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Q8DDY4

- FPG_VIBVU

UniProt

Q8DDY4 - FPG_VIBVU

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Protein

Formamidopyrimidine-DNA glycosylase

Gene
mutM, fpg, VV1_0821
Organism
Vibrio vulnificus (strain CMCP6)
Status
Reviewed - 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.UniRule annotation

Catalytic activityi

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

Cofactori

Binds 1 zinc ion per subunit By similarity.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei2 – 21Schiff-base intermediate with DNA By similarity
Active sitei3 – 31Proton donor By similarity
Active sitei57 – 571Proton donor; for beta-elimination activity By similarity
Binding sitei90 – 901DNA By similarity
Binding sitei109 – 1091DNA By similarity
Binding sitei150 – 1501DNA By similarity
Active sitei259 – 2591Proton donor; for delta-elimination activity By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri235 – 26935FPG-typeUniRule annotationAdd
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

BioCyciVVUL216895:GIYM-771-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:mutM
Synonyms:fpg
Ordered Locus Names:VV1_0821
OrganismiVibrio vulnificus (strain CMCP6)
Taxonomic identifieri216895 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000002275: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed By similarity
Chaini2 – 269268Formamidopyrimidine-DNA glycosylaseUniRule annotationPRO_0000170884Add
BLAST

Interactioni

Subunit structurei

Monomer By similarity.UniRule annotation

Protein-protein interaction databases

STRINGi216895.VV1_0821.

Structurei

3D structure databases

ProteinModelPortaliQ8DDY4.
SMRiQ8DDY4. Positions 2-268.

Family & Domainsi

Sequence similaritiesi

Belongs to the FPG family.

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG0266.
HOGENOMiHOG000020881.
KOiK10563.
OMAiDHVDLKL.
OrthoDBiEOG6QP131.

Family and domain databases

HAMAPiMF_00103. Fapy_DNA_glycosyl.
InterProiIPR015886. 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]
PfamiPF01149. Fapy_DNA_glyco. 1 hit.
PF06831. H2TH. 1 hit.
PF06827. zf-FPG_IleRS. 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.

Q8DDY4-1 [UniParc]FASTAAdd to Basket

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MPELPEVEVS RMGITPHLLN QTIQSLIFRT PKLRWVIPSE LKKLQGQVIR    50
HIGRRAKYLI IETDVGSAIV HLGMSGSLRV LDADFPAGKH DHVDLKLSNG 100
KVLRYNDPRR FGAWLYAAPG EDHDVLGNIG PEPLTNAFDG QYMFEKAQGK 150
RVAVKQFIMD NKIVVGVGNI YASESLFRSR ILPTRATMSL SAEEWQRLVS 200
HIKQTLQTAI EQGGTTLKDF SQADGKPGYF AQELQVYGKA GEPCPECGEA 250
IQEQKIGQRN TFYCSYCQC 269
Length:269
Mass (Da):30,091
Last modified:January 23, 2007 - v3
Checksum:i01DA42E2FA4695A7
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE016795 Genomic DNA. Translation: AAO09325.1.
RefSeqiNP_759798.1. NC_004459.3.

Genome annotation databases

EnsemblBacteriaiAAO09325; AAO09325; VV1_0821.
GeneIDi1177761.
KEGGivvu:VV1_0821.
PATRICi20158472. VBIVibVul94426_0806.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE016795 Genomic DNA. Translation: AAO09325.1 .
RefSeqi NP_759798.1. NC_004459.3.

3D structure databases

ProteinModelPortali Q8DDY4.
SMRi Q8DDY4. Positions 2-268.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 216895.VV1_0821.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAO09325 ; AAO09325 ; VV1_0821 .
GeneIDi 1177761.
KEGGi vvu:VV1_0821.
PATRICi 20158472. VBIVibVul94426_0806.

Phylogenomic databases

eggNOGi COG0266.
HOGENOMi HOG000020881.
KOi K10563.
OMAi DHVDLKL.
OrthoDBi EOG6QP131.

Enzyme and pathway databases

BioCyci VVUL216895:GIYM-771-MONOMER.

Family and domain databases

HAMAPi MF_00103. Fapy_DNA_glycosyl.
InterProi 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 ]
Pfami PF01149. Fapy_DNA_glyco. 1 hit.
PF06831. H2TH. 1 hit.
PF06827. zf-FPG_IleRS. 1 hit.
[Graphical view ]
SMARTi SM00898. Fapy_DNA_glyco. 1 hit.
[Graphical view ]
SUPFAMi SSF46946. SSF46946. 1 hit.
SSF81624. SSF81624. 1 hit.
TIGRFAMsi TIGR00577. fpg. 1 hit.
PROSITEi PS51068. FPG_CAT. 1 hit.
PS01242. ZF_FPG_1. 1 hit.
PS51066. ZF_FPG_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Complete genome sequence of Vibrio vulnificus CMCP6."
    Rhee J.H., Kim S.Y., Chung S.S., Kim J.J., Moon Y.H., Jeong H., Choy H.E.
    Submitted (DEC-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CMCP6.

Entry informationi

Entry nameiFPG_VIBVU
AccessioniPrimary (citable) accession number: Q8DDY4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 4, 2003
Last sequence update: January 23, 2007
Last modified: May 14, 2014
This is version 83 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

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