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Protein

Formamidopyrimidine-DNA glycosylase

Gene

mutM1

more
Organism
Xylella fastidiosa (strain Temecula1 / ATCC 700964)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

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).By similarity

Catalytic activityi

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

Cofactori

Zn2+By similarityNote: Binds 1 zinc ion per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei2 – 21Schiff-base intermediate with DNABy similarity
Active sitei3 – 31Proton donorBy similarity
Active sitei58 – 581Proton donor; for beta-elimination activityBy similarity
Binding sitei92 – 921DNABy similarity
Binding sitei111 – 1111DNABy similarity
Binding sitei152 – 1521DNABy similarity
Active sitei261 – 2611Proton donor; for delta-elimination activityBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri237 – 27135FPG-typeAdd
BLAST

GO - Molecular functioni

  1. damaged DNA binding Source: InterPro
  2. oxidized purine nucleobase lesion DNA N-glycosylase activity Source: UniProtKB-HAMAP
  3. zinc ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. base-excision repair Source: InterPro
  2. nucleotide-excision repair Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase, Lyase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciXFAS183190:GIX4-138-MONOMER.
XFAS183190:GIX4-53-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Formamidopyrimidine-DNA glycosylase (EC:3.2.2.23)
Short name:
Fapy-DNA glycosylase
Alternative name(s):
DNA-(apurinic or apyrimidinic site) lyase MutM (EC:4.2.99.18)
Short name:
AP lyase MutM
Gene namesi
Name:mutM1
Synonyms:fpg1
Ordered Locus Names:PD_0053
AND
Name:mutM2
Synonyms:fpg2
Ordered Locus Names:PD_0138
OrganismiXylella fastidiosa (strain Temecula1 / ATCC 700964)
Taxonomic identifieri183190 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXylella
ProteomesiUP000002516 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedBy similarity
Chaini2 – 271270Formamidopyrimidine-DNA glycosylasePRO_0000170889Add
BLAST

Interactioni

Subunit structurei

Monomer.By similarity

Protein-protein interaction databases

STRINGi183190.PD0138.

Family & Domainsi

Sequence similaritiesi

Belongs to the FPG family.Curated
Contains 1 FPG-type zinc finger.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri237 – 27135FPG-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG0266.
KOiK10563.
OMAiAKHILIF.
OrthoDBiEOG6QP131.

Family and domain databases

HAMAPiMF_00103. Fapy_DNA_glycosyl.
InterProiIPR015886. DNA_glyclase/AP_lyase_DNA-bd.
IPR015887. DNA_glyclase_Znf_dom_DNA_BS.
IPR012319. DNA_glycosylase/AP_lyase_cat.
IPR020629. Formamido-pyr_DNA_Glyclase.
IPR010979. Ribosomal_S13-like_H2TH.
IPR000214. Znf_DNA_glyclase/AP_lyase.
[Graphical view]
PfamiPF01149. Fapy_DNA_glyco. 1 hit.
PF06831. H2TH. 1 hit.
[Graphical view]
SMARTiSM00898. Fapy_DNA_glyco. 1 hit.
[Graphical view]
SUPFAMiSSF46946. SSF46946. 1 hit.
SSF81624. SSF81624. 1 hit.
TIGRFAMsiTIGR00577. fpg. 1 hit.
PROSITEiPS51068. FPG_CAT. 1 hit.
PS01242. ZF_FPG_1. 1 hit.
PS51066. ZF_FPG_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P64155-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPELPEVETT LRGLLPYLTN QLIYSLTLRR RTLRWDIPSH IESRLPGHRI
60 70 80 90 100
TTVCRRAKYL LIDTNAGGSL IIHLGMSGTL RLLAPETPLR PHDHVDIMLN
110 120 130 140 150
NRRVLRFNDP RRFGCLLWQE DGQIHPLLQR LGCEPLSDSF NGDYLYQCSR
160 170 180 190 200
ARNVSVKTFL MDQRIVVGVG NIYAAESLFR AGISPLCEAD KISLQRYRRL
210 220 230 240 250
AEVVKDILLY AINRGGTTLR DFLSPDGRPG YFKQELFVYG RQQQPCKQCG
260 270
SLLRQTTIRQ RTTVWCGHCQ G
Length:271
Mass (Da):31,091
Last modified:January 23, 2007 - v3
Checksum:i3FF8AFA1617695DF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009442 Genomic DNA. Translation: AAO27954.1.
AE009442 Genomic DNA. Translation: AAO28032.1.
RefSeqiNP_778305.1. NC_004556.1.
NP_778383.1. NC_004556.1.

Genome annotation databases

EnsemblBacteriaiAAO27954; AAO27954; PD_0053.
AAO28032; AAO28032; PD_0138.
KEGGixft:PD0053.
xft:PD0138.
PATRICi24147482. VBIXylFas71109_0076.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009442 Genomic DNA. Translation: AAO27954.1.
AE009442 Genomic DNA. Translation: AAO28032.1.
RefSeqiNP_778305.1. NC_004556.1.
NP_778383.1. NC_004556.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi183190.PD0138.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAO27954; AAO27954; PD_0053.
AAO28032; AAO28032; PD_0138.
KEGGixft:PD0053.
xft:PD0138.
PATRICi24147482. VBIXylFas71109_0076.

Phylogenomic databases

eggNOGiCOG0266.
KOiK10563.
OMAiAKHILIF.
OrthoDBiEOG6QP131.

Enzyme and pathway databases

BioCyciXFAS183190:GIX4-138-MONOMER.
XFAS183190:GIX4-53-MONOMER.

Family and domain databases

HAMAPiMF_00103. Fapy_DNA_glycosyl.
InterProiIPR015886. DNA_glyclase/AP_lyase_DNA-bd.
IPR015887. DNA_glyclase_Znf_dom_DNA_BS.
IPR012319. DNA_glycosylase/AP_lyase_cat.
IPR020629. Formamido-pyr_DNA_Glyclase.
IPR010979. Ribosomal_S13-like_H2TH.
IPR000214. Znf_DNA_glyclase/AP_lyase.
[Graphical view]
PfamiPF01149. Fapy_DNA_glyco. 1 hit.
PF06831. H2TH. 1 hit.
[Graphical view]
SMARTiSM00898. Fapy_DNA_glyco. 1 hit.
[Graphical view]
SUPFAMiSSF46946. SSF46946. 1 hit.
SSF81624. SSF81624. 1 hit.
TIGRFAMsiTIGR00577. fpg. 1 hit.
PROSITEiPS51068. FPG_CAT. 1 hit.
PS01242. ZF_FPG_1. 1 hit.
PS51066. ZF_FPG_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa."
    Van Sluys M.A., de Oliveira M.C., Monteiro-Vitorello C.B., Miyaki C.Y., Furlan L.R., Camargo L.E.A., da Silva A.C.R., Moon D.H., Takita M.A., Lemos E.G.M., Machado M.A., Ferro M.I.T., da Silva F.R., Goldman M.H.S., Goldman G.H., Lemos M.V.F., El-Dorry H., Tsai S.M.
    , Carrer H., Carraro D.M., de Oliveira R.C., Nunes L.R., Siqueira W.J., Coutinho L.L., Kimura E.T., Ferro E.S., Harakava R., Kuramae E.E., Marino C.L., Giglioti E., Abreu I.L., Alves L.M.C., do Amaral A.M., Baia G.S., Blanco S.R., Brito M.S., Cannavan F.S., Celestino A.V., da Cunha A.F., Fenille R.C., Ferro J.A., Formighieri E.F., Kishi L.T., Leoni S.G., Oliveira A.R., Rosa V.E. Jr., Sassaki F.T., Sena J.A.D., de Souza A.A., Truffi D., Tsukumo F., Yanai G.M., Zaros L.G., Civerolo E.L., Simpson A.J.G., Almeida N.F. Jr., Setubal J.C., Kitajima J.P.
    J. Bacteriol. 185:1018-1026(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Temecula1 / ATCC 700964.

Entry informationi

Entry nameiFPG_XYLFT
AccessioniPrimary (citable) accession number: P64155
Secondary accession number(s): Q9P9S8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: January 23, 2007
Last modified: April 29, 2015
This is version 78 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Multifunctional enzyme

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.