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(-) Description

Title :  DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE Y132F MUTANT COMPLEXED WITH LEFT END RECOGNITION AND CLEAVAGE SITE
 
Authors :  A. B. Hickman, J. A. James, O. Barabas, C. Pasternak, B. Ton-Hoang, M. Ch S. Sommer, F. Dyda
Date :  09 Aug 10  (Deposition) - 13 Oct 10  (Release) - 12 Jan 11  (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
    Mutation: YES
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
    Synonym: DRA2 TRANSPOSASE
 
Molecule 2 - DRA2 TRANSPOSASE LEFT END RECOGNITION SEQUENCE
    Chains: B, E
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - 5'-D(*TP*TP*GP*AP*TP*G)-3'
    Chains: C, F
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: DRA2 TRANSPOSON INTERNAL SEQUENCE
    Synonym: DRA2 TRANSPOSASE LEFT END CLEAVAGE SITE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric/Biological Unit (3, 18)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CD9Ligand/IonCADMIUM ION
3MG8Ligand/IonMAGNESIUM ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:67 , HIS A:69 , DT C:5 , DG C:6 , GLN D:136 , HOH D:2106BINDING SITE FOR RESIDUE CD A1001
02AC2SOFTWAREPRO A:114 , DC B:31 , HOH B:2066 , HOH B:2069 , HOH B:2072 , HOH B:2073 , HOH B:2074 , HOH B:2075 , HOH B:2076 , HOH B:2077BINDING SITE FOR RESIDUE CD A1002
03AC3SOFTWAREASP A:41 , HOH A:2030 , HOH A:2032 , HOH A:2034 , HOH A:2035 , DC B:27 , HOH B:2054 , HOH B:2055 , HOH B:2056 , HOH B:2057BINDING SITE FOR RESIDUE CD A1004
04AC4SOFTWAREASP A:66 , HOH A:2017BINDING SITE FOR RESIDUE CD A1006
05AC5SOFTWAREPRO A:7 , GLU A:9 , GLU A:38 , GLU A:123BINDING SITE FOR RESIDUE CD A1007
06AC6SOFTWAREGLN A:136 , MET D:64 , HIS D:67 , HIS D:69 , DT F:5 , DG F:6 , HOH F:2010BINDING SITE FOR RESIDUE CD D1001
07AC7SOFTWAREPRO D:114 , DC E:31 , HOH E:2056 , HOH E:2057 , HOH E:2060 , HOH E:2061 , HOH E:2062 , HOH E:2063 , HOH E:2065 , HOH E:2066BINDING SITE FOR RESIDUE CD D1002
08AC8SOFTWAREHIS A:137 , ASP D:45 , ASP D:49 , HOH D:2038 , HOH D:2039 , HOH D:2045 , HOH D:2046BINDING SITE FOR RESIDUE CD D1004
09AC9SOFTWAREASP D:41 , HOH D:2028 , HOH D:2029 , HOH D:2032 , HOH D:2033 , DT E:26 , HOH E:2041 , HOH E:2042BINDING SITE FOR RESIDUE CD E1002
10BC1SOFTWAREPRO A:114 , DC B:31 , HOH B:2066 , HOH B:2069 , HOH B:2072 , HOH B:2073 , HOH B:2074 , HOH B:2075 , HOH B:2076 , HOH B:2077BINDING SITE FOR RESIDUE MG A1141
11BC2SOFTWAREASP A:41 , HOH A:2030 , HOH A:2032 , HOH A:2034 , HOH A:2035 , DC B:27 , HOH B:2054 , HOH B:2055 , HOH B:2056 , HOH B:2057BINDING SITE FOR RESIDUE MG A1142
12BC3SOFTWAREPRO A:7 , GLU A:9 , GLU A:38 , GLU A:123BINDING SITE FOR RESIDUE MG A1143
13BC4SOFTWAREHOH B:2006 , HOH B:2009 , HOH B:2026 , HOH B:2081 , HOH B:2082 , HOH B:2083BINDING SITE FOR RESIDUE MG B1001
14BC5SOFTWAREHIS A:137 , ASP D:45 , ASP D:49 , HOH D:2038 , HOH D:2039 , HOH D:2045 , HOH D:2046BINDING SITE FOR RESIDUE MG D1137
15BC6SOFTWARETRP D:107BINDING SITE FOR RESIDUE ACT D1138
16BC7SOFTWAREHOH E:2003 , HOH E:2022 , HOH E:2072 , HOH E:2074 , HOH E:2075 , HOH E:2078BINDING SITE FOR RESIDUE MG E1001
17BC8SOFTWAREPRO D:114 , DC E:31 , HOH E:2056 , HOH E:2057 , HOH E:2060 , HOH E:2061 , HOH E:2062 , HOH E:2063 , HOH E:2065 , HOH E:2066BINDING SITE FOR RESIDUE MG E1038
18BC9SOFTWAREASP D:41 , HOH D:2028 , HOH D:2029 , HOH D:2032 , HOH D:2033 , DT E:26 , HOH E:2041 , HOH E:2042BINDING SITE FOR RESIDUE MG E1039

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XO6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XO6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XO6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XO6)

(-) Exons   (0, 0)

(no "Exon" information available for 2XO6)

(-) 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:134
 aligned with O83028_DEIRD | O83028 from UniProtKB/TrEMBL  Length:140

    Alignment length:134
                                    16        26        36        46        56        66        76        86        96       106       116       126       136    
         O83028_DEIRD     7 PLEMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIESQHDKE 140
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeeeeeeeeee.hhhh...hhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xo6 A   7 PLEMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKFIESQHDKE 140
                                    16        26        36        46        56        66        76        86        96       106       116       126       136    


Chain B from PDB  Type:DNA  Length:27
                                                           
                 2xo6 B  11 CGCACACTCGTGACTTCAGTCATGAGT  37
                                    20        30       


Chain C from PDB  Type:DNA  Length:6
                                      
                 2xo6 C   1 TTGATG   6


Chain D from PDB  Type:PROTEIN  Length:128
 aligned with O83028_DEIRD | O83028 from UniProtKB/TrEMBL  Length:140

    Alignment length:128
                                    18        28        38        48        58        68        78        88        98       108       118       128        
         O83028_DEIRD     9 EMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIESQ 136
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeee.hhhh...hhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xo6 D   9 EMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKFIESQ 136
                                    18        28        38        48        58        68        78        88        98       108       118       128        


Chain E from PDB  Type:DNA  Length:27
                                                           
                 2xo6 E  11 CGCACACTCGTGACTTCAGTCATGAGT  37
                                    20        30       


Chain F from PDB  Type:DNA  Length:6
                                      
                 2xo6 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 2XO6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XO6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2XO6)

(-) 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 2xqc

(-) 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