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Protein

Type-5 uracil-DNA glycosylase

Gene

udgb

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DNA glycosylase with broad substrate specificity. Can remove uracil from double-stranded DNA containing either a U/G, U/A, U/C or U/T base pair (PubMed:12000829, PubMed:17870091, PubMed:24838246). Can also excise hypoxanthine from double-stranded DNA containing G/I, T/I, and A/I base pairs, xanthine from both double-stranded and single stranded DNA, thymine from G/T mismatched DNA, 5'-hydroxymethyluracil and 5'-fluorouracil (PubMed:17870091, PubMed:24838246).3 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi13Iron-sulfur (4Fe-4S)Combined sources1 Publication1
Metal bindingi16Iron-sulfur (4Fe-4S)Combined sources1 Publication1
Metal bindingi115Iron-sulfur (4Fe-4S)Combined sources1 Publication1
Metal bindingi130Iron-sulfur (4Fe-4S)Combined sources1 Publication1

GO - Molecular functioni

  • 4 iron, 4 sulfur cluster binding Source: UniProtKB
  • deaminated base DNA N-glycosylase activity Source: UniProtKB
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • DNA repair Source: UniProtKB

Keywordsi

Molecular functionHydrolase
Biological processDNA damage, DNA repair
Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding

Enzyme and pathway databases

BioCyciTTHE300852:GH8R-1144-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Type-5 uracil-DNA glycosylaseCurated (EC:3.2.2.-3 Publications)
Alternative name(s):
TTUDGB1 Publication
Uracil/hypoxanthine/xanthine DNA glycosylaseCurated
Gene namesi
Name:udgb1 Publication
Ordered Locus Names:TTHA1149Imported
OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Taxonomic identifieri300852 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
Proteomesi
  • UP000000532 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi58L → D: 4-fold decrease in activity. 1 Publication1
Mutagenesisi75D → A: Loss of xanthine DNA glycosylase (XDG) activity. Decrease in uracil DNA glycosylase (UDG) and hypoxanthine DNA glycosylase (HDG) activities. Shows low activity for the removal of uracil from U/G or thymine from T/G. 2 Publications1
Mutagenesisi75D → E: Retains much of its activity. 1 Publication1
Mutagenesisi75D → N or Q: Loss of XDG activity, but retains much of its UDG and HDG activities. 1 Publication1
Mutagenesisi120N → A: Loss of XDG activity. Decrease in UDG and HDG activities. 1 Publication1
Mutagenesisi120N → D: Minimal effect on UDG and XDG activities. Strong reduction on HDG activity on A/I and T/I base pairs. 1 Publication1
Mutagenesisi120N → E: Strong decrease in UDG, HDG and XDG activities. 1 Publication1
Mutagenesisi120N → Q: Loss of XDG activity. Strong decrease in UDG and HDG activities. 1 Publication1
Mutagenesisi190H → A: Loss of UDG, HDG and XDG activities. 1 Publication1
Mutagenesisi190H → N or S: Strong decrease in UDG, HDG and XDG activities. 1 Publication1
Mutagenesisi195N → A, D, E or Q: Retains much of its activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004391871 – 219Type-5 uracil-DNA glycosylaseAdd BLAST219

Interactioni

Protein-protein interaction databases

STRINGi300852.TTHA1149.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2D3YX-ray1.55A1-219[»]
2DDGX-ray2.10A1-219[»]
2DEMX-ray1.95A1-219[»]
2DP6X-ray1.80A1-219[»]
ProteinModelPortaliQ5SJ65.
SMRiQ5SJ65.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5SJ65.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105E50. Bacteria.
COG1573. LUCA.
HOGENOMiHOG000196499.
OMAiHCAPPAN.
PhylomeDBiQ5SJ65.

Family and domain databases

Gene3Di3.40.470.10. 1 hit.
InterProiView protein in InterPro
IPR005122. Uracil-DNA_glycosylase-like.
PfamiView protein in Pfam
PF03167. UDG. 1 hit.
SMARTiView protein in SMART
SM00986. UDG. 1 hit.
SUPFAMiSSF52141. SSF52141. 1 hit.

Sequencei

Sequence statusi: Complete.

Q5SJ65-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDREAFVQTL TACRLCPRLV AWREEVVGRK RAFRGEPYWA RPVPGFGDPE
60 70 80 90 100
ARILLFGLAP GAHGSNRTGR PFTGDASGAF LYPLLHEAGL SSKPESLPGD
110 120 130 140 150
DLRLYGVYLT AAVRCAPPKN KPTPEELRAC ARWTEVELGL LPEVRVYVAL
160 170 180 190 200
GRIALEALLA HFGLRKSAHP FRHGAHYPLP GGRHLLASYH VSRQNTQTGR
210
LTREMFLEVL MEAKRLAGL
Length:219
Mass (Da):24,286
Last modified:December 21, 2004 - v1
Checksum:i10EE764537318207
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008226 Genomic DNA. Translation: BAD70972.1.
RefSeqiWP_011173217.1. NC_006461.1.
YP_144415.1. NC_006461.1.

Genome annotation databases

EnsemblBacteriaiBAD70972; BAD70972; BAD70972.
GeneIDi3169333.
KEGGittj:TTHA1149.
PATRICi23957257. VBITheThe93045_1128.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008226 Genomic DNA. Translation: BAD70972.1.
RefSeqiWP_011173217.1. NC_006461.1.
YP_144415.1. NC_006461.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2D3YX-ray1.55A1-219[»]
2DDGX-ray2.10A1-219[»]
2DEMX-ray1.95A1-219[»]
2DP6X-ray1.80A1-219[»]
ProteinModelPortaliQ5SJ65.
SMRiQ5SJ65.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi300852.TTHA1149.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD70972; BAD70972; BAD70972.
GeneIDi3169333.
KEGGittj:TTHA1149.
PATRICi23957257. VBITheThe93045_1128.

Phylogenomic databases

eggNOGiENOG4105E50. Bacteria.
COG1573. LUCA.
HOGENOMiHOG000196499.
OMAiHCAPPAN.
PhylomeDBiQ5SJ65.

Enzyme and pathway databases

BioCyciTTHE300852:GH8R-1144-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ5SJ65.

Family and domain databases

Gene3Di3.40.470.10. 1 hit.
InterProiView protein in InterPro
IPR005122. Uracil-DNA_glycosylase-like.
PfamiView protein in Pfam
PF03167. UDG. 1 hit.
SMARTiView protein in SMART
SM00986. UDG. 1 hit.
SUPFAMiSSF52141. SSF52141. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiUDGB_THET8
AccessioniPrimary (citable) accession number: Q5SJ65
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 15, 2017
Last sequence update: December 21, 2004
Last modified: March 15, 2017
This is version 70 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

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 one 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.