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(-) Description

Title :  HUMAN TDG N140A MUTANT IN A COMPLEX WITH 5-CARBOXYLCYTOSINE (5CAC)
 
Authors :  H. Hashimoto, X. Zhang, X. Cheng
Date :  28 Feb 13  (Deposition) - 29 May 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.58
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  5-Carboxylcytosine; Thymine Dna Glycosylase; Dna Modification; Dna 5Mc Oxidation; Epigenetic Regulation, Dna Demethylation, 5- Carboxylcytosine, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Hashimoto, X. Zhang, X. Cheng
Activity And Crystal Structure Of Human Thymine Dna Glycosylase Mutant N140A With 5-Carboxylcytosine Dna At Low Ph.
Dna Repair V. 12 535 2013
PubMed-ID: 23680598  |  Reference-DOI: 10.1016/J.DNAREP.2013.04.003

(-) Compounds

Molecule 1 - G/T MISMATCH-SPECIFIC THYMINE DNA GLYCOSYLASE
    ChainsA
    EC Number3.2.2.29
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPXC1057
    Expression System Taxid562
    FragmentUNP RESIDUES 111-308
    GeneTDG
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTHYMINE-DNA GLYCOSYLASE
 
Molecule 2 - OLIGONUCLEOTIDE
    ChainsC
    EngineeredYES
    Other DetailsDNA SYNTHESIS
    SyntheticYES
 
Molecule 3 - OLIGONUCLEOTIDE CONTAINING 5-CARBOXYLCYTOSINE
    ChainsD
    EngineeredYES
    Other DetailsDNA SYNTHESIS
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ACD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
11RT1Ligand/Ion4-AMINO-2-OXO-1,2-DIHYDROPYRIMIDINE-5-CARBOXYLIC ACID
2ORP1Mod. Nucleotide2-DEOXY-5-PHOSPHONO-RIBOSE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:138 , ILE A:139 , ALA A:140 , PRO A:141 , GLY A:142 , TYR A:152 , ASN A:191 , ASN A:230 , SER A:271 , ORP D:17BINDING SITE FOR RESIDUE 1RT D 417

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JGC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JGC)

(-) Exons   (0, 0)

(no "Exon" information available for 4JGC)

(-) 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    
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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:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh...........eeeee...hhhhhhhh........hhhhhhhhh.......hhhhhhhhhhhh.eeeee............hhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh.........ee..........eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jgc A 110 SFNGVSEAELLTKTLPDILTFNLDIVIIGIAPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERN 305
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299      

Chain C from PDB  Type:DNA  Length:28
                                                            
                 4jgc C   1 CAGCTCTGTACGTGAGCAGTGGACAGCT  28
                                    10        20        

Chain D from PDB  Type:DNA  Length:28
                                                            
                 4jgc D   1 AGCTGTCCACTGCTCAxGTACAGAGCTG  28
                                    10      | 20        
                                           17-ORP       

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  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 4JGC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4fnc HUMAN TDG IN A POST-REACTIVE COMPLEX WITH 5- HYDROXYMETHYLURACIL (5HMU)