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Conserved domains on  [gi|2159791220|ref|WP_230947426|]
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MULTISPECIES: uracil-DNA glycosylase [Burkholderia cepacia complex]

Protein Classification

uracil-DNA glycosylase( domain architecture ID 10178259)

uracil-DNA glycosylase is a DNA repair enzyme that catalyzes the removal of mismatched uracil from DNA to initiate DNA base excision repair pathway

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
UDG_like cd10035
uncharacterized family of the uracil-DNA glycosylase superfamily; Uracil-DNA glycosylases ...
 45-182 1.57e-40

uncharacterized family of the uracil-DNA glycosylase superfamily; Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil may arise from misincorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations; thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. UDG family 1 is the most efficient uracil-DNA glycosylase (UDG, also known as UNG) and shows a specificity for uracil in DNA. UDG family 2 includes thymine DNA glycosylase which removes uracil and thymine from G:U and G:T mismatches, and mismatch-specific uracil DNA glycosylase (MUG) which in Escherichia coli is highly specific to G:U mismatches, but also repairs G:T mismatches at high enzyme concentration. UDG family 3 includes Human SMUG1 which can remove uracil and its oxidized pyrimidine derivatives from, single-stranded DNA and double-stranded DNA with a preference for single-stranded DNA. Pedobacter heparinus SMUG2, which is UDG family 3 SMUG1-like, displays catalytic activities towards DNA containing uracil or hypoxanthine/xanthine. UDG family 4 includes Thermotoga maritima TTUDGA, a robust UDG which like family 1, acts on double-stranded and single-stranded uracil-containing DNA. UDG family 5 (UDGb) includes Thermus thermophilus HB8 TTUDGB which acts on double-stranded uracil-containing DNA; it is a hypoxanthine DNA glycosylase acting on double-stranded hypoxanthine-containing DNA except for the C/I base pair, as well as a xanthine DNA glycosylase which acts on both double-stranded and single-stranded xanthine-containing DNA. UDG family 6 hypoxanthine-DNA glycosylase lacks any detectable UDG activity; it excises hypoxanthine. Other UDG families include one represented by Bradyrhizobium diazoefficiens Blr0248 which prefers single-stranded DNA and removes uracil, 5-hydroxymethyl-uracil or xanthine from it.


:

Pssm-ID: 381685  Cd Length: 143  Bit Score: 135.07  E-value: 1.57e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2159791220  45 MGRDLGYRGGRRTGLALTDERRLDAVALSYpGAAANKATRGPVVAERTAAEIWAILERL---ERRPLLWNVFPFHPHEAD 121
Cdd:cd10035     1 VPEADGYRGGRFAGVLFTSERPLPKTAAPL-GGELGSGFISRDNDEPTATIVWRALAEAgidRRDPLLWNAVPWHPHKPG 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2159791220 122 DALTNRKFTARELAAVSELNAALFNWL-KIRRIICIGQDAATYAKAF--GVSVECVRHPSYGGV 182
Cdd:cd10035    80 NPLSNRTPTAAELRAGLPFLRELLELLpNLRVVVAVGRKAQRALARLepGIPVLAVRHPSPGGA 143
 
Name Accession Description Interval E-value
UDG_like cd10035
uncharacterized family of the uracil-DNA glycosylase superfamily; Uracil-DNA glycosylases ...
 45-182 1.57e-40

uncharacterized family of the uracil-DNA glycosylase superfamily; Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil may arise from misincorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations; thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. UDG family 1 is the most efficient uracil-DNA glycosylase (UDG, also known as UNG) and shows a specificity for uracil in DNA. UDG family 2 includes thymine DNA glycosylase which removes uracil and thymine from G:U and G:T mismatches, and mismatch-specific uracil DNA glycosylase (MUG) which in Escherichia coli is highly specific to G:U mismatches, but also repairs G:T mismatches at high enzyme concentration. UDG family 3 includes Human SMUG1 which can remove uracil and its oxidized pyrimidine derivatives from, single-stranded DNA and double-stranded DNA with a preference for single-stranded DNA. Pedobacter heparinus SMUG2, which is UDG family 3 SMUG1-like, displays catalytic activities towards DNA containing uracil or hypoxanthine/xanthine. UDG family 4 includes Thermotoga maritima TTUDGA, a robust UDG which like family 1, acts on double-stranded and single-stranded uracil-containing DNA. UDG family 5 (UDGb) includes Thermus thermophilus HB8 TTUDGB which acts on double-stranded uracil-containing DNA; it is a hypoxanthine DNA glycosylase acting on double-stranded hypoxanthine-containing DNA except for the C/I base pair, as well as a xanthine DNA glycosylase which acts on both double-stranded and single-stranded xanthine-containing DNA. UDG family 6 hypoxanthine-DNA glycosylase lacks any detectable UDG activity; it excises hypoxanthine. Other UDG families include one represented by Bradyrhizobium diazoefficiens Blr0248 which prefers single-stranded DNA and removes uracil, 5-hydroxymethyl-uracil or xanthine from it.


Pssm-ID: 381685  Cd Length: 143  Bit Score: 135.07  E-value: 1.57e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2159791220  45 MGRDLGYRGGRRTGLALTDERRLDAVALSYpGAAANKATRGPVVAERTAAEIWAILERL---ERRPLLWNVFPFHPHEAD 121
Cdd:cd10035     1 VPEADGYRGGRFAGVLFTSERPLPKTAAPL-GGELGSGFISRDNDEPTATIVWRALAEAgidRRDPLLWNAVPWHPHKPG 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2159791220 122 DALTNRKFTARELAAVSELNAALFNWL-KIRRIICIGQDAATYAKAF--GVSVECVRHPSYGGV 182
Cdd:cd10035    80 NPLSNRTPTAAELRAGLPFLRELLELLpNLRVVVAVGRKAQRALARLepGIPVLAVRHPSPGGA 143
 
Name Accession Description Interval E-value
UDG_like cd10035
uncharacterized family of the uracil-DNA glycosylase superfamily; Uracil-DNA glycosylases ...
 45-182 1.57e-40

uncharacterized family of the uracil-DNA glycosylase superfamily; Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil may arise from misincorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations; thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. UDG family 1 is the most efficient uracil-DNA glycosylase (UDG, also known as UNG) and shows a specificity for uracil in DNA. UDG family 2 includes thymine DNA glycosylase which removes uracil and thymine from G:U and G:T mismatches, and mismatch-specific uracil DNA glycosylase (MUG) which in Escherichia coli is highly specific to G:U mismatches, but also repairs G:T mismatches at high enzyme concentration. UDG family 3 includes Human SMUG1 which can remove uracil and its oxidized pyrimidine derivatives from, single-stranded DNA and double-stranded DNA with a preference for single-stranded DNA. Pedobacter heparinus SMUG2, which is UDG family 3 SMUG1-like, displays catalytic activities towards DNA containing uracil or hypoxanthine/xanthine. UDG family 4 includes Thermotoga maritima TTUDGA, a robust UDG which like family 1, acts on double-stranded and single-stranded uracil-containing DNA. UDG family 5 (UDGb) includes Thermus thermophilus HB8 TTUDGB which acts on double-stranded uracil-containing DNA; it is a hypoxanthine DNA glycosylase acting on double-stranded hypoxanthine-containing DNA except for the C/I base pair, as well as a xanthine DNA glycosylase which acts on both double-stranded and single-stranded xanthine-containing DNA. UDG family 6 hypoxanthine-DNA glycosylase lacks any detectable UDG activity; it excises hypoxanthine. Other UDG families include one represented by Bradyrhizobium diazoefficiens Blr0248 which prefers single-stranded DNA and removes uracil, 5-hydroxymethyl-uracil or xanthine from it.


Pssm-ID: 381685  Cd Length: 143  Bit Score: 135.07  E-value: 1.57e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2159791220  45 MGRDLGYRGGRRTGLALTDERRLDAVALSYpGAAANKATRGPVVAERTAAEIWAILERL---ERRPLLWNVFPFHPHEAD 121
Cdd:cd10035     1 VPEADGYRGGRFAGVLFTSERPLPKTAAPL-GGELGSGFISRDNDEPTATIVWRALAEAgidRRDPLLWNAVPWHPHKPG 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2159791220 122 DALTNRKFTARELAAVSELNAALFNWL-KIRRIICIGQDAATYAKAF--GVSVECVRHPSYGGV 182
Cdd:cd10035    80 NPLSNRTPTAAELRAGLPFLRELLELLpNLRVVVAVGRKAQRALARLepGIPVLAVRHPSPGGA 143
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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