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(-) Description

Title :  ENZYME-SUBSTRATE COMPLEX OF TDG CATALYTIC DOMAIN BOUND TO A G/U ANALOG
 
Authors :  L. S. Pidugu, E. Pozharski, S. S. Malik, A. C. Drohat
Date :  13 May 16  (Deposition) - 28 Sep 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Protein-Dna Complex, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. T. Coey, S. S. Malik, L. S. Pidugu, K. M. Varney, E. Pozharski, A. C. Drohat
Structural Basis Of Damage Recognition By Thymine Dna Glycosylase: Key Roles For N-Terminal Residues.
Nucleic Acids Res. V. 44 10248 2016
PubMed-ID: 27580719  |  Reference-DOI: 10.1093/NAR/GKW768

(-) Compounds

Molecule 1 - G/T MISMATCH-SPECIFIC THYMINE DNA GLYCOSYLASE
    ChainsA
    EC Number3.2.2.29
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneTDG
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsTDG
    SynonymTHYMINE-DNA GLYCOSYLASE,HTDG
 
Molecule 2 - DNA (28-MER)
    ChainsC
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 3 - DNA (28-MER)
    ChainsD
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 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
1UF21Mod. Nucleotide1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDINE-2,4(1H,3H)-DIONE

(-) Sites  (0, 0)

(no "Site" information available for 5JXY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:247 -Lys A:248
2Lys A:248 -Asn A:249

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JXY)

(-) 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.......hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhh.........ee..........eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jxy 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
                                                            
                 5jxy C   1 CAGCTCTGTACGTGAGCGATGGACAGCT  28
                                    10        20        

Chain D from PDB  Type:DNA  Length:28
                                                            
                 5jxy D   1 AGCTGTCCATCGCTCAxGTACAGAGCTG  28
                                    10      | 20        
                                           17-UF2       

   Legend:   → Mismatch (orange background)
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    → 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 5JXY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Lys A:248 - Asn A:249   [ RasMol ]  
    Val A:247 - Lys A:248   [ RasMol ]  
 

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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 4jgc 4xeg 4z3a 4z47 4z7b 4z7z 5cys 5ff8 5hf7 5t2w

(-) Related Entries Specified in the PDB File

3ufj 5hf7