Reviewed, UniProtKB/Swiss-Prot Q8U2D5 (AGOG_PYRFU)

Names and origin

Protein names

Recommended name:
    N-glycosylase/DNA lyase
Alternative name(s):
    AGOG
    8-oxoguanine DNA glycosylase
    EC=3.2.2.-
    DNA-(apurinic or apyrimidinic site) lyase
      Short name=AP lyase
    EC=4.2.99.18

Gene names

Ordered Locus Names:

PF0904

Organism

Pyrococcus furiosus [Complete proteome] [HAMAP]

Taxonomic identifier

2261 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus

Protein attributes

Sequence length	242 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	DNA repair enzyme that is part of the base excision repair (BER) pathway; protects from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine (GO), from single- and double-stranded DNA substrates By similarity. HAMAP MF_01168
Catalytic activity	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 MF_01168
Domain	Contains two alpha-helical subdomains, with the 8-oxoguanine binding site located in a cleft at their interface. Contains a helix-hairpin-helix (HhH) structural motif and a Gly/Pro-rich sequence followed by a conserved Asp (HhH-GPD motif). HAMAP MF_01168
Sequence similarities	Belongs to the archaeal N-glycosylase/DNA lyase (AGOG) family.

Ontologies

Keywords
Biological process	DNA damage DNA excision DNA repair
Molecular function	Hydrolase Lyase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	base-excision repair Inferred from electronic annotation. Source: HAMAP
Molecular function	DNA-(apurinic or apyrimidinic site) lyase activity Inferred from electronic annotation. Source: HAMAP oxidized base lesion DNA N-glycosylase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 242

242

N-glycosylase/DNA lyase HAMAP MF_01168

PRO_0000185114

Regions

Region

120 – 184

65

Helix-hairpin-helix HAMAP MF_01168

Sites

Active site

144

1

Schiff-base intermediate with DNA By similarity

Active site

176

1

Potential

Binding site

26

1

8-oxoguanine By similarity

Binding site

53

1

8-oxoguanine; via carbonyl oxygen By similarity

Binding site

64

1

8-oxoguanine By similarity

Binding site

148

1

8-oxoguanine By similarity

Binding site

174

1

8-oxoguanine; via carbonyl oxygen By similarity

Binding site

210

1

8-oxoguanine By similarity

Binding site

214

1

8-oxoguanine By similarity

Secondary structure

1

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242

Helix Strand Turn

Details...

Helix

2 – 22

21

Helix

25 – 34

10

Helix

39 – 51

13

Helix

60 – 71

12

Helix

79 – 86

8

Turn

87 – 89

3

Helix

97 – 112

16

Helix

116 – 124

9

Helix

126 – 137

12

Helix

144 – 160

17

Helix

177 – 184

8

Helix

191 – 202

12

Helix

206 – 217

12

Helix

227 – 239

13

Sequences

	Sequence		Length	Mass (Da)
	Q8U2D5-1 [UniParc]. Last modified June 1, 2002. Version 1. Checksum: 6FA190D348D3E823	FASTA	242	28,345
	10 20 30 40 50 60 MRELVEIIKG IGIEGAKEVE EKVDRQFYAL QYLFRHQDPE MFIKLVIANS LVSYQLTGRG 70 80 90 100 110 120 EDWWWEFARY FSGREVDSIW KAYGEFLPKS KNNRRLIEAK LNRIRKVEGF LSTLTLKDLE 130 140 150 160 170 180 GYYKNMKMLW KALIKIMGSR EDSKTIVFTV KMFGYASRIA FSRFIPYPME IPIPEDLRIK 190 200 210 220 230 240 SVTSKLTQEK PTKFWMKIGQ ESGVPPLHID SLIWPLLGNA DLTPLDIELR NKLMKLTELL GL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The complete sequence of the Pyrococcus furiosus genome." Weiss R.B., Dunn D.M., Robb F.T., Brown J.R. Submitted (FEB-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
[2]	"Conserved hypothetical protein Pfu-877259-001 from Pyrococcus furiosus." Chang J., Zhao M., Horanyi P., Xu H., Yang H., Liu Z.-J., Chen L., Zhou W., Habel J., Tempel W., Lee D., Lin D., Chang S.-H., Eneh J.C., Hopkins R.C., Jenney F.E., Lee H.-S., Li T. , Poole F.L., Shah C., Sugar F.J., Chen C.-Y., Arendall W.B., Richardson J.S., Richardson D.C., Rose J.P. Submitted (SEP-2004) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE009950 Genomic DNA. Translation: AAL81028.1.

RefSeq

NP_578633.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1XG7	X-ray	1.88	A/B	2-242	[»]

ModBase

Search...

Genome annotation databases

GeneID

1468768.

GenomeReviews

Gene locus PF0904 in contig AE009950_GR.

KEGG

pfu:PF0904.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

HBG539606.

OMA

PLHIDSI.

Enzyme and pathway databases

BRENDA

4.2.99.18. 321.

Family and domain databases

HAMAP

MF_01168. AGOG.
[Tree]

InterPro

IPR015254. N-Glyclase/DNA_lyase-like_arc.
IPR016544. N-Glyclase/DNA_lyase_arc.
[Graphical view]

Pfam

PF09171. DUF1886. 1 hit.
[Graphical view]

PIRSF

PIRSF008955. AGOG. 1 hit.

ProtoNet

Search...

Entry information

Entry name

AGOG_PYRFU

Accession

Primary (citable) accession number: Q8U2D5

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 10, 2006
Last sequence update:	June 1, 2002
Last modified:	January 19, 2010
This is version 41 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)