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Conserved domains on  [gi|2790392734|ref|WP_371109155|]
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uracil-DNA glycosylase family protein [Rhizobium sp. RCC_161_2]

Protein Classification

uracil-DNA glycosylase( domain architecture ID 10003975)

type-4 uracil-DNA glycosylase removes uracil bases that are present in DNA as a result of either deamination of cytosine or misincorporation of dUMP instead of dTMP

CATH:  3.40.470.10
EC:  3.2.2.27
Gene Ontology:  GO:0004844|GO:0006281|GO:0006284
PubMed:  19909758|11178247|11716455|10946227|25550433
SCOP:  4003607

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Udg4 COG1573
Uracil-DNA glycosylase [Replication, recombination and repair];
103-293 2.73e-71

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


:

Pssm-ID: 441181  Cd Length: 189  Bit Score: 218.14  E-value: 2.73e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734 103 RFAAESARSLNELKTALEAFNSCNLKNSARSTIFASGTPEGRVMVIGPMPSADDDREGAPFAGRTGLLLDKMLAAIGLKR 182
Cdd:COG1573     1 RAAAAAAETLEELREAVAACRRCPLVETRTQPVFGEGDPDARLMIVGEAPGAGEDRTGRPFVGRAGQLLDKMLAAAGLAR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734 183 DDILLTNVIPWRPPGNRAPSAPEIEICRPFIERQITLAEPKALLLLGNFTARHFFGSNETIHGLRGQWREVtisGRAIPA 262
Cdd:COG1573    81 EDVYITNAVKCRPPGNRKPTPEEIAACRPFLEREIALIRPKVIVALGATAAQALLGAGERITRLRGKWHEL---PGGIPL 157

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2790392734 263 IASLHPQELLTAPINKRLAWNDLLAFKTRID 293
Cdd:COG1573   158 LPTYHPSYLLRNPTTKREAWEDLLAARALLG 188
 
Name Accession Description Interval E-value
Udg4 COG1573
Uracil-DNA glycosylase [Replication, recombination and repair];
103-293 2.73e-71

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


Pssm-ID: 441181  Cd Length: 189  Bit Score: 218.14  E-value: 2.73e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734 103 RFAAESARSLNELKTALEAFNSCNLKNSARSTIFASGTPEGRVMVIGPMPSADDDREGAPFAGRTGLLLDKMLAAIGLKR 182
Cdd:COG1573     1 RAAAAAAETLEELREAVAACRRCPLVETRTQPVFGEGDPDARLMIVGEAPGAGEDRTGRPFVGRAGQLLDKMLAAAGLAR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734 183 DDILLTNVIPWRPPGNRAPSAPEIEICRPFIERQITLAEPKALLLLGNFTARHFFGSNETIHGLRGQWREVtisGRAIPA 262
Cdd:COG1573    81 EDVYITNAVKCRPPGNRKPTPEEIAACRPFLEREIALIRPKVIVALGATAAQALLGAGERITRLRGKWHEL---PGGIPL 157

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2790392734 263 IASLHPQELLTAPINKRLAWNDLLAFKTRID 293
Cdd:COG1573   158 LPTYHPSYLLRNPTTKREAWEDLLAARALLG 188
UDG-F4_TTUDGA_SPO1dp_like cd10030
Uracil DNA glycosylase family 4, includes Thermotoga maritima TTUDGA, Bacillus phage SPO1 DNA ...
 122-289 2.98e-69

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: 211.92  E-value: 2.98e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734 122 FNSCNLKNSARSTIFASGTPEGRVMVIGPMPSADDDREGAPFAGRTGLLLDKMLAAIGLKRDDILLTNVIPWRPPGNRAP 201
Cdd:cd10030     1 CTRCPLSKTRTNVVFGEGNPDAKLMFIGEAPGAEEDRQGRPFVGRAGKLLDKMLAAIGLSREDVYITNVVKCRPPGNRTP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734 202 SAPEIEICRPFIERQITLAEPKALLLLGNFTARHFFGSNETIHGLRGQWREVtisGRAIPAIASLHPQELLTAPINKRLA 281
Cdd:cd10030    81 TPEEIAACRPFLDRQIELIKPKVIVTLGRTAAQALLGKDAPISKLRGKWHEY---EKGIPVLPTYHPAALLRNPSLKRLA 157


                  ....*...
gi 2790392734 282 WNDLLAFK 289
Cdd:cd10030   158 WEDLKKLK 165
UDG_fam4 TIGR00758
uracil-DNA glycosylase, family 4; This well-conserved family of proteins is about 200 residues ...
 122-289 9.94e-56

uracil-DNA glycosylase, family 4; This well-conserved family of proteins is about 200 residues in length and homologous to the N-terminus of the DNA polymerase of phage SPO1 of Bacillus subtilis. The member from Thermus thermophilus HB8 is known to act as uracil-DNA glycosylase, an enzyme of DNA base excision repair. Its appearance as a domain of phage DNA polymerases could be consistent with uracil-DNA glycosylase activity. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129841  Cd Length: 173  Bit Score: 177.99  E-value: 9.94e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734 122 FNSCNLKNSARSTIFASGTPEGRVMVIGPMPSADDDREGAPFAGRTGLLLDKMLAAIGLKRDDILLTNVIPWRPPGNRAP 201
Cdd:TIGR00758   1 CRRCELHKTRTNAVPGDGNPDANIMFVGEAPGREEDRKGRPFVGRAGKLLDEMLAAIGLSRENVYITNVVKCRPPNNRDP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734 202 SAPEIEICRPFIERQITLAEPKALLLLGNFTARHFFGSNETIHGLRGQWREVTISGRAIPAIASLHPQELLTAPINKRLA 281
Cdd:TIGR00758  81 TPEEVEACAPYLVKQIELIRPKVIICLGRTAAQSILGKNDGITKIRGRVFEYRYIGTKIKITATYHPAALLRNPQLRREL 160


                  ....*...
gi 2790392734 282 WNDLLAFK 289
Cdd:TIGR00758 161 EEDFKKLK 168
UDG pfam03167
Uracil DNA glycosylase superfamily;
136-285 2.22e-36

Uracil DNA glycosylase superfamily;


Pssm-ID: 397331  Cd Length: 154  Bit Score: 127.46  E-value: 2.22e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734 136 FASGTPEGRVMVIGPMPSADDDREGAPFAGRTGLLLDKMLAAIGLKRD-----DILLTNVIPWRPPGNRAPSAPEIEICR 210
Cdd:pfam03167   1 PGFGPPNAKVLIVGEAPGADEDATGLPFVGRAGNLLWKLLNAAGLTRDlfspqGVYITNVVKCRPGNRRKPTSHEIDACW 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2790392734 211 PFIERQITLAEPKALLLLGNFTARHFFGSNEtIHGLRGQWREVtisgRAIPAIASLHPQELLTAPIN---KRLAWNDL 285
Cdd:pfam03167  81 PYLEAEIELLRPRVIVLLGKTAAKALLGLKK-ITKLRGKLIDL----KGIPVLPTPHPSPLLRNKLNpflKANAWEDL 153
UDG smart00986
Uracil DNA glycosylase superfamily;
136-286 6.85e-33

Uracil DNA glycosylase superfamily;


Pssm-ID: 214956  Cd Length: 156  Bit Score: 118.64  E-value: 6.85e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734  136 FASGTPEGRVMVIGPMPSADDDREGAPFAGRTGLLLDKMLAAIGLKRDDILLTNVIPWRPPG--NRAPSAPEIEICR-PF 212
Cdd:smart00986   1 PGTGDPNAKVLIVGQAPGASEEDRGGPFVGAAGLLLSVMLGVAGLPRLPPYLTNIVKCRPPDagNRRPTSWELQGCLlPW 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2790392734  213 IERQITLAEPKALLLLGNFTARHFFGSNE--TIHGLRGQWREvtISGRAIPAIASLHPQELLTA--PINKRLAWNDLL 286
Cdd:smart00986  81 LTVELALARPHLILLLGKFAAQALLGLLRrpLVFGLRGRVAQ--LKGKGHRVLPLPHPSPLNRNffPAKKFAAWNDLL 156
 
Name Accession Description Interval E-value
Udg4 COG1573
Uracil-DNA glycosylase [Replication, recombination and repair];
103-293 2.73e-71

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


Pssm-ID: 441181  Cd Length: 189  Bit Score: 218.14  E-value: 2.73e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734 103 RFAAESARSLNELKTALEAFNSCNLKNSARSTIFASGTPEGRVMVIGPMPSADDDREGAPFAGRTGLLLDKMLAAIGLKR 182
Cdd:COG1573     1 RAAAAAAETLEELREAVAACRRCPLVETRTQPVFGEGDPDARLMIVGEAPGAGEDRTGRPFVGRAGQLLDKMLAAAGLAR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734 183 DDILLTNVIPWRPPGNRAPSAPEIEICRPFIERQITLAEPKALLLLGNFTARHFFGSNETIHGLRGQWREVtisGRAIPA 262
Cdd:COG1573    81 EDVYITNAVKCRPPGNRKPTPEEIAACRPFLEREIALIRPKVIVALGATAAQALLGAGERITRLRGKWHEL---PGGIPL 157

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2790392734 263 IASLHPQELLTAPINKRLAWNDLLAFKTRID 293
Cdd:COG1573   158 LPTYHPSYLLRNPTTKREAWEDLLAARALLG 188
UDG-F4_TTUDGA_SPO1dp_like cd10030
Uracil DNA glycosylase family 4, includes Thermotoga maritima TTUDGA, Bacillus phage SPO1 DNA ...
 122-289 2.98e-69

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: 211.92  E-value: 2.98e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734 122 FNSCNLKNSARSTIFASGTPEGRVMVIGPMPSADDDREGAPFAGRTGLLLDKMLAAIGLKRDDILLTNVIPWRPPGNRAP 201
Cdd:cd10030     1 CTRCPLSKTRTNVVFGEGNPDAKLMFIGEAPGAEEDRQGRPFVGRAGKLLDKMLAAIGLSREDVYITNVVKCRPPGNRTP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734 202 SAPEIEICRPFIERQITLAEPKALLLLGNFTARHFFGSNETIHGLRGQWREVtisGRAIPAIASLHPQELLTAPINKRLA 281
Cdd:cd10030    81 TPEEIAACRPFLDRQIELIKPKVIVTLGRTAAQALLGKDAPISKLRGKWHEY---EKGIPVLPTYHPAALLRNPSLKRLA 157


                  ....*...
gi 2790392734 282 WNDLLAFK 289
Cdd:cd10030   158 WEDLKKLK 165
UDG_fam4 TIGR00758
uracil-DNA glycosylase, family 4; This well-conserved family of proteins is about 200 residues ...
 122-289 9.94e-56

uracil-DNA glycosylase, family 4; This well-conserved family of proteins is about 200 residues in length and homologous to the N-terminus of the DNA polymerase of phage SPO1 of Bacillus subtilis. The member from Thermus thermophilus HB8 is known to act as uracil-DNA glycosylase, an enzyme of DNA base excision repair. Its appearance as a domain of phage DNA polymerases could be consistent with uracil-DNA glycosylase activity. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129841  Cd Length: 173  Bit Score: 177.99  E-value: 9.94e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734 122 FNSCNLKNSARSTIFASGTPEGRVMVIGPMPSADDDREGAPFAGRTGLLLDKMLAAIGLKRDDILLTNVIPWRPPGNRAP 201
Cdd:TIGR00758   1 CRRCELHKTRTNAVPGDGNPDANIMFVGEAPGREEDRKGRPFVGRAGKLLDEMLAAIGLSRENVYITNVVKCRPPNNRDP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734 202 SAPEIEICRPFIERQITLAEPKALLLLGNFTARHFFGSNETIHGLRGQWREVTISGRAIPAIASLHPQELLTAPINKRLA 281
Cdd:TIGR00758  81 TPEEVEACAPYLVKQIELIRPKVIICLGRTAAQSILGKNDGITKIRGRVFEYRYIGTKIKITATYHPAALLRNPQLRREL 160


                  ....*...
gi 2790392734 282 WNDLLAFK 289
Cdd:TIGR00758 161 EEDFKKLK 168
UDG pfam03167
Uracil DNA glycosylase superfamily;
136-285 2.22e-36

Uracil DNA glycosylase superfamily;


Pssm-ID: 397331  Cd Length: 154  Bit Score: 127.46  E-value: 2.22e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734 136 FASGTPEGRVMVIGPMPSADDDREGAPFAGRTGLLLDKMLAAIGLKRD-----DILLTNVIPWRPPGNRAPSAPEIEICR 210
Cdd:pfam03167   1 PGFGPPNAKVLIVGEAPGADEDATGLPFVGRAGNLLWKLLNAAGLTRDlfspqGVYITNVVKCRPGNRRKPTSHEIDACW 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2790392734 211 PFIERQITLAEPKALLLLGNFTARHFFGSNEtIHGLRGQWREVtisgRAIPAIASLHPQELLTAPIN---KRLAWNDL 285
Cdd:pfam03167  81 PYLEAEIELLRPRVIVLLGKTAAKALLGLKK-ITKLRGKLIDL----KGIPVLPTPHPSPLLRNKLNpflKANAWEDL 153
UDG smart00986
Uracil DNA glycosylase superfamily;
136-286 6.85e-33

Uracil DNA glycosylase superfamily;


Pssm-ID: 214956  Cd Length: 156  Bit Score: 118.64  E-value: 6.85e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734  136 FASGTPEGRVMVIGPMPSADDDREGAPFAGRTGLLLDKMLAAIGLKRDDILLTNVIPWRPPG--NRAPSAPEIEICR-PF 212
Cdd:smart00986   1 PGTGDPNAKVLIVGQAPGASEEDRGGPFVGAAGLLLSVMLGVAGLPRLPPYLTNIVKCRPPDagNRRPTSWELQGCLlPW 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2790392734  213 IERQITLAEPKALLLLGNFTARHFFGSNE--TIHGLRGQWREvtISGRAIPAIASLHPQELLTA--PINKRLAWNDLL 286
Cdd:smart00986  81 LTVELALARPHLILLLGKFAAQALLGLLRrpLVFGLRGRVAQ--LKGKGHRVLPLPHPSPLNRNffPAKKFAAWNDLL 156
UDG-like cd09593
uracil-DNA glycosylases (UDG) and related enzymes; Uracil-DNA glycosylases (UDGs) initiate ...
 145-238 3.50e-08

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: 51.23  E-value: 3.50e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734 145 VMVIGPMPSADDDREGAPFAGRTGLLLDKMLAAIG----LKRDDILLTNVIPWRPPGNRAPSAPEIEICR-PFIERQITL 219
Cdd:cd09593     1 VLIVGQNPGPHGARAGGVPPGPSGNRLWRLLAAAGgtprLFRYGVGLTNTVPRGPPGAAAGSEKKELRFCgRWLRKLLEL 80

                          90
                  ....*....|....*....
gi 2790392734 220 AEPKALLLLGNFTARHFFG 238
Cdd:cd09593    81 LNPRVVVLLGKKAQEAYLA 99
UDG-F5_TTUDGB_like cd10031
Uracil DNA glycosylase family 5, includes Thermotoga maritima TTUDGB and similar proteins; ...
 139-229 2.37e-07

Uracil DNA glycosylase family 5, includes Thermotoga maritima TTUDGB and similar proteins; Uracil DNA glycosylase family 5 includes Thermus thermophilus HB8 TTUDGB (also called UDGb) which is not only a UDG acting on double-stranded uracil-containing DNA, but also 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 acting on both, double-stranded and single-stranded xanthine-containing DNA. TTUDGB also excises thymine from G:T mismatched DNA, and removes analogs of uracil from DNA, including 5-hydroxymethyluracil (hmU) and 5-fluorouracil (fU). This subfamily also contains Bradyrhizobium diazoefficiens family 5 homolog Blr5068 (UdgB) which has been found to efficiently excise uracil from ssDNA and dsDNA. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Similar to family 4 UDGs, members of this family possess four conserved cysteine residues required to coordinate the [4Fe-4S] iron-sulfur cluster. 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: 381681  Cd Length: 204  Bit Score: 50.16  E-value: 2.37e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2790392734 139 GTPEGRVMVIGPMPSADD-DREGAPFAG-RTGLLLDKMLAAIGL-------KRDDIL------LTNVIPWRPPGNRaPSA 203
Cdd:cd10031    35 GDPNARLLIVGLAPAAHGgNRTGRPFTGdRSGDFLYRALYEAGFanqptseSRDDGLelkdcyITAAVRCAPPQNK-PTP 113

                          90       100
                  ....*....|....*....|....*..
gi 2790392734 204 PEIEICRPFIERQI-TLAEPKALLLLG 229
Cdd:cd10031   114 EEIRNCRPFLEEELaLLKNLKVILALG 140
UDG_like cd10035
uncharacterized family of the uracil-DNA glycosylase superfamily; Uracil-DNA glycosylases ...
 162-230 1.38e-06

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: 46.85  E-value: 1.38e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2790392734 162 PFAGRTGLLLDKMLAAIGLKRDDILLTNVIPWRP--PG----NRAPSAPEIEICRPFIERQITL-AEPKALLLLGN 230
Cdd:cd10035    42 DNDEPTATIVWRALAEAGIDRRDPLLWNAVPWHPhkPGnplsNRTPTAAELRAGLPFLRELLELlPNLRVVVAVGR 117
 
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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