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(-) Description

Title :  CRYSTAL STRUCTURE OF THE IS608 TRANSPOSASE IN COMPLEX WITH LEFT END 26-MER DNA HAIRPIN AND A 6-MER DNA REPRESENTING THE LEFT END CLEAVAGE SITE
 
Authors :  O. Barabas, D. R. Ronning, C. Guynet, A. B. Hickman, B. Ton-Hoang, M. Chandler, F. Dyda
Date :  13 Dec 07  (Deposition) - 19 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Dna-Binding Protein, Protein-Dna Complex, Huh Motif, Dna Stem Loop, Transposition (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Barabas, D. R. Ronning, C. Guynet, A. B. Hickman, B. Ton-Hoang, M. Chandler, F. Dyda
Mechanism Of Is200/Is605 Family Dna Transposases: Activation And Transposon-Directed Target Site Selection.
Cell(Cambridge, Mass. ) V. 132 208 2008
PubMed-ID: 18243097  |  Reference-DOI: 10.1016/J.CELL.2007.12.029

(-) Compounds

Molecule 1 - TRANSPOSASE ORFA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET32B
    Fragment: RESIDUES 2-155
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
    Strain: PECAN2A
    Synonym: IS608 TRANSPOSASE
 
Molecule 2 - 5'-D(*DA*DA*DA*DG*DC*DC*DC*DC*DT*DA*DG*DC*DTP*DT *DT*DT*DA*DG*DC*DT*DA*DT*DG*DG*DG*DGP)-3'
    Chains: C, D
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
    Strain: PECAN2A
    Synonym: LEFT END 26-MER HAIRPIN
    Synthetic: YES
 
Molecule 3 - 5'-D(*DT*DA*DT*DT*DA*DCP)-3'
    Chains: E, F
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
    Strain: PECAN2A
    Synonym: 6-MER 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  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:2009 , DG C:39 , HOH C:2044 , HOH C:2045 , HOH C:2047 , HOH C:2050BINDING SITE FOR RESIDUE MG C1042
2AC2SOFTWAREDG D:39 , HOH D:2012 , HOH D:2045 , HOH D:2049 , HOH D:2052 , HOH D:2056BINDING SITE FOR RESIDUE MG D1042
3AC3SOFTWAREHOH E:2013 , HOH E:2014 , HOH E:2015 , HOH E:2018 , HOH F:2007 , HOH F:2008BINDING SITE FOR RESIDUE MG E1042

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VJV)

(-) 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:125
 aligned with Q933Z0_HELPX | Q933Z0 from UniProtKB/TrEMBL  Length:155

    Alignment length:125
                                    15        25        35        45        55        65        75        85        95       105       115       125     
         Q933Z0_HELPX     6 LYKSNHNVVYSCKYHIVWCPKYRRKVLVGAVEMRLKEIIQEVAKELRVEIIEMQTDKDHIHILADIDPSFGVMKFIKTAKGRSSRILRQEFNHLKTKLPTLWTNSCFISTVGGAPLNVVKQYIEN 130
               SCOP domains d2vjva1 A:6-130 ISHP608 transposase                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...eeee.eeeeee..hhhh...hhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vjv A   6 LYKSNHNVVYSCKYHIVWCPKYRRKVLVGAVEMRLKEIIQEVAKELRVEIIEMQTDKDHIHILADIDPSFGVMKFIKTAKGRSSRILRQEFNHLKTKLPTLWTNSCFISTVGGAPLNVVKQYIEN 130
                                    15        25        35        45        55        65        75        85        95       105       115       125     


Chain B from PDB  Type:PROTEIN  Length:125
 aligned with Q933Z0_HELPX | Q933Z0 from UniProtKB/TrEMBL  Length:155

    Alignment length:125
                                    15        25        35        45        55        65        75        85        95       105       115       125     
         Q933Z0_HELPX     6 LYKSNHNVVYSCKYHIVWCPKYRRKVLVGAVEMRLKEIIQEVAKELRVEIIEMQTDKDHIHILADIDPSFGVMKFIKTAKGRSSRILRQEFNHLKTKLPTLWTNSCFISTVGGAPLNVVKQYIEN 130
               SCOP domains d2vjvb1 B:6-130 ISHP608 transposase                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...eeee.eeeeee..hhhh...hhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vjv B   6 LYKSNHNVVYSCKYHIVWCPKYRRKVLVGAVEMRLKEIIQEVAKELRVEIIEMQTDKDHIHILADIDPSFGVMKFIKTAKGRSSRILRQEFNHLKTKLPTLWTNSCFISTVGGAPLNVVKQYIEN 130
                                    15        25        35        45        55        65        75        85        95       105       115       125     


Chain C from PDB  Type:DNA  Length:26
                                                          
                 2vjv C  16 AAAGCCCCTAGCTTTTAGCTATGGGG  41
                                    25        35      


Chain D from PDB  Type:DNA  Length:26
                                                          
                 2vjv D  16 AAAGCCCCTAGCTTTTAGCTATGGGG  41
                                    25        35      


Chain E from PDB  Type:DNA  Length:6
                                      
                 2vjv E  -6 TATTAC  -1


Chain F from PDB  Type:DNA  Length:6
                                      
                 2vjv F  -6 TATTAC  -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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q933Z0_HELPX | Q933Z0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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
        Q933Z0_HELPX | Q933Z0: 2a6m 2a6o 2vhg 2vic 2vih 2vju

(-) Related Entries Specified in the PDB File

2a6m CRYSTAL STRUCTURE OF THE ISHP608 TRANSPOSASE
2a6o CRYSTAL STRUCTURE OF THE ISHP608 TRANSPOSASE IN COMPLEXWITH STEM-LOOP DNA
2vhg CRYSTAL STRUCTURE OF THE ISHP608 TRANSPOSASE IN COMPLEX WITH RIGHT END 31-MER DNA
2vic CRYSTAL STRUCTURE OF THE ISHP608 TRANSPOSASE IN COMPLEX WITH LEFT 26-MER DNA AND MANGANESE
2vih CRYSTAL STRUCTURE OF THE IS608 TRANSPOSASE IN COMPLEX WITH LEFT END 26-MER DNA
2vju CRYSTAL STRUCTURE OF THE ISHP608 TRANSPOSASE IN COMPLEX WITH THE COMPLETE RIGHT END 35 -MER DNA AND MANGANESE