3BVS,2B6C


Conserved Protein Domain Family
AlkD_like_1

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cd07064: AlkD_like_1 
Click on image for an interactive view with Cn3D
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.
Statistics
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PSSM-Id: 132881
View PSSM: cd07064
Aligned: 42 rows
Threshold Bit Score: 220.543
Threshold Setting Gi: 62425335
Created: 15-Jan-2009
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                    #                                                                   
3BVS_A        17 HQNPEKAEPMARYMKNHFl--fLGIQTPERRQLLKDIIQIhtlpd--qkdfQIIIRELWDLPe---REFQAAALDIMqk- 88  Bacillus cereus
ZP_01690885   20 HANMEIAAQQKAYMKDNFe--fFGLKAPQRRAVQKPFLAKahlps--kaeaIEIVKALWQKPq---REFHHIAQELLkk- 91  Microscilla mar...
ZP_01108060   27 NSNAKIAEEQKAYMRNQFe--fYGIKTPVRREIQKPFLAKdflpp--kselQLIIKTLWNKPe---REYQFIGQELVhk- 98  Flavobacteriale...
Q3WFZ5        17 AADPARAPGMQAYMKSDMp--yRGVPKPVRTRVLRPVFAArtlad--plgwTATALALWREAa--yREERYAAIDLTghr 90  Frankia sp. EAN...
YP_001626430  19 QADAERAKSMAAYMKSYMp--yRGVPKPQVRKIMMTAARAypfad--aadlLSTATKLWREAn--cREERYIATALTef- 91  Renibacterium s...
YP_831912     17 AADPLRAVGSQSYMKSDMp--tLGVRVPEVRKITTGAAAQwpcrs--feelRDTVLELWRTAv--fREERYAAIDLTga- 89  Arthrobacter sp...
ZP_00997173   18 GANVERAVGQQRYMKSEMp--fLGLTSPQRHALLRPLLADpalrietrsgwERSIRELWDGAe--yREDRYAALALIrhr 93  Janibacter sp. ...
YP_001073963  15 AADPDRAPAMQAYMKSQMp--yYGIRLPDVRRLCGPVFDAhplgs-etsfeDAVERMFVEAThreeRYAAIQLARHRry- 90  Mycobacterium s...
ZP_01220341   18 VSNADDAISMQEYMKTEQp--fYGVKAPERKAVFKKAREHtdvad--fvqyRRLVLWLWSGVy---REELYLAMDVAey- 89  Photobacterium ...
ZP_00380470   22 RGSSVRAAKDQAYLKSELvhygVGVPDTRAVVRSALHTAEldh-----evlVELAEALWNPAp---IGIDAPVFDLRsaa 93  Brevibacterium ...
Feature 1                                    #   #                                  #            
3BVS_A        89 ------ykKHINETHIPFLEELIVTKSWWDSVDSIVPTFLGDIFlkhpelisayipkWIASDNIWLQRAAILFQLKYKqk 162 Bacillus cereus
ZP_01690885   92 ------yiKTFEATDIELLEWLIVRQSWWDTIDFIAPRLVGGYMkmypnqrqvcidqWLASGNIWLQRACVLFQLKYKkd 165 Microscilla mar...
ZP_01108060   99 ------ykKQFVKSDIALLEFMVTHKSWWDTVDYIAVKLIGPYFdmfpeqlkpiiekWLASGNMWLQRCCLLYQLKSKdk 172 Flavobacteriale...
Q3WFZ5        91 -----ayrAYQQAGTLEMYEEMVVTGAWWDYVDEIASHRVGPLLaadpaairpvvlrWSRDGDLWRRRTSIICQLSFKaa 165 Frankia sp. EAN...
YP_001626430  92 ------klAKGNLDFLPFYEEVVSAGAWWDHVDEMAHRILDLLLahgktm-dpkvrqWSTDSGFWFRRLAIISQLHAKts 164 Renibacterium s...
YP_831912     90 ------rpARGRLEMLPVYEEIIRTGAWWDLVDGVAHRICDLLQahrpel-drvlrsWSSDPDMWVRRAAITAQLGAKsa 162 Arthrobacter sp...
ZP_00997173   94 -----tyrSWRDPDVMPLVRHLIVTGAWWDYVDEVGNVVGDALLldpege-glrmraWAEDEDVWLRRSAIISQLRHGdd 167 Janibacter sp. ...
YP_001073963  91 -------rPFQTPDRIPLYRRLIIAGDWWDTVDEIAGNLIGPILvshpaevrpivlgWATDHNLWLRRTAIISQLSAKer 163 Mycobacterium s...
ZP_01220341   90 ------ykAFRTPDAFSIYEEMLETADNWDTVDKLSSNLIGDLIkdyref-eaklieWRQSDNMWLRRASLLAHLKHKnd 162 Photobacterium ...
ZP_00380470   94 tmvitqaqDHLGAGDSDFLERLLRQARTWALVDPLAGDVVGPLAeydlef-dpvlerWSGDEDFWIRRSALLAHLKPLqe 172 Brevibacterium ...
Feature 1                            ##      #                                    
3BVS_A       163 --mDEELLFWIIGQLHssKEFFIQKAIGWVLREYAKTNPDVVWEYVQNNel--aPLSKREAIKHI 223 Bacillus cereus
ZP_01690885  166 --lDTDFLEYVIGKLLgsQEFFINKAIGWILRDYSRIAPDWVTQFVQDTkg-lhSLSRREALRLM 227 Microscilla marina ATCC 23134
ZP_01108060  173 --mDTQRLSQIINLLLgsNEFFINKAIGWVLREYSRTNPKWVVKFVSNHkl--aPLSKREALRLL 233 Flavobacteriales bacterium HTC...
Q3WFZ5       166 --tDLDLLYACIDANLddRDFFIRKAIGWALRQYAWTDPAEVRRFVTARgdalsPLSRREALKNI 228 Frankia sp. EAN1pec
YP_001626430 165 --tDLGLLSDVIEPNMadPEFFVRKAIGWALRDYARTDPDWVRRFVAERsaalsPLSQREALKHL 227 Renibacterium salmoninarum ATC...
YP_831912    163 --tDPVLLASVIEPNLadREFFIRKAIGWALREYAKTDADWVRQFVARHetglsPLSRREALRNL 225 Arthrobacter sp. FB24
ZP_00997173  168 --tDARLLSDVIEPNLddREFFVRKAIGWALRQYARTDPAWVLAFVEAHgqrlsGLSRREALKHL 230 Janibacter sp. HTCC2649
YP_001073963 164 --tDLELLTCAIDANAgdTEFFIRKAIGWALRQYARTDPTWVLRFVAARedrlsGLSKREARKHL 226 Mycobacterium sp. JLS
ZP_01220341  163 --tNVPLLEETILLLAheKEFFIRKAIGWVLREYSKTNPDFVIEFVAKYnqqlsTLSKKEALKVI 225 Photobacterium profundum 3TCK
ZP_00380470  173 grgDFERFTRFADAMLeeKEFFIRKAIGWVLRETARTRPDMVFEWMLPRahrasGVTMREVVKHL 237 Brevibacterium linens BL2

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