P42371 (FPG_LACLC) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Formamidopyrimidine-DNA glycosylase
Short name=Fapy-DNA glycosylase
EC=3.2.2.23

Alternative name(s):
DNA-(apurinic or apyrimidinic site) lyase MutM
Short name=AP lyase MutM
EC=4.2.99.18

Gene names

Name:	mutM
Synonyms:	fpg

Organism

Lactococcus lactis subsp. cremoris (Streptococcus cremoris)

Taxonomic identifier

1359 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Lactobacillales › Streptococcaceae › Lactococcus › Lactococcus lactis

Protein attributes

Sequence length	273 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
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. Ref.1
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 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
Cofactor	Binds 1 zinc ion per subunit.
Subunit structure	Monomer.
Miscellaneous	The zinc finger is important for DNA binding. HAMAP-Rule MF_00103
Sequence similarities	Belongs to the FPG family. Contains 1 FPG-type zinc finger.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Domain	Zinc-finger
Ligand	DNA-binding Metal-binding Zinc
Molecular function	Glycosidase Hydrolase Lyase
Technical term	3D-structure Direct protein sequencing Multifunctional enzyme
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

Molecule processing

Initiator methionine

1

1

Removed Ref.1

Chain

2 – 273

272

Formamidopyrimidine-DNA glycosylase HAMAP-Rule MF_00103

PRO_0000170830

Regions

Zinc finger

238 – 272

35

FPG-type HAMAP-Rule MF_00103

Region

58 – 76

19

DNA binding HAMAP-Rule MF_00103

Region

162 – 172

11

DNA binding HAMAP-Rule MF_00103

Sites

Active site

2

1

Schiff-base intermediate with DNA Probable

Active site

3

1

Proton donor Probable

Active site

58

1

Proton donor; for beta-elimination activity Probable

Active site

262

1

Proton donor; for delta-elimination activity Probable

Binding site

92

1

DNA

Binding site

110

1

DNA

Experimental info

Mutagenesis

2

1

P → G: Loss of activity.

Secondary structure

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273

Helix Strand Turn

Details...

Helix

4 – 18

15

Beta strand

25 – 29

5

Helix

31 – 33

3

Helix

38 – 45

8

Beta strand

49 – 56

8

Beta strand

59 – 64

6

Turn

65 – 67

3

Beta strand

68 – 73

6

Turn

75 – 77

3

Beta strand

79 – 83

5

Beta strand

93 – 98

6

Beta strand

103 – 107

5

Beta strand

114 – 119

6

Helix

120 – 122

3

Helix

123 – 129

7

Helix

144 – 152

9

Helix

158 – 163

6

Beta strand

165 – 169

5

Helix

173 – 182

10

Helix

191 – 193

3

Helix

196 – 215

20

Beta strand

221 – 223

3

Turn

227 – 230

4

Helix

233 – 236

4

Turn

248 – 250

3

Beta strand

255 – 259

5

Beta strand

262 – 266

5

Turn

268 – 270

3

Sequences

	Sequence		Length	Mass (Da)
	P42371 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: EB16055C5E09840F	FASTA	273	31,310
	10 20 30 40 50 60 MPELPEVETV RRELEKRIVG QKIISIEATY PRMVLTGFEQ LKKELTGKTI QGISRRGKYL 70 80 90 100 110 120 IFEIGDDFRL ISHLRMEGKY RLATLDAPRE KHDHLTMKFA DGQLIYADVR KFGTWELIST 130 140 150 160 170 180 DQVLPYFLKK KIGPEPTYDE DFDEKLFREK LRKSTKKIKP YLLEQTLVAG LGNIYVDEVL 190 200 210 220 230 240 WLAKIHPEKE TNQLIESSIH LLHDSIIEIL QKAIKLGGSS IRTYSALGST GKMQNELQVY 250 260 270 GKTGEKCSRC GAEIQKIKVA GRGTHFCPVC QQK

References

[1]	"Repair of oxidative DNA damage in Gram-positive bacteria: the Lactococcus lactis Fpg protein." Duwat P., de Oliveira R., Ehrlich S.D., Boiteux S. Microbiology 141:411-417(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-22, FUNCTION. Strain: NCDO 763 / ML3.
[2]	"Use of degenerate primers for polymerase chain reaction cloning and sequencing of the Lactococcus lactis subsp. lactis recA gene." Duwat P., Ehrlich S.D., Gruss A. Appl. Environ. Microbiol. 58:2674-2678(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 194-273. Strain: NCDO 763 / ML3.
[3]	"Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA." Serre L., Pereira de Jesus K., Boiteux S., Zelwer C., Castaing B. EMBO J. 21:2854-2865(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 1-273 OF MUTANT GLY-2 IN COMPLEX WITH SUBSTRATE ANALOG.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X74298 Genomic DNA. Translation: CAA52351.1.
M88106 Genomic DNA. No translation available.

PIR

S39200.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1KFV	X-ray	2.55	A/B	3-273	[»]
1NNJ	X-ray	1.90	A	3-273	[»]
1PJI	X-ray	1.90	A	2-273	[»]
1PJJ	X-ray	1.90	A	3-273	[»]
1PM5	X-ray	1.95	A	2-273	[»]
1TDZ	X-ray	1.80	A	1-273	[»]
1XC8	X-ray	1.95	A	2-273	[»]
2XZF	X-ray	1.80	A	2-273	[»]
2XZU	X-ray	1.82	A	2-273	[»]
3C58	X-ray	1.90	A	2-273	[»]

ProteinModelPortal

P42371.

SMR

P42371. Positions 2-273.

ModBase

Search...

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

Search...

Other

EvolutionaryTrace

P42371.

Entry information

Entry name

FPG_LACLC

Accession

Primary (citable) accession number: P42371

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1995
Last sequence update:	January 23, 2007
Last modified:	April 3, 2013
This is version 102 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program