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(-) Description

Title :  STRUCTURE OF THE ENZYME-PRODUCT COMPLEX RESULTING FROM TDG ACTION ON A GU MISMATCH IN THE PRESENCE OF EXCESS BASE
 
Authors :  E. Pozharski, S. S. Malik, A. C. Drohat
Date :  01 Apr 15  (Deposition) - 16 Sep 15  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Protein-Dna Complex, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. S. Malik, C. T. Coey, K. M. Varney, E. Pozharski, A. C. Drohat
Thymine Dna Glycosylase Exhibits Negligible Affinity For Nucleobases That It Removes From Dna.
Nucleic Acids Res. V. 43 9541 2015
PubMed-ID: 26358812  |  Reference-DOI: 10.1093/NAR/GKV890

(-) 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 111-308
    Gene: TDG
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: THYMINE-DNA GLYCOSYLASE,HTDG
 
Molecule 2 - DNA
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA
    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  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2EDO3Ligand/Ion1,2-ETHANEDIOL
3ORP1Mod. Nucleotide2-DEOXY-5-PHOSPHONO-RIBOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:131 , LEU A:132 , GLN A:223 , ARG A:225binding site for residue EDO A 401
2AC2SOFTWARELEU A:254 , GLN A:255 , PRO A:256 , LYS A:258 , LEU A:265binding site for residue EDO A 402
3AC3SOFTWARELEU A:295 , GLN A:298 , LEU A:299 , ILE A:302 , HOH D:105binding site for residue EDO A 403
4AC4SOFTWAREGLY A:138 , ILE A:139 , ASN A:140 , TYR A:152 , ASN A:191 , HOH A:514 , HOH A:555 , HOH A:595 , ORP D:17binding site for residue ACY A 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z47)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Z47)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z47)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z47)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z47)

(-) 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:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh.............eeeee...hhhhhhhh........hhhhhhhhh.......hhhhhhhhhhhhheeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh........ee..........eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z47 A 111 FNGVSEAELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERNM 306
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300      


Chain C from PDB  Type:DNA  Length:28
                                                            
                 4z47 C   1 CAGCTCTGTACGTGAGCGATGGACAGCT  28
                                    10        20        


Chain D from PDB  Type:DNA  Length:28
                                                            
                 4z47 D   1 AGCTGTCCATCGCTCAxGTACAGAGCTG  28
                                    10      | 20        
                                           17-ORP
   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 4Z47)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z47)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z47)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4z47
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  TDG_HUMAN | Q13569
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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 4z7b 4z7z 5cys 5ff8 5hf7 5jxy 5t2w

(-) Related Entries Specified in the PDB File

4xeg 4z3a 4z7b 4z7z 5cys