2B6C,3BVS,1T06


Conserved Protein Domain Family
AlkD_like

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cd06561: AlkD_like 
Click on image for an interactive view with Cn3D
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.
Statistics
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PSSM-Id: 132880
View PSSM: cd06561
Aligned: 174 rows
Threshold Bit Score: 72.345
Threshold Setting Gi: 147918749
Created: 8-Jan-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Active site
Conserved site includes 7 residues -Click on image for an interactive view with Cn3D
Feature 1:Active site [active site]
Evidence:
  • Comment:site-specific mutagenesis within the recognition pocket identified several residues essential for DNA glycosylases activity

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1             #                                                                          
2B6C_A        17 AKXSAYXKhqf-----vfAGIPAPERQALSKQLlkesht---wpkeklCQEIEAYYQKteREYQYVAIDLalqnvqrfsL 88  Enterococcus fa...
ZP_02039803   15 ESYKQFNQklipg-tdhvIGVRMPALRKLAKGIaktdskq--yleeaqTEIDERSAHEe-IMLYGLVLGYakms-teqrM 89  Ruminococcus gn...
ZP_03302963   21 NGNKKFTEslhpg-ienvLGIRIPALRRLGAQIakdd-------wesyLQTADTYYMEe-RMLQGMVISNlkmkdieayL 91  Bacteroides dor...
YP_001557946  49 QKYKDFANklipq-vnnmIGIRLPILQEIAKQIakgd-------yegfLSHSNVQYFEe-VMVHGYVIGKlsni-piedI 118 Clostridium phy...
ZP_03292472   24 EKYRDFTLnlnpg-kekiIGIRIPELRKKAAEIskgdwr----kflyiSYKNDNGYIEe-EFIRGLVIGNvkncdieefI 97  Clostridium hir...
ZP_03485601   16 PKFQKFTSglipg-tdpiIGVRIPKLRTLAKKIaked-------wrgyLEHAACDTYEe-IMLQGLVLGYakge-idelL 85  Roseburia intes...
ZP_02423344   17 EKFRIFNEkivhtskyrvIGVRMPDLKAIAKEHrady--------keiFELPYDSFEE--IIIKGVAVGFadap-lcekE 85  Eubacterium sir...
NP_603702     31 IEYRDFNTkivvpvdceiIGIRTPILRDIAKKIaktssenflnlfeklFTKNKVKYYE--EKVLYGFLIGyskidfqerL 108 Fusobacterium n...
ZP_02074579   31 VEYGKFTAslspg-agniIGVRIPVLRKMAKEIasvn-------wkeyLDGARDDTFEe-VMLQGIVLGYargk-iddiL 100 Clostridium sp....
ZP_02206133   23 LEFGKYLAmnlpg-cgnvIGVRLDDLKEIAQQIaein-------wkeyLKHAPDDTLEd-VVLQGLVLGYaqgk-leeiL 92  Coprococcus eut...
Feature 1                       #   #                                            #               
2B6C_A        89 EEVVAFKAYvpqkAWWDSVDAWRKFFGSWVAlhltel-----------ptifalFYGAENFWNRRVALNLQLXlkek-tn 156 Enterococcus fa...
ZP_02039803   90 QALDMFVPKi---HNWAVCDSCCMGYKFMEKeqevwf------------sylrkYQNSSREFEVRFFIVSLLAhyineay 154 Ruminococcus gn...
ZP_03302963   92 SLVARFVTIi---NSWSVCDTFDFYGKQRFVdknkkrv----------wlflenWMKSDKEYEIRFGVVMAMAhyideey 158 Bacteroides dor...
YP_001557946 119 QEFISYHVPk--lDNWSTCDSFCSSLKITKKhpkevf------------dfilpYAHSNNSYEIRFFIVMCLNyyineey 184 Clostridium phy...
ZP_03292472   98 DYVDDFIGRi---DSWSVNDTFCSSLKITKKnmdrmh------------tfildNLKSKNPWRKRFSIVMLMDyylseey 162 Clostridium hir...
ZP_03485601   86 EYVRAFIPKi---HDWSVNDCFCATFKIAQKhrekvw------------nflmpYAKSDQEFEQRVVSVMLMDhflteey 150 Roseburia intes...
ZP_02423344   86 PYIIRYAEMi---DNWAECDCFCSCIKVKKSeeddll------------rlaegLMYRKEEFVSRVGTVLMFSkfsdept 150 Eubacterium sir...
NP_603702    109 KRIDFFINIi---DNWAVCDIVDSSFKFINKnkedfy------------tyltsKLSATNPWEQRFIFVMLLAycveeky 173 Fusobacterium n...
ZP_02074579  101 TYMGRFIPKi---DDWSICDTCCNTFKIANQyqqevwdflmpyldeqgvidgkpANERNREFELRFVAVMMLNyylnday 177 Clostridium sp....
ZP_02206133   93 AYADEFVPKi---DNWWVCDSFCANFKAASMyqeivwefimk--ymgdselnpeWRKKQQEVEVSIGQGGIAVgtwqdms 167 Coprococcus eut...
Feature 1                                            ##      #                                   
2B6C_A       157 qDLLKKAIIYDRt--------------------tEEFFIQKAIGWSLRQYSKTNPQWVEELXKELvls-----plaQREG 211 Enterococcus fa...
ZP_02039803  155 iEQVLEILNHTSh---------------------EGYYVKMAVAWAVSVCYVKFPIQTKRLLLANemd-----dftHNKA 208 Ruminococcus gn...
ZP_03302963  159 iNNVLQWMDRISh---------------------EGYYVKMAVAWALSVCYVKFPQKTVNYLKENhld-----dftYNKA 212 Bacteroides dor...
YP_001557946 185 vSIVDETLQSIIs---------------------DEYYVNMAICWAYTTMFYKDSNRVLQFLNKLkkqleteqnsrNRFI 243 Clostridium phy...
ZP_03292472  163 lDEIFDICDTIKd---------------------DEYYYKMAVAWLLSMCFVKFRDRTMAYFTSCnld-----dftYNKA 216 Clostridium hir...
ZP_03485601  151 iARVLSVWDRLDh---------------------PGYYRKMGVAWGVATAYAKYPKETHAFLLENhld-----detYNKA 204 Roseburia intes...
ZP_02423344  151 vRKALAIYDRLPs---------------------GEYYRDMAVAWGISVYCVRYPQLIVKYLEHSpis-----iavKLAA 204 Eubacterium sir...
NP_603702    174 lKDIFKICEKIKs---------------------DEYYVKMAKAWLLSVCYVKYKNETYKFLEKTkld-----vwtVNKS 227 Fusobacterium n...
ZP_02074579  178 iDKVLYAYDHMKn---------------------DGYYLKMGVAWGLAEAYVKCPEPTKVFLNNNhld-----dftFNKA 231 Clostridium sp....
ZP_02206133  168 dDFRLRFVAIMLkcyyvndryidkclyafehmqdGGYYAKDGVAFGLAESYFVFPDKTIDYIKNAkfedr--ilemAREK 245 Coprococcus eut...
Feature 1          
2B6C_A       212 SK 213 Enterococcus faecalis
ZP_02039803  209 IQ 210 Ruminococcus gnavus ATCC 29149
ZP_03302963  213 LQ 214 Bacteroides dorei DSM 17855
YP_001557946 244 LQ 245 Clostridium phytofermentans ISDg
ZP_03292472  217 LQ 218 Clostridium hiranonis DSM 13275
ZP_03485601  205 LQ 206 Roseburia intestinalis L1-82
ZP_02423344  205 AQ 206 Eubacterium siraeum DSM 15702
NP_603702    228 IQ 229 Fusobacterium nucleatum subsp. nucleatum ATCC 25586
ZP_02074579  232 IQ 233 Clostridium sp. L2-50
ZP_02206133  246 IE 247 Coprococcus eutactus ATCC 27759

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