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Conserved domains on  [gi|692357218|gb|KGG88842|]
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DNA polymerase [Comamonas thiooxydans]

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 ...
 184-300 1.21e-19

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 cd10030:

Pssm-ID: 444933  Cd Length: 165  Bit Score: 84.03  E-value: 1.21e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 692357218 184 GDAAKLLDNMLRALGLQEKpRVF--SAALHRAPPDADLSHA--QALQPALETLLRELRPDCVLVLGLASARAVLGRHDAL 259
Cdd:cd10030   44 GRAGKLLDKMLAAIGLSRE-DVYitNVVKCRPPGNRTPTPEeiAACRPFLDRQIELIKPKVIVTLGRTAAQALLGKDAPI 122

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 692357218 260 GRLRAEPHHI-AGVPTVVTYDPNYLLRAPQAKAGAWADLVQA 300
Cdd:cd10030  123 SKLRGKWHEYeKGIPVLPTYHPAALLRNPSLKRLAWEDLKKL 164
 
Name Accession Description Interval E-value
UDG-F4_TTUDGA_SPO1dp_like cd10030
Uracil DNA glycosylase family 4, includes Thermotoga maritima TTUDGA, Bacillus phage SPO1 DNA ...
 184-300 1.21e-19

Uracil DNA glycosylase family 4, includes Thermotoga maritima TTUDGA, Bacillus phage SPO1 DNA polymerase, and similar proteins; Uracil DNA glycosylase family 4 includes Thermotoga maritima TTUDGA, a robust uracil DNA glycosylase that shares narrow substrate specificity and high catalytic efficiency with family 1, acting on double-stranded and single-stranded uracil-containing DNA. Members of this family possess four conserved cysteine residues required to coordinate the [4Fe-4S] iron-sulfur cluster. This family also includes the N-terminal domain of Bacillus phage SPO1 DNA polymerase. Bacteriophage SPO1 is one of a group of large, lytic, tailed bacteriophages of Bacillus subtilis, and contains hydroxymethyluracil (hmUra) in place of thymine in their DNA. It has been speculated that this UDG domain may help discriminate between hmUra containing SPO1 DNA and thymine-containing host DNA. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil in DNA can arise as a result of mis-incorporation 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.


Pssm-ID: 381680  Cd Length: 165  Bit Score: 84.03  E-value: 1.21e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 692357218 184 GDAAKLLDNMLRALGLQEKpRVF--SAALHRAPPDADLSHA--QALQPALETLLRELRPDCVLVLGLASARAVLGRHDAL 259
Cdd:cd10030   44 GRAGKLLDKMLAAIGLSRE-DVYitNVVKCRPPGNRTPTPEeiAACRPFLDRQIELIKPKVIVTLGRTAAQALLGKDAPI 122

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 692357218 260 GRLRAEPHHI-AGVPTVVTYDPNYLLRAPQAKAGAWADLVQA 300
Cdd:cd10030  123 SKLRGKWHEYeKGIPVLPTYHPAALLRNPSLKRLAWEDLKKL 164
Udg4 COG1573
Uracil-DNA glycosylase [Replication, recombination and repair];
184-300 2.02e-17

Uracil-DNA glycosylase [Replication, recombination and repair];


Pssm-ID: 441181  Cd Length: 189  Bit Score: 78.70  E-value: 2.02e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 692357218 184 GDAAKLLDNMLRALGLQEKpRVF-SAALHRAPP---DADLSHAQALQPALETLLRELRPDCVLVLGLASARAVLGRHDAL 259
Cdd:COG1573   63 GRAGQLLDKMLAAAGLARE-DVYiTNAVKCRPPgnrKPTPEEIAACRPFLEREIALIRPKVIVALGATAAQALLGAGERI 141

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 692357218 260 GRLRAEPHHIA-GVPTVVTYDPNYLLRAPQAKAGAWADLVQA 300
Cdd:COG1573  142 TRLRGKWHELPgGIPLLPTYHPSYLLRNPTTKREAWEDLLAA 183
UDG pfam03167
Uracil DNA glycosylase superfamily;
159-297 1.32e-10

Uracil DNA glycosylase superfamily;


Pssm-ID: 397331  Cd Length: 154  Bit Score: 58.90  E-value: 1.32e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 692357218  159 EPAANPPLLSPAQRPAADSAQT--ALQGDAAKLLDNMLRALGLQEKP----RVF-SAALHRAPPDADLSHAQALQ---PA 228
Cdd:pfam03167   3 FGPPNAKVLIVGEAPGADEDATglPFVGRAGNLLWKLLNAAGLTRDLfspqGVYiTNVVKCRPGNRRKPTSHEIDacwPY 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 692357218  229 LETLLRELRPDCVLVLGLASARAVLGrHDALGRLRAEPHHIAGVPTVVTYDPNYLLRA---PQAKAGAWADL 297
Cdd:pfam03167  83 LEAEIELLRPRVIVLLGKTAAKALLG-LKKITKLRGKLIDLKGIPVLPTPHPSPLLRNklnPFLKANAWEDL 153
UDG smart00986
Uracil DNA glycosylase superfamily;
184-297 3.55e-06

Uracil DNA glycosylase superfamily;


Pssm-ID: 214956  Cd Length: 156  Bit Score: 46.23  E-value: 3.55e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 692357218   184 GDAAKLLDNMLRALGLQEKPRVFSAALHRAPPDA-----DLSHAQA-LQPALETLLRELRPDCVLVLGLASARAVLG--R 255
Cdd:smart00986  30 GAAGLLLSVMLGVAGLPRLPPYLTNIVKCRPPDAgnrrpTSWELQGcLLPWLTVELALARPHLILLLGKFAAQALLGllR 109

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 692357218   256 HDALGRLRAEPHHI--AGVPTVVTYDPNYLLRA--PQAKAGAWADL 297
Cdd:smart00986 110 RPLVFGLRGRVAQLkgKGHRVLPLPHPSPLNRNffPAKKFAAWNDL 155
 
Name Accession Description Interval E-value
UDG-F4_TTUDGA_SPO1dp_like cd10030
Uracil DNA glycosylase family 4, includes Thermotoga maritima TTUDGA, Bacillus phage SPO1 DNA ...
 184-300 1.21e-19

Uracil DNA glycosylase family 4, includes Thermotoga maritima TTUDGA, Bacillus phage SPO1 DNA polymerase, and similar proteins; Uracil DNA glycosylase family 4 includes Thermotoga maritima TTUDGA, a robust uracil DNA glycosylase that shares narrow substrate specificity and high catalytic efficiency with family 1, acting on double-stranded and single-stranded uracil-containing DNA. Members of this family possess four conserved cysteine residues required to coordinate the [4Fe-4S] iron-sulfur cluster. This family also includes the N-terminal domain of Bacillus phage SPO1 DNA polymerase. Bacteriophage SPO1 is one of a group of large, lytic, tailed bacteriophages of Bacillus subtilis, and contains hydroxymethyluracil (hmUra) in place of thymine in their DNA. It has been speculated that this UDG domain may help discriminate between hmUra containing SPO1 DNA and thymine-containing host DNA. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil in DNA can arise as a result of mis-incorporation 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.


Pssm-ID: 381680  Cd Length: 165  Bit Score: 84.03  E-value: 1.21e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 692357218 184 GDAAKLLDNMLRALGLQEKpRVF--SAALHRAPPDADLSHA--QALQPALETLLRELRPDCVLVLGLASARAVLGRHDAL 259
Cdd:cd10030   44 GRAGKLLDKMLAAIGLSRE-DVYitNVVKCRPPGNRTPTPEeiAACRPFLDRQIELIKPKVIVTLGRTAAQALLGKDAPI 122

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 692357218 260 GRLRAEPHHI-AGVPTVVTYDPNYLLRAPQAKAGAWADLVQA 300
Cdd:cd10030  123 SKLRGKWHEYeKGIPVLPTYHPAALLRNPSLKRLAWEDLKKL 164
Udg4 COG1573
Uracil-DNA glycosylase [Replication, recombination and repair];
184-300 2.02e-17

Uracil-DNA glycosylase [Replication, recombination and repair];


Pssm-ID: 441181  Cd Length: 189  Bit Score: 78.70  E-value: 2.02e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 692357218 184 GDAAKLLDNMLRALGLQEKpRVF-SAALHRAPP---DADLSHAQALQPALETLLRELRPDCVLVLGLASARAVLGRHDAL 259
Cdd:COG1573   63 GRAGQLLDKMLAAAGLARE-DVYiTNAVKCRPPgnrKPTPEEIAACRPFLEREIALIRPKVIVALGATAAQALLGAGERI 141

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 692357218 260 GRLRAEPHHIA-GVPTVVTYDPNYLLRAPQAKAGAWADLVQA 300
Cdd:COG1573  142 TRLRGKWHELPgGIPLLPTYHPSYLLRNPTTKREAWEDLLAA 183
UDG pfam03167
Uracil DNA glycosylase superfamily;
159-297 1.32e-10

Uracil DNA glycosylase superfamily;


Pssm-ID: 397331  Cd Length: 154  Bit Score: 58.90  E-value: 1.32e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 692357218  159 EPAANPPLLSPAQRPAADSAQT--ALQGDAAKLLDNMLRALGLQEKP----RVF-SAALHRAPPDADLSHAQALQ---PA 228
Cdd:pfam03167   3 FGPPNAKVLIVGEAPGADEDATglPFVGRAGNLLWKLLNAAGLTRDLfspqGVYiTNVVKCRPGNRRKPTSHEIDacwPY 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 692357218  229 LETLLRELRPDCVLVLGLASARAVLGrHDALGRLRAEPHHIAGVPTVVTYDPNYLLRA---PQAKAGAWADL 297
Cdd:pfam03167  83 LEAEIELLRPRVIVLLGKTAAKALLG-LKKITKLRGKLIDLKGIPVLPTPHPSPLLRNklnPFLKANAWEDL 153
UDG smart00986
Uracil DNA glycosylase superfamily;
184-297 3.55e-06

Uracil DNA glycosylase superfamily;


Pssm-ID: 214956  Cd Length: 156  Bit Score: 46.23  E-value: 3.55e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 692357218   184 GDAAKLLDNMLRALGLQEKPRVFSAALHRAPPDA-----DLSHAQA-LQPALETLLRELRPDCVLVLGLASARAVLG--R 255
Cdd:smart00986  30 GAAGLLLSVMLGVAGLPRLPPYLTNIVKCRPPDAgnrrpTSWELQGcLLPWLTVELALARPHLILLLGKFAAQALLGllR 109

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 692357218   256 HDALGRLRAEPHHI--AGVPTVVTYDPNYLLRA--PQAKAGAWADL 297
Cdd:smart00986 110 RPLVFGLRGRVAQLkgKGHRVLPLPHPSPLNRNffPAKKFAAWNDL 155
 
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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