1EBM,1PU7,3F10,1XQP,1KEA,3KNT,3S6I,4OFE,7YHQ,8FAY,6Q0C,4B21,1ORN,3OGD


Conserved Protein Domain Family
HhH_GPD_SF
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cd00056: HhH_GPD_SF (This model is not part of the current CDD release)
HhH-GPD motif found in the HhH-GDP superfamily of DNA glycosylases
The HhH-GDP superfamily of DNA glycosylases contains a diverse range of structurally related DNA repair proteins found in bacteria, archaea, and eukaryotes. They recognize and remove damaged or modified DNA bases, initiating the base excision repair (BER) process. Some members are involved in gene regulation and cell cycle control. The superfamily is characterized by containing a structural signature, the HhH-GPD motif, which is also known as the helix-hairpin-helix followed by a Gly/Pro-rich loop and a conserved aspartate. This motif is involved in the recognition and excision of damaged DNA bases. The conserved aspartic acid plays a crucial role in the catalytic activity of the enzyme. Members of this superfamily, such as MutY, EndoIII/Nth, OGG1, OGG2, AGOG, AlkA/TAG II/MagII, MagIII, MBD4, TDG/MIG, and DEMETER, have diverse substrate preferences and they can recognize and excise a variety of damaged bases, including those arising from alkylation, oxidation, and deamination.
Links
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Statistics
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PSSM-Id: 527620
Aligned: 14 rows
Threshold Bit Score: 72.0198
Created: 1-Nov-2000
Updated: 14-Jul-2025
Structure
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Program:
Drawing:
Aligned Rows:
Download Cn3D
 
active siteDNA binding
Conserved site includes 11 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Comment:Some family member may not display significant catalytic activity.
  • Structure:4B21: Schizosaccharomyces pombe Mag2 binds beta-D-glucopyranose, contacts at 4A
  • Structure:6Q0C: Geobacillus stearothermophilus A/G-specific adenine glycosylase in complex with EDO, contacts at 4A
  • Structure:1ORN: Geobacillus stearothermophilus endonuclease III in complex with PED, contacts at 4A
  • Structure:1PU7: Helicobacter pylori MagIII bound to 3,9-dimethyladenine, contacts at 4A
  • Structure:1XQP: Pyrobaculum aerophilum 8-oxoguanine DNA glycosylase in complex with 8HG, contacts at 4A
Scroll to Sequence Alignment Display
Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1           #  #    #  #                                                              
1EBM_A    130 IECLFSFICSSNnnIARITGMVERLcqafgprliqlddvt---------------------------------------- 169 human
1PU7_A     31 FEALLGAVLTQNtkFEAVLKSLENLknafilendde-------------------------------------------- 66  Helicobacter pylori
3F10_A    116 FEILLSFIISANnrIPMIKKCINNIsekagkkleykgki----------------------------------------- 154 Clostridium acetob...
3KNT_A     38 FKELCFCILTANftAEGGIRIQKEIgdgf--------------------------------------------------- 66  Methanocaldococcus...
3S6I_A     51 YEELIRAVASQQlhSKAANAIFNRFksisnngqfp--------------------------------------------- 85  Schizosaccharomyce...
4OFE_A     69 WKLLIATIFLNKtsGKMAIPVLWKFlekypsa------------------------------------------------ 100 human
7YHQ_A    168 VDSVVGVFLTQNvsDHLSSSAFMSLasqfpvpfvpssnfdagtssmpsiqityldseetmssppdhnhscqkptlkekgk 247 synthetic construct
6Q0C_A     37 YKVWVSEVMLQQtrVETVIPYFEQFidrfptl------------------------------------------------ 68  Geobacillus stearo...
4B21_A     61 YEGIIRAITSQKlsDAATNSIINKFctqcsdndef--------------------------------------------- 95  fission yeast
1ORN_A     34 FELLIAVVLSAQctDALVNKVTKRLfekyrtp------------------------------------------------ 65  Geobacillus stearo...

Feature 1                                                                                     
1EBM_A    170 ------------------------------yhgfpslqalagpevEAHLRKLGl-------GYRARYVSASAraileeqg 212 human
1PU7_A     67 -----------------------------------inlkkiayieFSKLAECVrps--gfyNQKAKRLIDLSgnilkdfq 109 Helicobacter pylori
3F10_A    155 -------------------------------yyafptvdklheftEKDFEECTa-------GFRAKYLKDTVdriyngel 196 Clostridium acetob...
3KNT_A     67 -----------------------------------------ltlpREELEEKLknlghrfyRKRAEYIVLARrfknikdi 105 Methanocaldococcus...
3S6I_A     86 ------------------------------------tpeeirdmdFEIMRACGf------sARKIDSLKSIAeatisgli 123 Schizosaccharomyce...
4OFE_A    101 --------------------------------------evartadWRDVSELLkpl--glyDLRAKTIVKFSdeyltkq- 139 human
7YHQ_A    248 kvlkeekkafdwdclrreaqaragirektrstmdtvdwkairaadVKEVAETIksr--gmnHKLAERIQGFLdrlvndhg 325 synthetic construct
6Q0C_A     69 --------------------------------------ealadadEDEVLKAWegl---gyYSRVRNLHAAVkevktryg 107 Geobacillus stearo...
4B21_A     96 -----------------------------------ptpkqimetdVETLHECGf------sKLKSQEIHIVAeaalnkqi 134 fission yeast
1ORN_A     66 --------------------------------------hdyiavpLEELEQDIrsi--glyRNKARNIQKLCamlidkyn 105 Geobacillus stearo...

Feature 1                                 #   #   #         # # ##       
1EBM_A    213 glawlqqlressyeeahkalcilPGVGTQVADCICLMaldk-pqaVPVDVHMWHIAQRD 270 human
1PU7_A    110 sfenf------kqevtrewlldqKGIGKESADAILCYaca--kevMVVDKYSYLFLKKL 160 Helicobacter pylori
3F10_A    197 nleyik---slndnecheelkkfMGVGPQVADCIMLFsmqk-ysaFPVDTWVKKAMMSL 251 Clostridium acetobutylicum
3KNT_A    106 vesfe-----nekvareflvrniKGIGYQEASHFLRNvgy--ddvAIIDRHILRELYEN 157 Methanocaldococcus jannaschii
3S6I_A    124 ptkeeae--rlsneelierltqiKGIGRWTVEMLLIFslnrddvmPADDLSIRNGYRYL 180 Schizosaccharomyces pombe 972h-
4OFE_A    140 ----------------wkypielHGIGKYGNDSYRIFcvnewkqvHPENHKLNKYHDWL 182 human
7YHQ_A    326 sidlewl-rdvppdkakeyllsfNGLGLKSVECVRLLtlh--hlaFPVDTNVGRIAVRL 381 synthetic construct
6Q0C_A    108 gkv----------pddpdefsrlKGVGPYTVGAVLSLayg--vpePAVDGNVMRVLSRL 154 Geobacillus stearothermophilus
4B21_A    135 pskseie--kmseeelmeslskiKGVKRWTIEMYSIFtlgrldimPADDSTLKNEAKEF 191 fission yeast
1ORN_A    106 gev----------prdrdelmklPGVGRKTANVVVSVafg--vpaIAVDTHVERVSKRL 152 Geobacillus stearothermophilus

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