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(-) Description

Title :  STRUCTURE DETERMINATION OF DNA METHYLATION LESIONS N1-MEA AND N3-MEC IN DUPLEX DNA USING A CROSS-LINKED HOST-GUEST SYSTEM
 
Authors :  L. Lu, C. Yi, X. Jian, G Zheng, C. He
Date :  29 Apr 09  (Deposition) - 31 Mar 10  (Release) - 04 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Protein-Dna Complex, Dioxygenase, Dna Damage, Dna Repair, Iron, Metal-Binding, Nucleus, Oxidoreductase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Lu, C. Yi, X. Jian, G. Zheng, C. He
Structure Determination Of Dna Methylation Lesions N1-Mea And N3-Mec In Duplex Dna Using A Cross-Linked Protein-Dna System.
Nucleic Acids Res. V. 38 4415 2010
PubMed-ID: 20223766  |  Reference-DOI: 10.1093/NAR/GKQ129

(-) Compounds

Molecule 1 - ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB HOMOLOG 2
    ChainsA
    EC Number1.14.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentTRUNCATION WITH N-TERMINAL 55 AMINO ACID DELETED
    GeneABH2, ALKB HUMAN HOMOLOG 2(ABH2), ALKBH2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymALKYLATED DNA REPAIR PROTEIN ALKB HOMOLOG 2, OXY DC1
 
Molecule 2 - 5'-D(*CP*TP*GP*TP*AP*TP*(2YR)P*AP*TP*(6MA)P*GP*CP*G)-3'
    ChainsB
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 3 - 5'-D(*TP*CP*GP*CP*TP*AP*TP*AP*AP*TP*AP*CP*A)-3'
    ChainsC
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
12YR1Mod. Nucleotide2'-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE 5'-(DIHYDROGENPHOSPHATE)
26MA1Mod. NucleotideN6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE
3GOL1Ligand/IonGLYCEROL
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:101 , TYR A:122 , PHE A:124 , SER A:125 , ILE A:168 , GLY A:169 , HIS A:171 , CYS A:175 , HOH A:403 , DT B:264 , DA B:266 , HOH B:305 , HOH B:309 , HOH B:311BINDING SITE FOR RESIDUE 2YR B 265
2AC2SOFTWAREGLU A:77 , ILE A:81 , ARG A:98 , ARG A:140 , HOH A:425 , HOH A:459 , HOH A:468BINDING SITE FOR RESIDUE GOL A 301
3AC3SOFTWARE6MA B:268 , DG B:269 , HOH B:312 , DA C:277 , DT C:278 , HOH C:416 , HOH C:430BINDING SITE FOR RESIDUE TRS C 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H8R)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His A:228 -Pro A:229

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048223R203HALKB2_HUMANPolymorphism33962311AR203H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FE2OG_OXYPS51471 Fe(2+) 2-oxoglutarate dioxygenase domain profile.ALKB2_HUMAN152-257  1A:152-257

(-) Exons   (0, 0)

(no "Exon" information available for 3H8R)

(-) 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:204
 aligned with ALKB2_HUMAN | Q6NS38 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:204
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254    
          ALKB2_HUMAN    55 PSWRHIRAEGLDCSYTVLFGKAEADEIFQELEKEVEYFTGALARVQVFGKWHSVPRKQATYGDAGLTYTFSGLTLSPKPWIPVLERIRDHVSGVTGQTFNFVLINRYKDGCDHIGEHRDDERELAPGSPIASVSFGACRDFVFRHKDSRGKSPSRRVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKILL 258
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee..eeeeeee..hhhhhhhhhhhhhhhh...hhhh.eeee..eeee...eeeeee.....eee..eee.....hhhhhhhhhhhhhhhh....eeeeeee......eeee............eeeeeee..eeeeeee.hhh..........eeeee...eeeee..hhhhheeeee.........eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------H------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------FE2OG_OXY  PDB: A:152-257 UniProt: 152-257                                                                - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3h8r A  55 HSWRHIRAEGLDSSYTVLFGKAEADEIFQELEKEVEYFTGALARVQVFGKWHSVPRKQATYGDAGLTYTFSGLTLSPKPWIPVLERIRDHVSGVTGQTFNFVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSRGKSPSRRVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKILL 258
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254    

Chain B from PDB  Type:DNA  Length:13
                                             
                 3h8r B 259 CTGTATxATaGCG 271
                                  |268   
                                265-2YR  
                                   268-6MA

Chain C from PDB  Type:DNA  Length:13
                                             
                 3h8r C 272 TCGCTATAATACA 284
                                   281   

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3H8R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H8R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H8R)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ALKB2_HUMAN | Q6NS38)
molecular function
    GO:0043734    DNA-N1-methyladenine dioxygenase activity    Catalysis of the oxidative demethylation of N1-methyladenine and N3-methylcytosine in DNA, with concomitant decarboxylation of 2-oxoglutarate and releases oxidized methyl group on N1-methyladenine and N3-methylcytosine as formaldehyde.
    GO:0051747    cytosine C-5 DNA demethylase activity    Catalysis of the reaction: methyl-dCpdG DNA + H2O = dCpdG DNA + methanol. This reaction is the hydrolytic removal of the methyl group on the 5 position of cytosine in DNA.
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016706    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors    Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.
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:0080111    DNA demethylation    The removal of a methyl group from one or more nucleotides within an DNA molecule.
    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: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.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0035511    oxidative DNA demethylation    Removal of the methyl group from one or more nucleotides within a DNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.
    GO:0070989    oxidative demethylation    The process of removing one or more methyl groups from a molecule, involving the oxidation (i.e. electron loss) of one or more atoms in the substrate.
cellular component
    GO:0015630    microtubule cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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
        ALKB2_HUMAN | Q6NS383btx 3bty 3btz 3bu0 3buc 3h8o 3h8x 3rzg 3rzh 3rzj 3rzk 3rzl 3rzm 3s57 3s5a 4mg2 4mgt

(-) Related Entries Specified in the PDB File

3h8o 3h8x