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(-) Description

Title :  DUPLEX INTERROGATION BY A DIRECT DNA REPAIR PROTEIN IN THE SEARCH OF DAMAGE
 
Authors :  C. Yi, B. Chen, B. Qi, W. Zhang, G. Jia, L. Zhang, C. Li, A. Dinner, C. Yang,
Date :  11 May 11  (Deposition) - 06 Jun 12  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Protein-Dna Complex, Jelly-Roll, Demethylase, Nucleus, Oxidoreductase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Yi, B. Chen, B. Qi, W. Zhang, G. Jia, L. Zhang, C. J. Li, A. R. Dinner, C. G. Yang, C. He
Duplex Interrogation By A Direct Dna Repair Protein In Search Of Base Damage
Nat. Struct. Mol. Biol. V. 19 671 2012
PubMed-ID: 22659876  |  Reference-DOI: 10.1038/NSMB.2320

(-) Compounds

Molecule 1 - ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB HOMOLOG 2
    ChainsA
    EC Number1.14.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 56-261
    GeneALKBH2, ABH2
    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*CP*TP*(ME6)P*AP*CP*TP*GP*CP*G)-3'
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 3 - 5'-D(*TP*CP*GP*CP*AP*GP*TP*GP*AP*GP*AP*CP*A)-3'
    ChainsC
    EngineeredYES
    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
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2ME61Mod. Nucleotide[(2R,3S,5R)-5-(4-AZANYL-3-METHYL-2-OXO-PYRIMIDIN-3-IUM-1-YL)-3-HYDROXY-OXOLAN-2-YL]METHYL DIHYDROGENPHOSPHATE
3MN1Ligand/IonMANGANESE (II) ION
4XL31Ligand/IonPROPANE-1-THIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:171 , ASP A:173 , HIS A:236 , AKG A:262BINDING SITE FOR RESIDUE MN A 1
2AC2SOFTWAREMN A:1 , LEU A:157 , ASN A:159 , TYR A:161 , HIS A:171 , ASP A:173 , HIS A:236 , ARG A:248 , ASN A:250 , THR A:252 , ARG A:254 , ME6 B:265BINDING SITE FOR RESIDUE AKG A 262
3AC3SOFTWARECYS A:169 , DC B:267BINDING SITE FOR RESIDUE XL3 A 263

(-) SS Bonds  (0, 0)

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

(-) 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 3RZJ)

(-) 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:203
 aligned with ALKB2_HUMAN | Q6NS38 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:210
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258
          ALKB2_HUMAN    49 GGHSAGPSWRHIRAEGLDCSYTVLFGKAEADEIFQELEKEVEYFTGALARVQVFGKWHSVPRKQATYGDAGLTYTFSGLTLSPKPWIPVLERIRDHVSGVTGQTFNFVLINRYKDGCDHIGEHRDDERELAPGSPIASVSFGACRDFVFRHKDSRGKSPSRRVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKILL 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
                 3rzj A  53 GSH----SWRHIRAEGLDSSYTVLFGKAEADEIFQELEKEVEYFTGALARVQVFGKWHSVPRKQATYGDAGLTYTFSGLTLSPKPWIPVLERIRDHVSGVTGQTFNFVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSR---PSRRVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKILL 258
                              |    |58        68        78        88        98       108       118       128       138       148       158       168       178       188       198    |  208       218       228       238       248       258
                             55   56                                                                                                                                                203 207                                                   

Chain B from PDB  Type:DNA  Length:13
                                             
                 3rzj B 259 CTGTCTcACTGCG 271
                                  |268   
                                265-ME6  

Chain C from PDB  Type:DNA  Length:13
                                             
                 3rzj C 272 TCGCAGTGAGACA 284
                                   281   

   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 3RZJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 3h8r 3h8x 3rzg 3rzh 3rzk 3rzl 3rzm 3s57 3s5a 4mg2 4mgt

(-) Related Entries Specified in the PDB File

3rzg 3rzh 3rzk 3rzl 3rzm