glyclase_Znf_dom_DNA_BS.
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

« Hide

        10         20         30         40         50
MPQLPEVETI RRTLLPLIVG KTIEDVRIFW PNIIRHPRDS EAFAARMIGQ
60 70 80 90 100
TVRGLERRGK FLKFLLDRDA LISHLRMEGR YAVASALEPL EPHTHVVFCF
110 120 130 140 150
TDGSELRYRD VRKFGTMHVY AKEEADRRPP LAELGPEPLS PAFSPAVLAE
160 170 180 190 200
RAVKTKRSVK ALLLDQTVVA GFGNIYVDES LFRAGILPGR PAASLSSKEI
210 220 230 240 250
ERLHEEMVAT IGEAVMKGGS TVRTYVNTQG EAGTFQHHLY VYGRQGNPCK
260 270
RCGTPIEKTV VAGRGTHYCP RCQR
Length:274
Mass (Da):30,689
Last modified:September 13, 2004 - v1
Checksum:iC260712E9E1B7FD9
GO

Cross-referencesi

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi3.2.2.23. 623.

Miscellaneous databases

EvolutionaryTraceiP84131.

Family and domain databases

HAMAPiMF_00103. Fapy_DNA_glycosyl.
InterProiIPR015886. DNA_glyclase/AP_lyase_DNA-bd.
IPR015887. DNA_glyclase_Znf_dom_DNA_BS.
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]
ProtoNetiSearch...

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: June 24, 2015
This is version 86 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources, Multifunctional enzymeUniRule annotationSAAS annotation

External Data

Dasty 3

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 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.