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(-) Description

Title :  UNPRECEDENTED SCULPTING OF DNA AT ABASIC SITES BY DNA GLYCOSLASE HOMOLOG MAG2
 
Authors :  B. Dalhus, L. Nilsen, H. Korvald, J. Huffman, R. J. Forstrom, C. T. Mcmur I. Alseth, J. A. Tainer, M. Bjoras
Date :  12 Jul 12  (Deposition) - 09 Jan 13  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,X,Y
Keywords :  Hydrolase-Dna Complex, Hydrolase, Helix-Hairpin-Helix Dna Glycosylase Homologue (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Dalhus, L. Nilsen, H. Korvald, J. Huffman, R. J. Forstrom, C. T. Mcmurray, I. Alseth, J. A. Tainer, M. Bjoras
Sculpting Of Dna At Abasic Sites By Dna Glycosylase Homolog Mag2.
Structure V. 21 154 2013
PubMed-ID: 23245849  |  Reference-DOI: 10.1016/J.STR.2012.11.004

(-) Compounds

Molecule 1 - MAG2, DNA-3-METHYLADENINE GLYCOSYLASE 2
    ChainsA
    EC Number3.2.2.21
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    Organism ScientificSCHIZOSACCHAROMYCES POMBE
    Organism Taxid4896
    Synonym3-METHYLADENINE DNA GLYCOSIDASE 2,3MEA DNA GLYCOSYLASE 2
 
Molecule 2 - 5'-D(*GP*CP*TP*AP*CP*(3DR)P*AP*AP*TP*CP*GP)-3'
    ChainsX
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SynonymABASIC DNA
    SyntheticYES
 
Molecule 3 - 5'-D(*CP*GP*AP*TP*TP*GP*GP*TP*AP*GP*CP)-3'
    ChainsY
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit AXY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 4B23)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B23)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:192 -Pro A:193

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B23)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALKYLBASE_DNA_GLYCOSPS00516 Alkylbase DNA glycosidases alkA family signature.MAG2_SCHPO138-162  1A:138-162

(-) Exons   (0, 0)

(no "Exon" information available for 4B23)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:207
 aligned with MAG2_SCHPO | O94468 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:207
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       
           MAG2_SCHPO     3 KDSDYKRAEKHLSSIDNKWSSLVKKVGPCTLTPHPEHAPYEGIIRAITSQKLSDAATNSIINKFCTQCSDNDEFPTPKQIMETDVETLHECGFSKLKSQEIHIVAEAALNKQIPSKSEIEKMSEEELMESLSKIKGVKRWTIEMYSIFTLGRLDIMPADDSTLKNEAKEFFGLSSKPQTEEVEKLTKPCKPYRTIAAWYLWQIPKLH 209
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhhhhhhh..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh......hhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..........hhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------ALKYLBASE_DNA_GLYCOS     ----------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b23 A   3 KDSDYKRAEKHLSSIDNKWSSLVKKVGPCTLTPHPEHAPYEGIIRAITSQKLSDAATNSIINKFCTQCSDNDEFPTPKQIMETDVETLHECGFSKLKSQEIHIVAEAALNKQIPSKSEIEKMSEEELMESLSKIKGVKRWTIEMYSIFTLGRLDIMPADDSTLKNEAKEFFGLSSKPQTEEVEKLTKPCKPYRTIAAWYLWQIPKLH 209
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       

Chain X from PDB  Type:DNA  Length:11
                                           
                 4b23 X   1 GCTACxAATCG  11
                                 |  10 
                                 6-3DR 

Chain Y from PDB  Type:DNA  Length:11
                                           
                 4b23 Y  12 CGATTGGTAGC  22
                                    21 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4B23)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B23)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B23)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MAG2_SCHPO | O94468)
molecular function
    GO:0019104    DNA N-glycosylase activity    Catalysis of the removal of damaged bases by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic/apyrimidinic (AP) site.
    GO:0008725    DNA-3-methyladenine glycosylase activity    Catalysis of the reaction: DNA containing 3-methyladenine + H2O = DNA with abasic site + 3-methyladenine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 3-methyladenine and the deoxyribose sugar to remove the 3-methyladenine, leaving an abasic site.
    GO:0052822    DNA-3-methylguanine glycosylase activity    Catalysis of the reaction: DNA containing 3-methylguanine + H2O = DNA with abasic site + 3-methylguanine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 3-methylguanine and the deoxyribose sugar to remove the 3-methylguanine, leaving an abasic site.
    GO:0052821    DNA-7-methyladenine glycosylase activity    Catalysis of the reaction: DNA containing 7-methyladenine + H2O = DNA with abasic site + 7-methyladenine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 7-methyladenine and the deoxyribose sugar to remove the 7-methyladenine, leaving an abasic site.
    GO:0043916    DNA-7-methylguanine glycosylase activity    Catalysis of the reaction: DNA containing 7-methylguanine + H2O = DNA with abasic site + 7-methylguanine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 7-methylguanine and the deoxyribose sugar to remove the 7-methylguanine, leaving an abasic site.
    GO:0003905    alkylbase DNA N-glycosylase activity    Catalysis of the reaction: DNA with alkylated base + H2O = DNA with abasic site + alkylated base. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar to remove an alkylated base, leaving an apyrimidinic or apurinic site.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0006307    DNA dealkylation involved in DNA repair    The repair of alkylation damage, e.g. the removal of the alkyl group at the O6-position of guanine by O6-alkylguanine-DNA alkyltransferase (AGT).
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006284    base-excision repair    In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
    GO:0006285    base-excision repair, AP site formation    The formation of an AP site, a deoxyribose sugar with a missing base, by DNA glycosylase which recognizes an altered base in DNA and catalyzes its hydrolytic removal. This sugar phosphate is the substrate recognized by the AP endonuclease, which cuts the DNA phosphodiester backbone at the 5' side of the altered site to leave a gap which is subsequently repaired.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MAG2_SCHPO | O944684b21 4b22 4b24 4hsb

(-) Related Entries Specified in the PDB File

4b21 UNPRECEDENTED SCULPTING OF DNA AT ABASIC SITES BY DNA GLYCOSYLASE HOMOLOG MAG2
4b22 UNPRECEDENTED SCULPTING OF DNA AT ABASIC SITES BY DNA GLYCOSYLASE HOMOLOG MAG2
4b24 UNPRECEDENTED SCULPTING OF DNA AT ABASIC SITES BY DNA GLYCOSYLASE HOMOLOG MAG2