Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

P84131 (P84131_GEOSE) Unreviewed, UniProtKB/TrEMBL

Last modified March 19, 2014. Version 73. Feed History...

Clusters with 100%, 90%, 50% identity | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry infoCustomize order

Names and origin

Protein namesRecommended name:
Formamidopyrimidine-DNA glycosylase HAMAP-Rule MF_00103

Short name=Fapy-DNA glycosylase HAMAP-Rule MF_00103
EC=3.2.2.23 HAMAP-Rule MF_00103
Alternative name(s):
DNA-(apurinic or apyrimidinic site) lyase MutM HAMAP-Rule MF_00103
Gene names
Name:mutM HAMAP-Rule MF_00103
Synonyms:fpg HAMAP-Rule MF_00103
OrganismGeobacillus stearothermophilus (Bacillus stearothermophilus) PDB 1R2Y PDB 1R2Z
Taxonomic identifier1422 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

Protein attributes

Sequence length274 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. HAMAP-Rule MF_00103 SAAS SAAS000191

Catalytic activity

Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine. HAMAP-Rule MF_00103 SAAS SAAS000191

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. HAMAP-Rule MF_00103 SAAS SAAS000191

Cofactor

Binds 1 zinc ion per subunit By similarity. HAMAP-Rule MF_00103 SAAS SAAS000191

Subunit structure

Monomer By similarity. HAMAP-Rule MF_00103 SAAS SAAS000191

Sequence similarities

Belongs to the FPG family. HAMAP-Rule MF_00103

Contains 1 FPG-type zinc finger. HAMAP-Rule MF_00103

Contains FPG-type zinc finger. SAAS SAAS000191

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Regions

Zinc finger240 – 27435FPG-type By similarity HAMAP-Rule MF_00103

Sites

Active site21Schiff-base intermediate with DNA By similarity HAMAP-Rule MF_00103
Active site601Proton donor; for beta-elimination activity By similarity HAMAP-Rule MF_00103
Active site2641Proton donor; for delta-elimination activity By similarity HAMAP-Rule MF_00103
Metal binding2491Zinc PDB 1R2Y PDB 1R2Z PDB 3SAR PDB 1L1Z PDB 3SAS PDB 3SAT PDB 3SAU PDB 3SAV PDB 3SAW PDB 3SBJ PDB 3U6C PDB 3U6D PDB 3U6E PDB 3U6L PDB 3U6M PDB 3U6O PDB 3U6P PDB 2F5N PDB 2F5O PDB 2F5P PDB 2F5Q PDB 2F5S PDB 3GO8 PDB 3GP1 PDB 3GPP PDB 3GPU PDB 3GPX PDB 3GPY PDB 3GQ3 PDB 3GQ4 PDB 3GQ5 PDB 3JR4 PDB 3JR5 PDB 3U6Q PDB 3U6S PDB 4G4N PDB 4G4O PDB 4G4Q PDB 4G4R
Metal binding2521Zinc PDB 1R2Y PDB 1R2Z PDB 3SAR PDB 3SAS PDB 3SAT PDB 3SAU PDB 3SAV PDB 3SAW PDB 3SBJ PDB 3U6C PDB 3U6D PDB 3U6E PDB 3U6L PDB 3U6M PDB 3U6O PDB 3U6P PDB 2F5N PDB 2F5O PDB 2F5P PDB 2F5Q PDB 2F5S PDB 3GO8 PDB 3GP1 PDB 3GPP PDB 3GPU PDB 3GPX PDB 3GPY PDB 3GQ3 PDB 3GQ4 PDB 3GQ5 PDB 3JR4 PDB 3JR5 PDB 3U6Q PDB 3U6S PDB 4G4N PDB 4G4O PDB 4G4Q PDB 4G4R
Metal binding2691Zinc PDB 1R2Y PDB 1R2Z PDB 3SAR PDB 1L1Z PDB 3SAS PDB 3SAT PDB 3SAU PDB 3SAV PDB 3SAW PDB 3SBJ PDB 3U6C PDB 3U6D PDB 3U6E PDB 3U6L PDB 3U6M PDB 3U6O PDB 3U6P PDB 2F5N PDB 2F5O PDB 2F5P PDB 2F5Q PDB 2F5S PDB 3GO8 PDB 3GP1 PDB 3GPP PDB 3GPU PDB 3GPX PDB 3GPY PDB 3GQ3 PDB 3GQ4 PDB 3GQ5 PDB 3JR4 PDB 3JR5 PDB 3U6Q PDB 3U6S PDB 4G4N PDB 4G4O PDB 4G4Q PDB 4G4R
Metal binding2721Zinc PDB 1R2Y PDB 1R2Z PDB 3SAR PDB 1L1Z PDB 3SAS PDB 3SAT PDB 3SAU PDB 3SAV PDB 3SAW PDB 3SBJ PDB 3U6C PDB 3U6D PDB 3U6E PDB 3U6L PDB 3U6M PDB 3U6O PDB 3U6P PDB 2F5N PDB 2F5O PDB 2F5P PDB 2F5Q PDB 2F5S PDB 3GO8 PDB 3GP1 PDB 3GPP PDB 3GPU PDB 3GPX PDB 3GPY PDB 3GQ3 PDB 3GQ4 PDB 3GQ5 PDB 3JR4 PDB 3JR5 PDB 3U6Q PDB 3U6S PDB 4G4N PDB 4G4O PDB 4G4Q PDB 4G4R
Binding site931DNA By similarity HAMAP-Rule MF_00103
Binding site1121DNA By similarity HAMAP-Rule MF_00103

Sequences

Sequence LengthMass (Da)Tools
P84131 [UniParc].

Last modified September 13, 2004. Version 1.
Checksum: C260712E9E1B7FD9

FASTA27430,689
        10         20         30         40         50         60 
MPQLPEVETI RRTLLPLIVG KTIEDVRIFW PNIIRHPRDS EAFAARMIGQ TVRGLERRGK 

        70         80         90        100        110        120 
FLKFLLDRDA LISHLRMEGR YAVASALEPL EPHTHVVFCF TDGSELRYRD VRKFGTMHVY 

       130        140        150        160        170        180 
AKEEADRRPP LAELGPEPLS PAFSPAVLAE RAVKTKRSVK ALLLDQTVVA GFGNIYVDES 

       190        200        210        220        230        240 
LFRAGILPGR PAASLSSKEI ERLHEEMVAT IGEAVMKGGS TVRTYVNTQG EAGTFQHHLY 

       250        260        270 
VYGRQGNPCK RCGTPIEKTV VAGRGTHYCP RCQR 

« Hide

References

[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]"Strandwise translocation of a DNA glycosylase on undamaged DNA."
Qi Y., Nam K., Spong M.C., Banerjee A., Sung R.J., Zhang M., Karplus M., Verdine G.L.
Proc. Natl. Acad. Sci. U.S.A. 109:1086-1091(2012) [PubMed] [Europe PMC] [Abstract]
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.

Cross-references

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1L1ZX-ray1.70A1-274[»]
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[»]
ProteinModelPortalP84131.
SMRP84131. Positions 2-274.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

HAMAPMF_00103. Fapy_DNA_glycosyl.
InterProIPR015886. 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]
PfamPF01149. Fapy_DNA_glyco. 1 hit.
PF06831. H2TH. 1 hit.
PF06827. zf-FPG_IleRS. 1 hit.
[Graphical view]
SMARTSM00898. Fapy_DNA_glyco. 1 hit.
[Graphical view]
SUPFAMSSF46946. SSF46946. 1 hit.
SSF81624. SSF81624. 1 hit.
TIGRFAMsTIGR00577. fpg. 1 hit.
PROSITEPS51068. FPG_CAT. 1 hit.
PS01242. ZF_FPG_1. 1 hit.
PS51066. ZF_FPG_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP84131.

Entry information

Entry nameP84131_GEOSE
AccessionPrimary (citable) accession number: P84131
Entry history
Integrated into UniProtKB/TrEMBL: September 13, 2004
Last sequence update: September 13, 2004
Last modified: March 19, 2014
This is version 73 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)