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(-) Description

Title :  CRYSTAL STRUCTURE OF TATD IN COMPLEX WITH TRINUCLEOTIDE DNA
 
Authors :  Y. Chen, C. -L. Li, Y. -Y. Hsiao, Y. Duh, H. S. Yuan
Date :  23 Apr 14  (Deposition) - 27 Aug 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.89
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Repair, Dna Processing, Exonuclease, Tim Barrel, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. C. Chen, C. L. Li, Y. Y. Hsiao, Y. Duh, H. S. Yuan
Structure And Function Of Tatd Exonuclease In Dna Repair.
Nucleic Acids Res. V. 42 10776 2014
PubMed-ID: 25114049  |  Reference-DOI: 10.1093/NAR/GKU732

(-) Compounds

Molecule 1 - TAT-LINKED QUALITY CONTROL PROTEIN TATD
    Chains: A
    EC Number: 3.1.15.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TATD, MTTC, YIGW, YIGX, B4483, JW5931
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: DEOXYRIBONUCLEASE TATD,DNASE TATD
 
Molecule 2 - DNA (5'-D(*GP*CP*T)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4PE8)

(-) Sites  (0, 0)

(no "Site" information available for 4PE8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PE8)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:90 -Glu A:91
2Ala A:204 -Pro A:205
3Thr A:213 -Pro A:214

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PE8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PE8)

(-) Exons   (0, 0)

(no "Exon" information available for 4PE8)

(-) 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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhh.hhhhhhhhhhh.....eee...hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhh...eeeeeeeeee......hhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh.hhhhh..eee.....hhhhhhhhhh..eeeeehhhhhh...hhhhhhhh.......eee.....................hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pe8 A   1 MFDIGVNLTSSQFAKDRDDVVACAFDAGVNGLLITGTNLRESQQAQKLARQYSSCWSTAGVHPHDSSQWQAATEEAIIELAAQPEVVAIGECGLDFNRNFSTPEEQERAFVAQLRIAADLNMPVFMHCRDAHERFMTLLEPWLDKLPGAVLHCFTGTREEMQACVAHGIYIGITGWVCDERRGLELRELLPLIPAEKLLIETDAPYLLPRDLTPKPSSRRNEPAHLPHILQRIAHWRGEDAAWLAATTDANVKTLFGIAF 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260


Chain B from PDB  Type:DNA  Length:3
                                   
                 4pe8 B  -1 GCT   1
   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 4PE8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PE8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PE8)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:204 - Pro A:205   [ RasMol ]  
    Gly A:90 - Glu A:91   [ RasMol ]  
    Thr A:213 - Pro A:214   [ RasMol ]  
 

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  TATD_ECOLI | P27859
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  3.1.15.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        TATD_ECOLI | P27859: 1xwy 4p5u

(-) Related Entries Specified in the PDB File

4p5u TATD APOPROTEIN