P84131 (P84131_GEOSE) Unreviewed, UniProtKB/TrEMBL

Names and origin

Protein names

Recommended 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

Organism

Geobacillus stearothermophilus (Bacillus stearothermophilus) PDB 1R2Y PDB 1R2Z

Taxonomic identifier

1422 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Geobacillus

Protein attributes

Sequence length	274 AA.
Sequence status	Complete.
Protein existence	Evidence 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 SAAS015886
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 SAAS015886 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 SAAS015886
Cofactor	Binds 1 zinc ion per subunit By similarity. HAMAP-Rule MF_00103 SAAS SAAS015886
Subunit structure	Monomer By similarity. HAMAP-Rule MF_00103 SAAS SAAS015886
Sequence similarities	Belongs to the FPG family. HAMAP-Rule MF_00103 Contains 1 FPG-type zinc finger. HAMAP-Rule MF_00103 SAAS SAAS015886

Ontologies

Keywords
Biological process	DNA damage DNA repair HAMAP-Rule MF_00103 SAAS SAAS015886
Domain	Zinc-finger HAMAP-Rule MF_00103 SAAS SAAS015886
Ligand	DNA-binding HAMAP-Rule MF_00103 SAAS SAAS015886 Metal-binding Zinc
Molecular function	Glycosidase HAMAP-Rule MF_00103 SAAS SAAS015886 Hydrolase Lyase HAMAP-Rule MF_00103 SAAS SAAS015886
Technical term	3D-structure 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 Multifunctional enzyme HAMAP-Rule MF_00103 SAAS SAAS015886
Gene Ontology (GO)
Biological_process	base-excision repair Inferred from electronic annotation. Source: InterPro nucleotide-excision repair Inferred from electronic annotation. Source: InterPro
Molecular_function	damaged DNA binding Inferred from electronic annotation. Source: InterPro oxidized purine nucleobase lesion DNA N-glycosylase activity Inferred from electronic annotation. Source: HAMAP zinc ion binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Regions
	Zinc finger	240 – 274	35	FPG-type By similarity HAMAP-Rule MF_00103
Sites
	Active site	2	1	Schiff-base intermediate with DNA By similarity HAMAP-Rule MF_00103
	Active site	60	1	Proton donor; for beta-elimination activity By similarity HAMAP-Rule MF_00103
	Active site	264	1	Proton donor; for delta-elimination activity By similarity HAMAP-Rule MF_00103
	Metal binding	249	1	Zinc PDB 1R2Y PDB 1R2Z 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
	Metal binding	252	1	Zinc PDB 1R2Y PDB 1R2Z 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
	Metal binding	269	1	Zinc PDB 1R2Y PDB 1R2Z 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
	Metal binding	272	1	Zinc PDB 1R2Y PDB 1R2Z 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
	Binding site	93	1	DNA By similarity HAMAP-Rule MF_00103
	Binding site	112	1	DNA By similarity HAMAP-Rule MF_00103

Sequences

	Sequence		Length	Mass (Da)
	P84131 [UniParc]. Last modified September 13, 2004. Version 1. Checksum: C260712E9E1B7FD9	FASTA	274	30,689
	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

References

[1]	"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.
[2]	"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.
[3]	"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 4-274 IN COMPLEX WITH ZINC.
[4]	"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.
[5]	"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.
[6]	"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 4-274.
[7]	"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. 0:0-0(2013) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 4-274.

Cross-references

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
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	4-274	[»]
3GP1	X-ray	2.05	A	4-274	[»]
3GPP	X-ray	2.15	A	4-274	[»]
3GPU	X-ray	1.62	A	4-274	[»]
3GPX	X-ray	1.78	A	4-274	[»]
3GPY	X-ray	1.85	A	2-274	[»]
3GQ3	X-ray	1.83	A	4-274	[»]
3GQ4	X-ray	1.70	A	2-274	[»]
3GQ5	X-ray	1.90	A	4-274	[»]
3JR4	X-ray	2.60	A	2-274	[»]
3JR5	X-ray	1.70	A	2-274	[»]
3SAR	X-ray	1.95	A	4-274	[»]
3SAS	X-ray	2.05	A	4-274	[»]
3SAT	X-ray	2.15	A	4-274	[»]
3SAU	X-ray	1.65	A	4-274	[»]
3SAV	X-ray	2.12	A	4-274	[»]
3SAW	X-ray	2.35	A	4-274	[»]
3SBJ	X-ray	2.10	A	4-274	[»]
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	4-274	[»]
4G4O	X-ray	1.95	A	2-274	[»]
4G4Q	X-ray	1.86	A	4-274	[»]
4G4R	X-ray	1.95	A	2-274	[»]

ProteinModelPortal

P84131.

SMR

P84131. Positions 2-274.

ModBase

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Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

HAMAP

MF_00103. Fapy_DNA_glycosyl.

InterPro

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]

Pfam

PF01149. Fapy_DNA_glyco. 1 hit.
PF06831. H2TH. 1 hit.
PF06827. zf-FPG_IleRS. 1 hit.
[Graphical view]

SMART

SM00898. Fapy_DNA_glyco. 1 hit.
[Graphical view]

SUPFAM

SSF81624. Form_DNAglyc_cat. 1 hit.
SSF46946. Ribosomal_H2TH. 1 hit.

TIGRFAMs

TIGR00577. fpg. 1 hit.

PROSITE

PS51068. FPG_CAT. 1 hit.
PS01242. ZF_FPG_1. 1 hit.
PS51066. ZF_FPG_2. 1 hit.
[Graphical view]

ProtoNet

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Other

EvolutionaryTrace

P84131.

Entry information

Entry name

P84131_GEOSE

Accession

Primary (citable) accession number: P84131

Entry history

Integrated into UniProtKB/TrEMBL:	September 13, 2004
Last sequence update:	September 13, 2004
Last modified:	May 1, 2013
This is version 65 of the entry and version 1 of the sequence. [Complete history]

Entry status

Unreviewed (UniProtKB/TrEMBL)