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(-) Description

Title :  DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE RIGHT END DNA COMPLEX
 
Authors :  A. B. Hickman, J. A. James, O. Barabas, C. Pasternak, B. Ton-Hoang, M. Ch S. Sommer, F. Dyda
Date :  26 Jul 10  (Deposition) - 13 Oct 10  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
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, B, E, F
    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 RIGHT END RECOGNITION SITE
    Chains: C, D, G, H
    Engineered: YES
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
    Other Details: ISDRA2 TRANSPOSON SEQUENCE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:114 , HOH A:2038 , DC C:31 , HOH C:2022 , HOH C:2026 , HOH C:2027BINDING SITE FOR RESIDUE MG C 1045
2AC2SOFTWAREHOH A:2004 , PRO B:114 , DC D:31 , HOH D:2014 , HOH D:2016 , HOH D:2018BINDING SITE FOR RESIDUE MG D 1045
3AC3SOFTWAREPRO E:114 , HOH E:2021 , DC G:31 , HOH G:2006 , HOH G:2009 , HOH G:2010BINDING SITE FOR RESIDUE MG E 1139
4AC4SOFTWAREPRO F:114 , DC H:31 , HOH H:2006 , HOH H:2007 , HOH H:2008 , HOH H:2009BINDING SITE FOR RESIDUE MG H 1045

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XMA)

(-) 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:139
 aligned with O83028_DEIRD | O83028 from UniProtKB/TrEMBL  Length:140

    Alignment length:139
                               1                                                                                                                                       
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127         
         O83028_DEIRD     - ---MTYVILPLEMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIESQ 136
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee...eeeeeeeeeeee.hhhh...hhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xma A  -2 GSHMTYVILPLEMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIESQ 136
                                     7        17        27        37        47        57        67        77        87        97       107       117       127         


Chain B from PDB  Type:PROTEIN  Length:135
 aligned with O83028_DEIRD | O83028 from UniProtKB/TrEMBL  Length:140

    Alignment length:135
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     
         O83028_DEIRD     2 TYVILPLEMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIESQ 136
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeeeeeee.hhhh...hhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xma B   2 TYVILPLEMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIESQ 136
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     


Chain C from PDB  Type:DNA  Length:34
                                                                  
                 2xma C  11 GAGAATCACGCGACTTTAGTCGTGTGAGGTTCAA  44
                                    20        30        40    


Chain D from PDB  Type:DNA  Length:34
                                                                  
                 2xma D  11 GAGAATCACGCGACTTTAGTCGTGTGAGGTTCAA  44
                                    20        30        40    


Chain E from PDB  Type:PROTEIN  Length:141
 aligned with O83028_DEIRD | O83028 from UniProtKB/TrEMBL  Length:140

    Alignment length:141
                               1                                                                                                                                         
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137 
         O83028_DEIRD     - ---MTYVILPLEMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIESQHD 138
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............................hhhh....hhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xma E  -2 GSHMTYVILPLEMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIESQHD 138
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137 


Chain F from PDB  Type:PROTEIN  Length:139
 aligned with O83028_DEIRD | O83028 from UniProtKB/TrEMBL  Length:140

    Alignment length:139
                               1                                                                                                                                       
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127         
         O83028_DEIRD     - ---MTYVILPLEMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIESQ 136
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee..eeeeeeeeeeeee.hhh...hhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xma F  -2 GSHMTYVILPLEMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIESQ 136
                                     7        17        27        37        47        57        67        77        87        97       107       117       127         


Chain G from PDB  Type:DNA  Length:34
                                                                  
                 2xma G  11 GAGAATCACGCGACTTTAGTCGTGTGAGGTTCAA  44
                                    20        30        40    


Chain H from PDB  Type:DNA  Length:33
                                                                 
                 2xma H  12 AGAATCACGCGACTTTAGTCGTGTGAGGTTCAA  44
                                    21        31        41
   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 2XMA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,E,F   (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 2xo6 2xqc

(-) Related Entries Specified in the PDB File

2xm3 DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE LEFT END DNA COMPLEX