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Conserved domains on  [gi|1189398122|ref|NP_001338166|]
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single-strand selective monofunctional uracil DNA glycosylase isoform 2 [Homo sapiens]

Protein Classification

uracil-DNA glycosylase family protein( domain architecture ID 1526)

uracil-DNA glycosylase family protein may be a DNA repair enzyme that catalyzes the removal of mismatched uracil from DNA to initiate DNA base excision repair pathway

EC:  3.2.2.-
PubMed:  11178247|19909758
SCOP:  4003607

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
UDG-like super family cl00483
uracil-DNA glycosylases (UDG) and related enzymes; Uracil-DNA glycosylases (UDGs) initiate ...
 29-135 1.47e-71

uracil-DNA glycosylases (UDG) and related enzymes; 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.


The actual alignment was detected with superfamily member cd19374:

Pssm-ID: 444933  Cd Length: 232  Bit Score: 215.44  E-value: 1.47e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1189398122  29 ESFLEEELRLNAELSQLQFSEPVGIIYNPVEYAWEPHRNYVTRYCQGPKEVLFLGMNPGPFGMAQTGVPFGEVSMVRDWL 108
Cdd:cd19374     1 EKLLEIARRLSEELDALRFSEPVAHVYNPLEYAWEPHEAYLRRYGNGGKKVLFLGMNPGPWGMAQTGVPFGEVAAVRDWL 80

                          90       100
                  ....*....|....*....|....*..
gi 1189398122 109 GIVGPVLTPPQEHPKRPVLGLECPQSE 135
Cdd:cd19374    81 GIEGPVGKPEKEHPKRPVEGFECPRSE 107
 
Name Accession Description Interval E-value
UDG-F3_SMUG1-like cd19374
Uracil DNA glycosylase family 3 subfamily, includes single-strand-selective monofunctional ...
 29-135 1.47e-71

Uracil DNA glycosylase family 3 subfamily, includes single-strand-selective monofunctional uracil-DNA glycosylase 1 and similar proteins; Uracil DNA glycosylase family 3 includes Human SMUG1 that can remove uracil and its oxidized pyrimidine derivatives from both, single-stranded DNA and double-stranded DNA, with a preference for single-stranded DNA substrates. The SMUG-targeted mismatched uracil derivatives include 5-hydroxyuracil, 5-hydroxymethyluracil and 5-formyluracil. Also included in this subfamily is Geobacter metallireducens SMUG1 which has dual substrate specificities for DNA with uracil or xanthine. UDG catalyzes the removal of uracil from DNA to initiate the DNA base excision repair pathway. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or deamination of cytosine. Uracil mispaired with guanine in DNA 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.


Pssm-ID: 381689  Cd Length: 232  Bit Score: 215.44  E-value: 1.47e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1189398122  29 ESFLEEELRLNAELSQLQFSEPVGIIYNPVEYAWEPHRNYVTRYCQGPKEVLFLGMNPGPFGMAQTGVPFGEVSMVRDWL 108
Cdd:cd19374     1 EKLLEIARRLSEELDALRFSEPVAHVYNPLEYAWEPHEAYLRRYGNGGKKVLFLGMNPGPWGMAQTGVPFGEVAAVRDWL 80

                          90       100
                  ....*....|....*....|....*..
gi 1189398122 109 GIVGPVLTPPQEHPKRPVLGLECPQSE 135
Cdd:cd19374    81 GIEGPVGKPEKEHPKRPVEGFECPRSE 107
 
Name Accession Description Interval E-value
UDG-F3_SMUG1-like cd19374
Uracil DNA glycosylase family 3 subfamily, includes single-strand-selective monofunctional ...
 29-135 1.47e-71

Uracil DNA glycosylase family 3 subfamily, includes single-strand-selective monofunctional uracil-DNA glycosylase 1 and similar proteins; Uracil DNA glycosylase family 3 includes Human SMUG1 that can remove uracil and its oxidized pyrimidine derivatives from both, single-stranded DNA and double-stranded DNA, with a preference for single-stranded DNA substrates. The SMUG-targeted mismatched uracil derivatives include 5-hydroxyuracil, 5-hydroxymethyluracil and 5-formyluracil. Also included in this subfamily is Geobacter metallireducens SMUG1 which has dual substrate specificities for DNA with uracil or xanthine. UDG catalyzes the removal of uracil from DNA to initiate the DNA base excision repair pathway. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or deamination of cytosine. Uracil mispaired with guanine in DNA 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.


Pssm-ID: 381689  Cd Length: 232  Bit Score: 215.44  E-value: 1.47e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1189398122  29 ESFLEEELRLNAELSQLQFSEPVGIIYNPVEYAWEPHRNYVTRYCQGPKEVLFLGMNPGPFGMAQTGVPFGEVSMVRDWL 108
Cdd:cd19374     1 EKLLEIARRLSEELDALRFSEPVAHVYNPLEYAWEPHEAYLRRYGNGGKKVLFLGMNPGPWGMAQTGVPFGEVAAVRDWL 80

                          90       100
                  ....*....|....*....|....*..
gi 1189398122 109 GIVGPVLTPPQEHPKRPVLGLECPQSE 135
Cdd:cd19374    81 GIEGPVGKPEKEHPKRPVEGFECPRSE 107
UDG-like cd09593
uracil-DNA glycosylases (UDG) and related enzymes; Uracil-DNA glycosylases (UDGs) initiate ...
 79-99 5.90e-03

uracil-DNA glycosylases (UDG) and related enzymes; 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: 381677  Cd Length: 125  Bit Score: 35.06  E-value: 5.90e-03
                          10        20
                  ....*....|....*....|.
gi 1189398122  79 VLFLGMNPGPFGMAQTGVPFG 99
Cdd:cd09593     1 VLIVGQNPGPHGARAGGVPPG 21
UDG-F3-like_SMUG2 cd19375
Uracil DNA glycosylase family 3-like subfamily, includes single-strand-selective ...
 77-98 7.67e-03

Uracil DNA glycosylase family 3-like subfamily, includes single-strand-selective monofunctional uracil-DNA glycosylase 2 and similar proteins; Uracil DNA glycosylase family 3-like, which includes Pedobacter heparinus SMUG2, displays catalytic activities towards DNA containing uracil or hypoxanthine/xanthine. UDG catalyzes the removal of uracil from DNA to initiate the DNA base excision repair pathway. Uracil in DNA can arise as a result of misincorporation of dUMP residues by DNA polymerase or deamination of cytosine. Uracil mispaired with guanine in DNA 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.


Pssm-ID: 381690  Cd Length: 218  Bit Score: 35.50  E-value: 7.67e-03
                          10        20
                  ....*....|....*....|..
gi 1189398122  77 KEVLFLGMNPGPFGMAQTGVPF 98
Cdd:cd19375    50 KRVLILGINPGRFGAGVTGIPF 71
 
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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