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(-) Description

Title :  STRUCTURE OF THYMINE DNA GLYCOSYLASE BOUND TO SUBSTRATE ANALOG 2'-F-5-FORMYL-DC
 
Authors :  L. S. Pidugu, E. Pozharski, A. C. Drohat
Date :  24 Aug 16  (Deposition) - 09 Nov 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Protein-Dna Complex, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. S. Pidugu, J. W. Flowers, C. T. Coey, E. Pozharski, M. M. Greenberg, A. C. Drohat
Structural Basis For Excision Of 5-Formylcytosine By Thymin Dna Glycosylase.
Biochemistry V. 55 6205 2016
PubMed-ID: 27805810  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B00982

(-) Compounds

Molecule 1 - G/T MISMATCH-SPECIFIC THYMINE DNA GLYCOSYLASE
    Chains: A
    EC Number: 3.2.2.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 82-308
    Gene: TDG
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: THYMINE-DNA GLYCOSYLASE,HTDG
 
Molecule 2 - DNA (28-MER)
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (27-MER)
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ACD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1XFC1Mod. Nucleotide4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-2-OXO-1,2-DIHYDROPYRIMIDINE-5-CARBALDEHYDE

(-) Sites  (0, 0)

(no "Site" information available for 5T2W)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5T2W)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:154 -Pro A:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5T2W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T2W)

(-) Exons   (0, 0)

(no "Exon" information available for 5T2W)

(-) 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:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh.............eeeee...hhhhhhhh........hhhhhhhhh.......hhhhhhhhhhhhheeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh........ee..........eeeee...........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t2w A 108 VDRFNGVSEAELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGI 302
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297     


Chain C from PDB  Type:DNA  Length:28
                                                            
                 5t2w C   1 CAGCTCTGTACGTGAGCGATGGACAGCT  28
                                    10        20        


Chain D from PDB  Type:DNA  Length:27
                                                           
                 5t2w D   2 GCTGTCCATCGCTCAxGTACAGAGCTG  28
                                    11     |  21       
                                          17-XFC
   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 5T2W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T2W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T2W)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:154 - Pro A:155   [ RasMol ]  
 

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  5t2w
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  3.2.2.29
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 Related Entries

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

UniProtKB/Swiss-Prot
        TDG_HUMAN | Q13569: 1wyw 2d07 2rba 3ufj 3uo7 3uob 4fnc 4jgc 4xeg 4z3a 4z47 4z7b 4z7z 5cys 5ff8 5hf7 5jxy

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5T2W)