Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
E [auth A]SCOP2B SuperfamilyDNA-glycosylase 8038321 3000905 SCOP2B (2022-06-29)
E [auth A]SCOP2B SuperfamilyTATA-box binding protein-like 8036364 3000705 SCOP2B (2022-06-29)
F [auth B]SCOP2B SuperfamilyTATA-box binding protein-like 8036364 3000705 SCOP2B (2022-06-29)
F [auth B]SCOP2B SuperfamilyDNA-glycosylase 8038321 3000905 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
E [auth A]HhH-GPDe1dizA1 A: alpha arraysX: HhH/H2THH: SAM/DNA-glycosylaseT: DNA-glycosylaseF: HhH-GPDECOD (1.6)
E [auth A]AlkA_Ne1dizA2 A: a+b two layersX: TBP-likeH: TATA-box binding protein-like (From Topology)T: TATA-box binding protein-likeF: AlkA_NECOD (1.6)
F [auth B]HhH-GPDe1dizB1 A: alpha arraysX: HhH/H2THH: SAM/DNA-glycosylaseT: DNA-glycosylaseF: HhH-GPDECOD (1.6)
F [auth B]AlkA_Ne1dizB2 A: a+b two layersX: TBP-likeH: TATA-box binding protein-like (From Topology)T: TATA-box binding protein-likeF: AlkA_NECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
E [auth A],
F [auth B]
PF06029AlkA N-terminal domain (AlkA_N)AlkA N-terminal domain- Domain
E [auth A],
F [auth B]
PF00730HhH-GPD superfamily base excision DNA repair protein (HhH-GPD)HhH-GPD superfamily base excision DNA repair proteinThis family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate [2]. This includes endonucle ...This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate [2]. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases such as Swiss:P53397. The methyl-CPG binding protein MBD4 Swiss:Q9Z2D7 also contains a related domain [1] that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth C],
C [auth E]
DNA (5'-D(*GP*AP*CP*AP*TP*GP*AP*(NRI)P*TP*GP*CP*CP*T)-3')---
B [auth D],
D [auth F]
DNA (5'-D(*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3')---
E [auth A],
F [auth B]
3-METHYLADENINE DNA GLYCOSYLASE II

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

ChainsEnzyme NameDescriptionCatalytic Residues
DNA-3-methyladenine glycosylase II  M-CSA #313

A variety of environmental toxins can react with DNA and chemically alkylate the bases. This blocks the replicative polymerases and interferes with binding of regulatory proteins to DNA resulting in widespread cellular responses including activation of cell cycle checkpoints and programmed cell death. There are a number of repair strategies - direct reversal, nucleotide excision repair and base excision repair. Most single base modifications are corrected using base excision repair. Firstly a lesion specific DNA glycosylase removes the damaged base by hydrolysis of the deoxyribose glycosidic bond of alkylated DNA. The abasic site is then excised and filled by DNA polymerase.

AlkA lacks an obvious residue that could fulfill the role of a general acid to protonate the leaving group and later activate a water molecule. It is thought that AlkA's positively charged, alkylated substrates might not require this type of assistance. The lack of a general acid in AlkA's active site provides a means of catalytic selectivity. Positively charged bases, which do not require protonation and have a weakened glycosylic bond, can be removed effectively, and in turn it may function as a general base to activate a nearby water molecule. Unmodified bases require protonation by a general acid prior to hydrolysis and therefore are poor substrates. [PMID:10675345]

Defined by 3 residues: TRP:E-218 [auth A-218]TYR:E-222 [auth A-222]ASP:E-238 [auth A-238]
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