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(-) Description

Title :  CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(II), 2-OXOGLUTARATE AND METHYLATED TRINUCLEOTIDE T-MEA-T
 
Authors :  B. Yu, J. F. Hunt
Date :  29 Jun 09  (Deposition) - 25 Aug 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Jellyroll, Protein-Dna Complex, Dioxygenase, Dna Damage, Dna Repair, Iron, Metal-Binding, Oxidoreductase, Oxidoreductase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Yu, J. F. Hunt
Enzymological And Structural Studies Of The Mechanism Of Promiscuous Substrate Recognition By The Oxidative Dna Repair Enzyme Alkb.
Proc. Natl. Acad. Sci. Usa V. 106 14315 2009
PubMed-ID: 19706517  |  Reference-DOI: 10.1073/PNAS.0812938106

(-) Compounds

Molecule 1 - ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB
    ChainsA
    EC Number1.14.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET26B
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 12-216
    GeneAIDD, ALKB, B2212, JW2200
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK-12
    SynonymALKYLATED DNA REPAIR PROTEIN ALKB
 
Molecule 2 - DNA (5'-D(P*TP*(MA7)P*T)-3')
    ChainsB
    EngineeredYES
    Other DetailsOLIGONUCLEOTIDE TRIMER CHEMICALLY SYNTHESIZED WITH METHYL ADDUCT ON N1 OF CENTRAL ADENINE BASE
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2FE21Ligand/IonFE (II) ION
3MA71Mod. Nucleotide1N-METHYLADENOSINE-5'-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:118 , ASN A:120 , TYR A:122 , LEU A:128 , HIS A:131 , ASP A:133 , HIS A:187 , ILE A:189 , ARG A:204 , ASN A:206 , ARG A:210 , FE2 A:300 , HOH A:601 , HOH A:617 , MA7 B:502BINDING SITE FOR RESIDUE AKG A 400
2AC2SOFTWAREHIS A:131 , ASP A:133 , HIS A:187 , AKG A:400 , HOH A:601BINDING SITE FOR RESIDUE FE2 A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I2O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3I2O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I2O)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FE2OG_OXYPS51471 Fe(2+) 2-oxoglutarate dioxygenase domain profile.ALKB_ECOLI113-213  1A:113-213

(-) Exons   (0, 0)

(no "Exon" information available for 3I2O)

(-) 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:199
 aligned with ALKB_ECOLI | P05050 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:199
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204         
           ALKB_ECOLI    15 LAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAG 213
               SCOP domains d3i2oa_ A: automated matches                                                                                                                                                                            SCOP domains
               CATH domains 3i2oA00 A:15-213 Clavaminate synthase-like domains                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee......hhhhhhhhhhhhhhhh...............eeeee...eeeee..eeeee.............hhhhhhhhhhhhhhh........eeeeeee.....eeee...........eeeeeee..eeeee.........eeeee....eeee.hhhhhh.eee..............eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------FE2OG_OXY  PDB: A:113-213 UniProt: 113-213                                                            PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i2o A  15 LAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAG 213
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204         

Chain B from PDB  Type:DNA  Length:3
                                   
                 3i2o B 501 TaT 503
                             | 
                           502-MA7

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I2O)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ALKB_ECOLI | P05050)
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:0035515    oxidative RNA demethylase activity    Catalysis of the removal of a methyl group from one or more nucleosides within a RNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.
    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.
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:0042245    RNA repair    Any process that results in the repair of damaged RNA.
    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: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.
    GO:0035552    oxidative single-stranded DNA demethylation    Removal of the methyl group from one or more nucleotides within a single-stranded DNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.
    GO:0035553    oxidative single-stranded RNA demethylation    Removal of the methyl group from one or more nucleotides within a single-stranded RNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ALKB_ECOLI | P050502fd8 2fdf 2fdg 2fdh 2fdi 2fdj 2fdk 3bi3 3bie 3bkz 3i3m 3i3q 3i49 3khb 3khc 3o1m 3o1o 3o1p 3o1r 3o1s 3o1t 3o1u 3o1v 3t3y 3t4h 3t4v 4jht 4nid 4nig 4nih 4nii 4rfr 4zhn

(-) Related Entries Specified in the PDB File

2fd8 SAME PROTEIN COMPLEX AT LOWER RESOLUTION
2iuw HOMOLOGUE
3buc HOMOLOGUE
3i3m
3i3q
3i49