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(-) Description

Title :  DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE COMPLEXED WITH LEFT END RECOGNITION AND CLEAVAGE SITE AND ZN
 
Authors :  A. B. Hickman, J. A. James, O. Barabas, C. Pasternak, B. Ton-Hoang, M. Ch S. Sommer, F. Dyda
Date :  01 Sep 10  (Deposition) - 13 Oct 10  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Dna Binding Protein-Dna Complex, Transposition, Mobile Element (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. B. Hickman, J. A. James, O. Barabas, C. Pasternak, B. Ton-Hoang, M. Chandler, S. Sommer, F. Dyda
Dna Recognition And The Precleavage State During Single-Stranded Dna Transposition In D. Radiodurans.
Embo J. V. 29 3840 2010
PubMed-ID: 20890269  |  Reference-DOI: 10.1038/EMBOJ.2010.241

(-) Compounds

Molecule 1 - TRANSPOSASE
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
    Synonym: DRA2 TRANSPOSASE
 
Molecule 2 - DRA2 TRANSPOSASE LEFT END RECOGNITION SEQUENCE
    Chains: B, E
    Engineered: YES
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
    Other Details: ISDRA2 TRANSPOSON INTERNAL SEQUENCE
    Synthetic: YES
 
Molecule 3 - 5'-D(TP*TP*GP*AP*TP*GP)-3'
    Chains: C, F
    Engineered: YES
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
    Synonym: DRA2 TRANSPOSASE LEFT END CLEAVAGE SITE, F
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric/Biological Unit (1, 9)
No.NameCountTypeFull Name
1ZN9Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:67 , HIS A:69 , DT C:5 , DG C:6 , HIS D:137BINDING SITE FOR RESIDUE ZN A 1138
2AC2SOFTWAREPRO A:114 , HOH A:2133 , HOH A:2134 , HOH A:2135 , HOH A:2136 , DC B:31BINDING SITE FOR RESIDUE ZN A 1139
3AC3SOFTWAREASP A:45 , ASP A:49 , GLU D:134 , ASP D:138BINDING SITE FOR RESIDUE ZN A 1140
4AC4SOFTWAREHOH B:2057 , HOH B:2058 , HOH B:2059 , HOH B:2060 , HOH B:2061 , HOH B:2062BINDING SITE FOR RESIDUE ZN B 1038
5AC5SOFTWAREDG C:3 , HOH C:2019 , HOH C:2020 , HOH C:2021 , HOH C:2022 , HOH C:2023BINDING SITE FOR RESIDUE ZN C 1007
6AC6SOFTWAREHIS A:137 , HIS D:67 , HIS D:69 , DT F:5 , DG F:6BINDING SITE FOR RESIDUE ZN D 1141
7AC7SOFTWAREASP D:45 , HOH D:2125 , HOH D:2126 , HOH D:2127 , HOH D:2128 , HOH D:2129BINDING SITE FOR RESIDUE ZN D 1142
8AC8SOFTWAREPRO D:114 , DC E:31 , HOH E:2095 , HOH E:2096 , HOH E:2097 , HOH E:2098BINDING SITE FOR RESIDUE ZN E 1038
9AC9SOFTWAREHOH E:2099 , HOH E:2100 , HOH E:2101 , HOH E:2102 , HOH E:2103 , HOH E:2104BINDING SITE FOR RESIDUE ZN E 1039

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XQC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XQC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XQC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XQC)

(-) Exons   (0, 0)

(no "Exon" information available for 2XQC)

(-) 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:129
 aligned with O83028_DEIRD | O83028 from UniProtKB/TrEMBL  Length:140

    Alignment length:129
                                    18        28        38        48        58        68        78        88        98       108       118       128         
         O83028_DEIRD     9 EMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIESQH 137
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eeeeeeeeeeee.hhhh...hhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xqc A   9 EMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIESQH 137
                                    18        28        38        48        58        68        78        88        98       108       118       128         


Chain B from PDB  Type:DNA  Length:27
                                                           
                 2xqc B  11 CGCACACTCGTGACTTCAGTCATGAGT  37
                                    20        30       


Chain C from PDB  Type:DNA  Length:6
                                      
                 2xqc C   1 TTGATG   6


Chain D from PDB  Type:PROTEIN  Length:132
 aligned with O83028_DEIRD | O83028 from UniProtKB/TrEMBL  Length:140

    Alignment length:132
                                    18        28        38        48        58        68        78        88        98       108       118       128       138  
         O83028_DEIRD     9 EMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIESQHDKE 140
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeeeeeeee.hhhh...hhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xqc D   9 EMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIESQHDKE 140
                                    18        28        38        48        58        68        78        88        98       108       118       128       138  


Chain E from PDB  Type:DNA  Length:27
                                                           
                 2xqc E  11 CGCACACTCGTGACTTCAGTCATGAGT  37
                                    20        30       


Chain F from PDB  Type:DNA  Length:6
                                      
                 2xqc F   1 TTGATG   6
   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 2XQC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XQC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2XQC)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,D   (O83028_DEIRD | O83028)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004803    transposase activity    Catalysis of the transposition of transposable elements or transposons. Transposases are involved in recombination required for transposition and are site-specific for the transposon/transposable element.
biological process
    GO:0070895    negative regulation of transposon integration    Any process that stops, prevents, or reduces the frequency, rate or extent of transposon integration, a process in which a transposable element is incorporated into another DNA molecule.
    GO:0006313    transposition, DNA-mediated    Any process involved in a type of transpositional recombination which occurs via a DNA intermediate.

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 Related Entries

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

UniProtKB/TrEMBL
        O83028_DEIRD | O83028: 2xm3 2xma 2xo6

(-) Related Entries Specified in the PDB File

2xm3 DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE LEFT END DNA COMPLEX
2xma DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE RIGHT END DNA COMPLEX
2xo6 DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE Y132F MUTANT COMPLEXED WITH LEFT END RECOGNITION AND CLEAVAGE SITE