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Conserved domains on  [gi|446285068|ref|WP_000362923|]
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MULTISPECIES: DNA alkylation repair protein [Streptococcus]

Protein Classification

DNA alkylation repair protein( domain architecture ID 10162603)

DNA alkylation repair protein such as alkylpurine DNA glycosylase AlkD, may not require a base-flipping mechanism for either DNA-binding or catalysis

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AlkD_like_1 cd07064
A new structural DNA glycosylase containing HEAT-like repeats; This domain represents a new ...
 14-219 3.38e-98

A new structural DNA glycosylase containing HEAT-like repeats; This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity. The known structures for members of this family, AlkC and AlkD from Bacillus cereus, are distant homologues and are composed of six variant HEAT (Huntington/Elongation/ A subunit/Target of rapamycin) repeats. HEAT motifs are ~45-amino acid sequences that form antiparallel alpha-helices, which are packed by a conserved hyrophobic interface and are tandemly repeated to form superhelical alpha-structures. AlkD and AlkC are specific for removal of 3-methyladenine (3mA) and 7-methylguanine (7mG) from the DNA by base excision repair. Homologues of AlkC and AlkD were also identified in other organisms.


:

Pssm-ID: 132881  Cd Length: 208  Bit Score: 284.10  E-value: 3.38e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446285068  14 ASDKEVSKQQEAYLRHHFKCYGIKSPERRMLYKELIKAAKRQ-AKIDWQLLDKCWQSDYREYHHFVLDYLLAMSQFITYN 92
Cdd:cd07064    1 HADPERAAAMKAYMKNQFPFYGIKTPERRALSKPFLKESKLPdKEELWELVLELWQQPEREYQYVAIDLLRKYKKFLTPE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446285068  93 DCSRLEFYARHQQWWDSIDVLTKVFGNLSLKDDKVM-NLLSEWSLDQDFWMRRLAIEHQLGFKEKTNTDILSLFILRNTG 171
Cdd:cd07064   81 DLPLLEELITTKSWWDTVDSLAKVVGGILLADYPEFePVMDEWSTDENFWLRRTAILHQLKYKEKTDTDLLFEIILANLG 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 446285068 172 SQEFFINKAIGWALRDYSKYNKVWVKDFISNHYDELSTLSIREGSKYL 219
Cdd:cd07064  161 SKEFFIRKAIGWALREYSKTNPDWVRDFVAAHKLRLSPLSRREALKYL 208
 
Name Accession Description Interval E-value
AlkD_like_1 cd07064
A new structural DNA glycosylase containing HEAT-like repeats; This domain represents a new ...
 14-219 3.38e-98

A new structural DNA glycosylase containing HEAT-like repeats; This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity. The known structures for members of this family, AlkC and AlkD from Bacillus cereus, are distant homologues and are composed of six variant HEAT (Huntington/Elongation/ A subunit/Target of rapamycin) repeats. HEAT motifs are ~45-amino acid sequences that form antiparallel alpha-helices, which are packed by a conserved hyrophobic interface and are tandemly repeated to form superhelical alpha-structures. AlkD and AlkC are specific for removal of 3-methyladenine (3mA) and 7-methylguanine (7mG) from the DNA by base excision repair. Homologues of AlkC and AlkD were also identified in other organisms.


Pssm-ID: 132881  Cd Length: 208  Bit Score: 284.10  E-value: 3.38e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446285068  14 ASDKEVSKQQEAYLRHHFKCYGIKSPERRMLYKELIKAAKRQ-AKIDWQLLDKCWQSDYREYHHFVLDYLLAMSQFITYN 92
Cdd:cd07064    1 HADPERAAAMKAYMKNQFPFYGIKTPERRALSKPFLKESKLPdKEELWELVLELWQQPEREYQYVAIDLLRKYKKFLTPE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446285068  93 DCSRLEFYARHQQWWDSIDVLTKVFGNLSLKDDKVM-NLLSEWSLDQDFWMRRLAIEHQLGFKEKTNTDILSLFILRNTG 171
Cdd:cd07064   81 DLPLLEELITTKSWWDTVDSLAKVVGGILLADYPEFePVMDEWSTDENFWLRRTAILHQLKYKEKTDTDLLFEIILANLG 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 446285068 172 SQEFFINKAIGWALRDYSKYNKVWVKDFISNHYDELSTLSIREGSKYL 219
Cdd:cd07064  161 SKEFFIRKAIGWALREYSKTNPDWVRDFVAAHKLRLSPLSRREALKYL 208
DNA_alkylation pfam08713
DNA alkylation repair enzyme; Proteins in this family are predicted to be DNA alkylation ...
 7-219 1.54e-61

DNA alkylation repair enzyme; Proteins in this family are predicted to be DNA alkylation repair enzymes. The structure of a hypothetical protein in this family shows it to adopt a supercoiled alpha helical structure.


Pssm-ID: 378033  Cd Length: 212  Bit Score: 191.30  E-value: 1.54e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446285068    7 LERKFKAASDKEVSKQQEAYLRHHFKCYGIKSPERRMLYKELIKAAKRQAKidWQLLDKCWQSDYREYHHFVLDYLLAMS 86
Cdd:pfam08713   1 IQAELEALADPEKAAEMQRYFKEGFPFLGVRTPERRKIAKDFFKELKLEDR--LELAEELWQSPYREERYLALDLLTQAR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446285068   87 QFITYNDCSRLEFYARHQQWWDSIDVLT-KVFGNLSLKDDKVMNLLSEWSLDQDFWMRRLAIEHQLGFKEKTNTDILSLF 165
Cdd:pfam08713  79 KKLTEADLDLYESWVETINNWDTVDGLApHIVGRYLADRPERLDLLEEWAKSENLWLRRAAIVSTLPFKKKTDFELLLEI 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 446285068  166 ILRNTGSQEFFINKAIGWALRDYSKYNKVWVKDFISNHYDELSTLSIREGSKYL 219
Cdd:pfam08713 159 AELLLGDKEFFIQKAIGWALREYSKTDPDLVRAFLEKHAKRMPRLSLREAIEKL 212
AlkD COG4912
3-methyladenine DNA glycosylase AlkD [Replication, recombination and repair];
1-219 6.72e-50

3-methyladenine DNA glycosylase AlkD [Replication, recombination and repair];


Pssm-ID: 443940 [Multi-domain]  Cd Length: 216  Bit Score: 161.60  E-value: 6.72e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446285068   1 MDLFLSLERKFKAASDKEVSKQQEAYLRHHFKCYGIKSPERRMLYKELIKAakrqakIDWQLLDKCWQSDYREYHHFVLD 80
Cdd:COG4912    1 ESTLEEIRAELEALADPERAAFMARYGKEGDPFLGVRVPDLRKLAKRIKKE------LDHELAEELWASGYHEARLLALL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446285068  81 YLLAMsQFITYNDCSRLEFYARHQQWWDSIDVL-TKVFGNLsLKDDKVMNLLSEWSLDQDFWMRRLAIEHQLGF-KEKTN 158
Cdd:COG4912   75 ILDPK-KKRDEETLELLEAWVPTIDNWDLVDSLaPKVVGKL-LLDPEALELLLEWAKSDNEWVRRAAIVLLLAFaRKGDD 152

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446285068 159 TDILSLF--ILRNTGSQEFFINKAIGWALRDYSKYNKVWVKDFISNHYDELSTLSIREGSKYL 219
Cdd:COG4912  153 TDFELLLeiIERLLHDEEDFVQKAIGWALREIGKRDPELVEAFLEKHDARLPRLTLRYAIEKL 215
 
Name Accession Description Interval E-value
AlkD_like_1 cd07064
A new structural DNA glycosylase containing HEAT-like repeats; This domain represents a new ...
 14-219 3.38e-98

A new structural DNA glycosylase containing HEAT-like repeats; This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity. The known structures for members of this family, AlkC and AlkD from Bacillus cereus, are distant homologues and are composed of six variant HEAT (Huntington/Elongation/ A subunit/Target of rapamycin) repeats. HEAT motifs are ~45-amino acid sequences that form antiparallel alpha-helices, which are packed by a conserved hyrophobic interface and are tandemly repeated to form superhelical alpha-structures. AlkD and AlkC are specific for removal of 3-methyladenine (3mA) and 7-methylguanine (7mG) from the DNA by base excision repair. Homologues of AlkC and AlkD were also identified in other organisms.


Pssm-ID: 132881  Cd Length: 208  Bit Score: 284.10  E-value: 3.38e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446285068  14 ASDKEVSKQQEAYLRHHFKCYGIKSPERRMLYKELIKAAKRQ-AKIDWQLLDKCWQSDYREYHHFVLDYLLAMSQFITYN 92
Cdd:cd07064    1 HADPERAAAMKAYMKNQFPFYGIKTPERRALSKPFLKESKLPdKEELWELVLELWQQPEREYQYVAIDLLRKYKKFLTPE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446285068  93 DCSRLEFYARHQQWWDSIDVLTKVFGNLSLKDDKVM-NLLSEWSLDQDFWMRRLAIEHQLGFKEKTNTDILSLFILRNTG 171
Cdd:cd07064   81 DLPLLEELITTKSWWDTVDSLAKVVGGILLADYPEFePVMDEWSTDENFWLRRTAILHQLKYKEKTDTDLLFEIILANLG 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 446285068 172 SQEFFINKAIGWALRDYSKYNKVWVKDFISNHYDELSTLSIREGSKYL 219
Cdd:cd07064  161 SKEFFIRKAIGWALREYSKTNPDWVRDFVAAHKLRLSPLSRREALKYL 208
DNA_alkylation pfam08713
DNA alkylation repair enzyme; Proteins in this family are predicted to be DNA alkylation ...
 7-219 1.54e-61

DNA alkylation repair enzyme; Proteins in this family are predicted to be DNA alkylation repair enzymes. The structure of a hypothetical protein in this family shows it to adopt a supercoiled alpha helical structure.


Pssm-ID: 378033  Cd Length: 212  Bit Score: 191.30  E-value: 1.54e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446285068    7 LERKFKAASDKEVSKQQEAYLRHHFKCYGIKSPERRMLYKELIKAAKRQAKidWQLLDKCWQSDYREYHHFVLDYLLAMS 86
Cdd:pfam08713   1 IQAELEALADPEKAAEMQRYFKEGFPFLGVRTPERRKIAKDFFKELKLEDR--LELAEELWQSPYREERYLALDLLTQAR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446285068   87 QFITYNDCSRLEFYARHQQWWDSIDVLT-KVFGNLSLKDDKVMNLLSEWSLDQDFWMRRLAIEHQLGFKEKTNTDILSLF 165
Cdd:pfam08713  79 KKLTEADLDLYESWVETINNWDTVDGLApHIVGRYLADRPERLDLLEEWAKSENLWLRRAAIVSTLPFKKKTDFELLLEI 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 446285068  166 ILRNTGSQEFFINKAIGWALRDYSKYNKVWVKDFISNHYDELSTLSIREGSKYL 219
Cdd:pfam08713 159 AELLLGDKEFFIQKAIGWALREYSKTDPDLVRAFLEKHAKRMPRLSLREAIEKL 212
AlkD COG4912
3-methyladenine DNA glycosylase AlkD [Replication, recombination and repair];
1-219 6.72e-50

3-methyladenine DNA glycosylase AlkD [Replication, recombination and repair];


Pssm-ID: 443940 [Multi-domain]  Cd Length: 216  Bit Score: 161.60  E-value: 6.72e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446285068   1 MDLFLSLERKFKAASDKEVSKQQEAYLRHHFKCYGIKSPERRMLYKELIKAakrqakIDWQLLDKCWQSDYREYHHFVLD 80
Cdd:COG4912    1 ESTLEEIRAELEALADPERAAFMARYGKEGDPFLGVRVPDLRKLAKRIKKE------LDHELAEELWASGYHEARLLALL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446285068  81 YLLAMsQFITYNDCSRLEFYARHQQWWDSIDVL-TKVFGNLsLKDDKVMNLLSEWSLDQDFWMRRLAIEHQLGF-KEKTN 158
Cdd:COG4912   75 ILDPK-KKRDEETLELLEAWVPTIDNWDLVDSLaPKVVGKL-LLDPEALELLLEWAKSDNEWVRRAAIVLLLAFaRKGDD 152

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446285068 159 TDILSLF--ILRNTGSQEFFINKAIGWALRDYSKYNKVWVKDFISNHYDELSTLSIREGSKYL 219
Cdd:COG4912  153 TDFELLLeiIERLLHDEEDFVQKAIGWALREIGKRDPELVEAFLEKHDARLPRLTLRYAIEKL 215
AlkD_like cd06561
A new structural DNA glycosylase; This domain represents a new and uncharacterized structural ...
 21-217 1.19e-44

A new structural DNA glycosylase; This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity.


Pssm-ID: 132880 [Multi-domain]  Cd Length: 197  Bit Score: 147.46  E-value: 1.19e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446285068  21 KQQEAYLRHHF---KCYGIKSPERRMLYKELIKAAKrqAKIDWQLLDKCWQSDYREYHHFVLDYLLAMsqFITYNDCSRL 97
Cdd:cd06561    1 EKMKKFMKNLGpgdPFLGVRTPDLRKIAKEFKKEDK--LEEDHELAEALWHEEIREAQYLALDLLDKK--ELKEEDLERF 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446285068  98 EFYARHQQWWDSIDVLTKVFGNLSLKDDKVMNLLSEWSLDQDFWMRRLAIEHQLGFKEK-TNTDILSLFILRNTGSQEFF 176
Cdd:cd06561   77 EPWIEYIDNWDLVDSLCANLLGKLLYAEPELDLLEEWAKSENEWVRRAAIVLLLRLIKKeTDFDLLLEIIERLLHDEEYF 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 446285068 177 INKAIGWALRDYSKYNKVWVKDFISNHYDELSTLSIREGSK 217
Cdd:cd06561  157 VQKAVGWALREYGKKDPERVIAFLEKNGLSMPRLTLRYAIE 197
 
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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