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(-) Description

Title :  STRUCTURE OF HUMAN THYMINE DNA GLYCOSYLASE BOUND TO ABASIC AND UNDAMAGED DNA
 
Authors :  A. Maiti, E. Pozharski, A. C. Drohat
Date :  18 Sep 07  (Deposition) - 17 Jun 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.79
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Dna Complex, Dna Damage, Dna Repair, Glycosidase, Hydrolase, Nucleus, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Maiti, M. T. Morgan, E. Pozharski, A. C. Drohat
Crystal Structure Of Human Thymine Dna Glycosylase Bound To Dna Elucidates Sequence-Specific Mismatch Recognition.
Proc. Natl. Acad. Sci. Usa V. 105 8890 2008
PubMed-ID: 18587051  |  Reference-DOI: 10.1073/PNAS.0711061105

(-) Compounds

Molecule 1 - G/T MISMATCH-SPECIFIC THYMINE DNA GLYCOSYLASE
    ChainsA, B
    EC Number3.2.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    FragmentCORE DOMAIN
    GeneTDG
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
 
Molecule 2 - DNA (5'- D(*DCP*DAP*DGP*DCP*DTP*DCP*DTP*DGP*DTP*DAP*DCP*DGP*DTP*DGP*DAP*DGP*DC P*DAP*DGP*DTP*DGP*DGP*DA)-3')
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 3 - DNA (5'-D(*DCP*DCP*DAP*DCP*DTP*DGP*DCP*DTP*DCP*DAP*(3DR) P*DGP*DTP*DAP*DCP*DAP*DGP*DAP*DGP*DCP*DTP*DGP*DT)-3')
    ChainsD
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

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  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:140 , GLY A:142 , GLY A:156 , ASN A:157 , SER A:200 , SER A:273 , DA D:10 , DG D:12BINDING SITE FOR RESIDUE 3DR D 11

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RBA)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Gly A:154 -Pro A:155
2Pro A:155 -Gly A:156
3Gly A:199 -Ser A:200
4Gly A:301 -Ile A:302
5Ile A:302 -Glu A:303
6Gly B:154 -Pro B:155
7Gln B:278 -Phe B:279
8Phe B:279 -Pro B:280

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018892G199STDG_HUMANPolymorphism4135113A/BG199S

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RBA)

(-) Exons   (6, 12)

Asymmetric/Biological Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003928721ENSE00002180300chr12:104359593-104359838246TDG_HUMAN1-880--
1.2ENST000003928722ENSE00001735126chr12:104370696-104370838143TDG_HUMAN8-56490--
1.3aENST000003928723aENSE00001772150chr12:104373609-104373850242TDG_HUMAN56-136812A:123-136
B:123-136
14
14
1.4ENST000003928724ENSE00001675345chr12:104374671-10437474070TDG_HUMAN137-160242A:137-160
B:137-160
24
24
1.5ENST000003928725ENSE00001666484chr12:104376577-104376712136TDG_HUMAN160-205462A:160-205
B:160-205
46
46
1.6ENST000003928726ENSE00000937845chr12:104376914-10437699683TDG_HUMAN205-233292A:205-233
B:205-233
29
29
1.7ENST000003928727ENSE00000937846chr12:104377073-10437716795TDG_HUMAN233-264322A:233-264
B:233-264
32
32
1.8ENST000003928728ENSE00000937847chr12:104378527-104378698172TDG_HUMAN265-322582A:265-304
B:265-304
40
40
1.9ENST000003928729ENSE00000937848chr12:104379381-104379506126TDG_HUMAN322-364430--
1.10ENST0000039287210ENSE00001301388chr12:104380726-1043826551930TDG_HUMAN364-410470--

(-) 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:182
 aligned with TDG_HUMAN | Q13569 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:182
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302  
            TDG_HUMAN   123 TLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIER 304
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhh........hhhhhhhhh..........hhhhhhhhhheeeee............hhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhh.........ee..........eeeee...........hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------S--------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a     Exon 1.4  PDB: A:137-160--------------------------------------------Exon 1.6  PDB: A:205-233     -------------------------------Exon 1.8  PDB: A:265-304 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.5  PDB: A:160-205 UniProt: 160-205     ---------------------------Exon 1.7  PDB: A:233-264        ---------------------------------------- Transcript 1 (2)
                 2rba A 123 TLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIER 304
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302  

Chain B from PDB  Type:PROTEIN  Length:182
 aligned with TDG_HUMAN | Q13569 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:182
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302  
            TDG_HUMAN   123 TLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIER 304
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --UDG-2rbaB01 B:125-293                                                                                                                                                    ----------- Pfam domains (1)
           Pfam domains (2) --UDG-2rbaB02 B:125-293                                                                                                                                                    ----------- Pfam domains (2)
         Sec.struct. author ...........eeeee...hhhhhhhh........hhhhhhhhh.......hhhhhhhhhhhhheeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhh............eeeeee......eeeee...............hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------S--------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a     Exon 1.4  PDB: B:137-160--------------------------------------------Exon 1.6  PDB: B:205-233     -------------------------------Exon 1.8  PDB: B:265-304 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.5  PDB: B:160-205 UniProt: 160-205     ---------------------------Exon 1.7  PDB: B:233-264        ---------------------------------------- Transcript 1 (2)
                 2rba B 123 TLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIER 304
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302  

Chain C from PDB  Type:DNA  Length:23
                                                       
                 2rba C   1 CAGCTCTGTACGTGAGCAGTGGA  23
                                    10        20   

Chain D from PDB  Type:DNA  Length:23
                                                       
                 2rba D   1 CCACTGCTCAxGTACAGAGCTGT  23
                                    10|       20   
                                     11-3DR        

   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 2RBA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2RBA)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Family: UDG (24)
1aUDG-2rbaB01B:125-293
1bUDG-2rbaB02B:125-293

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TDG_HUMAN | Q13569)
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:0001104    RNA polymerase II transcription cofactor activity    Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to modulate transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between regulatory transcription factors and the basal RNAP II transcription machinery.
    GO:0032183    SUMO binding    Interacting selectively and non-covalently with the small ubiquitin-like protein SUMO.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    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.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0030983    mismatched DNA binding    Interacting selectively and non-covalently with double-stranded DNA containing one or more mismatches.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0005080    protein kinase C binding    Interacting selectively and non-covalently with protein kinase C.
    GO:0008263    pyrimidine-specific mismatch base pair DNA N-glycosylase activity    Catalysis of the removal of mismatched pyrimidine bases in DNA. Enzymes with this activity recognize and remove pyrimidines present in mismatches 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 apyrimidinic (AP) site.
    GO:0004844    uracil DNA N-glycosylase activity    Catalysis of the cleavage of the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar, releasing a free base and leaving an apyrimidinic (AP) site. Enzymes with this activity recognize and remove uracil bases in DNA that result from the deamination of cytosine or the misincorporation of dUTP opposite an adenine.
biological process
    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: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.
    GO:0045008    depyrimidination    The disruption of the bond between the sugar in the backbone and the C or T base, causing the base to be removed and leaving a depyrimidinated sugar.
    GO:0009790    embryo development    The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006298    mismatch repair    A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
    GO:0035562    negative regulation of chromatin binding    Any process that stops or reduces the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0032091    negative regulation of protein binding    Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
    GO:0040029    regulation of gene expression, epigenetic    Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0016605    PML body    A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TDG_HUMAN | Q135691wyw 2d07 3ufj 3uo7 3uob 4fnc 4jgc 4xeg 4z3a 4z47 4z7b 4z7z 5cys 5ff8 5hf7 5jxy 5t2w

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2RBA)