Summary: 8-oxoguanine DNA glycosylase, N-terminal domain

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Wikipedia: Oxoguanine glycosylase
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Oxoguanine glycosylase Edit Wikipedia article

8-oxoguanine DNA glycosylase

PDB rendering based on 1ebm.

Available structures

PDB

Ortholog search: PDBe, RCSB

List of PDB id codes
1EBM, 1FN7, 1HU0, 1KO9, 1LWV, 1LWW, 1LWY, 1M3H, 1M3Q, 1N39, 1N3A, 1N3C, 1YQK, 1YQL, 1YQM, 1YQR, 2I5W, 2NOB, 2NOE, 2NOF, 2NOH, 2NOI, 2NOL, 2NOZ, 2XHI, 3IH7, 3KTU

Identifiers

Symbols

OGG1; HMMH; HOGG1; MUTM; OGH1

External IDs

OMIM: 601982 MGI: 1097693 HomoloGene: 1909 GeneCards: OGG1 Gene

EC number

4.2.99.18

Gene Ontology
Molecular function	• damaged DNA binding • endonuclease activity • protein binding • microtubule binding • oxidized purine nucleobase lesion DNA N-glycosylase activity • 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
Cellular component	• nucleus • nucleoplasm • nucleolus • mitochondrion • nuclear matrix • nuclear speck
Biological process	• acute inflammatory response • DNA repair • base-excision repair • base-excision repair, AP site formation • nucleotide-excision repair • regulation of transcription, DNA-dependent • response to oxidative stress • response to radiation • response to estradiol stimulus • regulation of protein import into nucleus, translocation • response to drug • depurination • response to ethanol • response to folic acid • cellular response to cadmium ion
Sources: Amigo / QuickGO

RNA expression pattern

More reference expression data

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 3:
9.79 – 9.83 Mb

Chr 6:
113.33 – 113.34 Mb

PubMed search

[1]

[2]

8-oxoguanine DNA glycosylase, N-terminal domain

structure of catalytically inactive q315a human 8-oxoguanine glycosylase complexed to 8-oxoguanine dna

Identifiers

Symbol

OGG_N

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

8-Oxoguanine glycosylase also known as OGG1 is a DNA glycosylase enzyme that, in humans, is encoded by the OGG1 gene. It is involved in base excision repair. It is found in bacterial, archaeal and eukaryotic species.

[edit] Function

OGG1 is the primary enzyme responsible for the excision of 7,8-dihydro-8-oxoguanine (8-oxoG), a mutagenic base byproduct that occurs as a result of exposure to reactive oxygen species (ROS). OGG1 is a bifunctional glycosylase, as it is able to both cleave the glycosidic bond of the mutagenic lesion and cause a strand break in the DNA backbone. Alternative splicing of the C-terminal region of this gene classifies splice variants into two major groups, type 1 and type 2, depending on the last exon of the sequence. Type 1 alternative splice variants end with exon 7 and type 2 end with exon 8. All variants have the N-terminal region in common. Many alternative splice variants for this gene have been described, but the full-length nature for every variant has not been determined. In eukaryotes, the N-terminus of this gene contains a mitochondrial targeting signal, essential for mitochondrial localization.^[1] A conserved N-terminal domain contributes residues to the 8-oxoguanine binding pocket. This domain is organised into a single copy of a TBP-like fold.^[2]

Despite the presumed importance of this enzyme, mice lacking Ogg1 have been generated and found to have a normal lifespan,^[3] and despite some early reports, do not show increased mutagenesis or cancer incidence.^{[citation needed]}^{[dubious – discuss]} Interestingly, mice lacking Ogg1 have been shown to be prone to increased body weight and obesity, as well as high-fat diet induced insulin resistance.^[4] There is some controversy as to whether deletion of Ogg1 actually leads to increased 8-oxo-dG levels: the HPLC-EC assay suggests up to 6 fold higher levels of 8-oxo-dG in nuclear DNA and 20-fold higher in mitochondrial DNA whereas the fappy-glycosylase assay indicates no change.^{[citation needed]}

[edit] Interactions

Oxoguanine glycosylase has been shown to interact with XRCC1^[5] and PKC alpha.^[6]

[edit] References

^ "Entrez Gene: OGG1 8-oxoguanine DNA glycosylase". http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=4968.
^ Bjoras M, Seeberg E, Luna L, Pearl LH, Barrett TE (March 2002). "Reciprocal "flipping" underlies substrate recognition and catalytic activation by the human 8-oxo-guanine DNA glycosylase". J. Mol. Biol. 317 (2): 171–7. doi:10.1006/jmbi.2002.5400. PMID 11902834.
^ Klungland A, Rosewell I, Hollenbach S, Larsen E, Daly G, Epe B, Seeberg E, Lindahl T, Barnes DE (November 1999). "Accumulation of premutagenic DNA lesions in mice defective in removal of oxidative base damage". Proc. Natl. Acad. Sci. U.S.A. 96 (23): 13300–5. doi:10.1073/pnas.96.23.13300. PMC 23942. PMID 10557315. //www.ncbi.nlm.nih.gov/pmc/articles/PMC23942/.
^ Sampath H, Vartanian V, Rollins MR, Sakumi K, Nakabeppu Y, Lloyd RS (December 2012). "8-Oxoguanine DNA glycosylase (OGG1) deficiency increases susceptibility to obesity and metabolic dysfunction". PLoS ONE 7 (12): e51697. doi:10.1371/journal.pone.0051697. PMC 3524114. PMID 23284747. //www.ncbi.nlm.nih.gov/pmc/articles/PMC3524114/.
^ Marsin S, Vidal AE, Sossou M, Ménissier-de Murcia J, Le Page F, Boiteux S, de Murcia G, Radicella JP (November 2003). "Role of XRCC1 in the coordination and stimulation of oxidative DNA damage repair initiated by the DNA glycosylase hOGG1". J. Biol. Chem. 278 (45): 44068–74. doi:10.1074/jbc.M306160200. PMID 12933815.
^ Dantzer F, Luna L, Bjørås M, Seeberg E (June 2002). "Human OGG1 undergoes serine phosphorylation and associates with the nuclear matrix and mitotic chromatin in vivo". Nucleic Acids Res. 30 (11): 2349–57. doi:10.1093/nar/30.11.2349. PMC 117190. PMID 12034821. //www.ncbi.nlm.nih.gov/pmc/articles/PMC117190/.

[edit] Further reading

Boiteux S, Radicella JP (2000). "The human OGG1 gene: structure, functions, and its implication in the process of carcinogenesis.". Arch. Biochem. Biophys. 377 (1): 1–8. doi:10.1006/abbi.2000.1773. PMID 10775435.
Park J, Chen L, Tockman MS et al. (2004). "The human 8-oxoguanine DNA N-glycosylase 1 (hOGG1) DNA repair enzyme and its association with lung cancer risk". Pharmacogenetics 14 (2): 103–9. doi:10.1097/00008571-200402000-00004. PMID 15077011.
Hung RJ, Hall J, Brennan P, Boffetta P (2006). "Genetic polymorphisms in the base excision repair pathway and cancer risk: a HuGE review". Am. J. Epidemiol. 162 (10): 925–42. doi:10.1093/aje/kwi318. PMID 16221808.
Mirbahai L, Kershaw RM, Green RM, Hayden RE, Meldrum RA, Hodges NJ. (2010). "Use of a molecular beacon to track the activity of base excision repair protein OGG1 in live cells". DNA Repair 9 (2): 144–152. doi:10.1016/j.dnarep.2009.11.009. PMID 20042377.

[edit] External links

oxoguanine glycosylase 1, human at the US National Library of Medicine Medical Subject Headings (MeSH)

PDB gallery

1ebm: CRYSTAL STRUCTURE OF THE HUMAN 8-OXOGUANINE GLYCOSYLASE (HOGG1) BOUND TO A SUBSTRATE OLIGONUCLEOTIDE

1fn7: COUPLING OF DAMAGE RECOGNITION AND CATALYSIS BY A HUMAN BASE-EXCISION DNA REPAIR PROTEIN

1hu0: CRYSTAL STRUCTURE OF AN HOGG1-DNA BOROHYDRIDE TRAPPED INTERMEDIATE COMPLEX

1ko9: Native Structure of the Human 8-oxoguanine DNA Glycosylase hOGG1

1lwv: Borohydride-trapped hOgg1 Intermediate Structure Co-Crystallized with 8-aminoguanine

1lww: Borohydride-trapped hOgg1 Intermediate Structure Co-Crystallized with 8-bromoguanine

1lwy: hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine

1m3h: Crystal Structure of Hogg1 D268E Mutant with Product Oligonucleotide

1m3q: Crystal Structure of hogg1 D268E Mutant with Base-Excised DNA and 8-aminoguanine

1n39: Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase

1n3a: Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase

1n3c: Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase

1yqk: Human 8-oxoguanine glycosylase crosslinked with guanine containing DNA

1yql: Catalytically inactive hOGG1 crosslinked with 7-deaza-8-azaguanine containing DNA

1yqm: Catalytically inactive human 8-oxoguanine glycosylase crosslinked to 7-deazaguanine containing DNA

1yqr: Catalytically inactive human 8-oxoguanine glycosylase crosslinked to oxoG containing DNA

2i5w: Structure of hOGG1 crosslinked to DNA sampling a normal G adjacent to an oxoG

2nob: Structure of catalytically inactive H270A human 8-oxoguanine glycosylase crosslinked to 8-oxoguanine DNA

2noe: Structure of catalytically inactive G42A human 8-oxoguanine glycosylase complexed to 8-oxoguanine DNA

2nof: Structure of Q315F human 8-oxoguanine glycosylase proximal crosslink to 8-oxoguanine DNA

2noh: Structure of catalytically inactive Q315A human 8-oxoguanine glycosylase complexed to 8-oxoguanine DNA

2noi: Structure of G42A human 8-oxoguanine glycosylase crosslinked to undamaged G-containing DNA

2nol: Structure of catalytically inactive human 8-oxoguanine glycosylase distal crosslink to oxoG DNA

2noz: Structure of Q315F human 8-oxoguanine glycosylase distal crosslink to 8-oxoguanine DNA

Hydrolase: sugar hydrolases (EC 3.2)

3.2.1: Glycoside hydrolases

Disaccharidase	Sucrase/Sucrase-isomaltase/Invertase Maltase Trehalase Lactase

Glucosidases	Cellulase Alpha-glucosidase Acid Neutral AB Neutral C Beta-glucosidase cytosolic Debranching enzyme

Other	Amylase Alpha-amylase Chitinase Lysozyme Neuraminidase NEU1 NEU2 NEU3 NEU4 Bacterial neuraminidase Viral neuraminidase Galactosidases Alpha Beta alpha-Mannosidase Glucuronidase Hyaluronidase Pullulanase Glucosylceramidase lysosomal non-lysosomal Galactosylceramidase Alpha-N-acetylgalactosaminidase NAGA Alpha-N-acetylglucosaminidase Fucosidase Hexosaminidase HEXA HEXB Iduronidase Maltase-glucoamylase Heparanase HPSE2

3.2.2: Hydrolysing
N-Glycosyl compounds

DNA glycosylases: Oxoguanine glycosylase

B
enzm
1.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
- 10
- 11
- 13
- 14
- 15-18
2.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
2.7.10
2.7.11-12
3.1
- - 3.1.3.48
- 2
- 3
- 4
  - 3.4.21
- 5
- 6
- 7
- 22
- 23
- 24
4.1
- 2
- 3
- 4
- 5
- 6
5.1
- 2
- 3
- 4
- 99
6.1-3
- 4
- 5-6

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8-oxoguanine DNA glycosylase, N-terminal domain Provide feedback

The presence of 8-oxoguanine residues in DNA can give rise to G-C to T-A transversion mutations. This enzyme is found in archaeal, bacterial and eukaryotic species, and is specifically responsible for the process which leads to the removal of 8-oxoguanine residues. It has DNA glycosylase activity ( EC:3.2.2.23) and DNA lyase activity ( EC:4.2.99.18) [1]. The region featured in this family is the N-terminal domain, which is organised into a single copy of a TBP-like fold. The domain contributes residues to the 8-oxoguanine binding pocket [2].

Literature references

Bruner SD, Norman DP, Verdine GL; , Nature 2000;403:859-866.: Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA. PUBMED:10706276 EPMC:10706276
Bjoras M, Seeberg E, Luna L, Pearl LH, Barrett TE; , J Mol Biol 2002;317:171-177.: Reciprocal "flipping" underlies substrate recognition and catalytic activation by the human 8-oxo-guanine DNA glycosylase. PUBMED:11902834 EPMC:11902834

External database links

PANDIT:	PF07934
Pseudofam:	PF07934
SCOP:	1ebm
SYSTERS:	OGG_N

This tab holds annotation information from the InterPro database.

InterPro entry IPR012904

The presence of 8-oxoguanine residues in DNA can give rise to G-C to T-A transversion mutations. This enzyme is found in archaeal, bacterial and eukaryotic species, and is specifically responsible for the process which leads to the removal of 8-oxoguanine residues. It has DNA glycosylase activity (EC) and DNA lyase activity (EC) [PUBMED:10706276]. The region featured in this family is the N-terminal domain, which is organised into a single copy of a TBP-like fold. The domain contributes residues to the 8-oxoguanine binding pocket [PUBMED:11902834].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Molecular function	damaged DNA binding (GO:0003684)
Molecular function	oxidized purine base lesion DNA N-glycosylase activity (GO:0008534)
Biological process	nucleotide-excision repair (GO:0006289)

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan TBP-like (CL0407), which contains the following 3 members:

AlkA_N OGG_N TBP

Alignments

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	Seed (95)	Full (767)	Representative proteomes				NCBI (723)	Meta (56)
	Seed (95)	Full (767)	RP15 (121)	RP35 (203)	RP55 (278)	RP75 (324)	NCBI (723)	Meta (56)
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¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (95)	Full (767)	Representative proteomes				NCBI (723)	Meta (56)
	Seed (95)	Full (767)	RP15 (121)	RP35 (203)	RP55 (278)	RP75 (324)	NCBI (723)	Meta (56)
Alignment:
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Sequence:	Inserts lower case All upper case
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Download/view:	Download View

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	Seed (95)	Full (767)	Representative proteomes				NCBI (723)	Meta (56)
	Seed (95)	Full (767)	RP15 (121)	RP35 (203)	RP55 (278)	RP75 (324)	NCBI (723)	Meta (56)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download	Download

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation

Seed source:

Pfam-B_29151 (release 14.0)

Previous IDs:

none

Type:

Family

Author:

Fenech M

Number in seed:

95

Number in full:

767

Average length of the domain:

113.40 aa

Average identity of full alignment:

26 %

Average coverage of the sequence by the domain:

34.56 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	20.1	20.1
Trusted cut-off	20.1	20.3
Noise cut-off	19.5	18.9

Model length:

117

Family (HMM) version:

7

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Species distribution

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Interactive tree

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Interactions

There is 1 interaction for this family. More...

HhH-GPD

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the OGG_N domain has been found. There are 31 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: OGG_N (PF07934)

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