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(-) Description

Title :  DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE LEFT END DNA COMPLEX
 
Authors :  A. B. Hickman, J. A. James, O. Barabas, C. Pasternak, B. Ton-Hoang, M. Ch S. Sommer, F. Dyda
Date :  22 Jul 10  (Deposition) - 13 Oct 10  (Release) - 12 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R
Biol. Unit 1:  C,D,K,L,M,N  (1x)
Biol. Unit 2:  A,B,G,H,I,J  (1x)
Biol. Unit 3:  E,F,O,P,Q,R  (1x)
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, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
    Other Details: ISDRA2 INSERTION SEQUENCE
    Synonym: DRA2 TRANSPOSASE
 
Molecule 2 - DRA2 TRANSPOSASE BINDING ELEMENT
    Chains: G, I, K, M, O, Q
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - 5'-D(*TP*TP*AP*GP*T)-3'
    Chains: H, J, L, N, P, R
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: ISDRA2 INSERTION SEQUENCE LEFT END FLANK
    Synonym: DRA2 TRANSPOSASE LEFT END CLEAVAGE SITE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112131415161718
Asymmetric Unit : ABCDEFGHIJKLMNOPQR
Biological Unit 1 (1x):   CD      KLMN    
Biological Unit 2 (1x): AB    GHIJ        
Biological Unit 3 (1x):     EF        OPQR

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL4Ligand/IonGLYCEROL
3MG12Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU B:62 , VAL B:63BINDING SITE FOR RESIDUE ACT B1135
02AC2SOFTWAREPRO E:114 , HOH E:2034 , DC O:31 , HOH O:2017 , HOH O:2019 , HOH O:2020BINDING SITE FOR RESIDUE MG E1135
03AC3SOFTWAREPRO F:114 , HOH F:2023 , DC Q:31 , HOH Q:2018 , HOH Q:2019 , HOH Q:2020BINDING SITE FOR RESIDUE MG F1135
04AC4SOFTWARECYS A:27 , CYS A:117 , HOH A:2013 , DC G:15 , DA G:16 , HOH G:2035 , DT H:5BINDING SITE FOR RESIDUE GOL G1038
05AC5SOFTWAREPRO A:114 , HOH B:2003 , DC G:31 , HOH G:2024 , HOH G:2026 , HOH G:2028BINDING SITE FOR RESIDUE MG G1039
06AC6SOFTWAREHOH G:2012 , HOH G:2013 , HOH G:2030 , HOH G:2032 , HOH G:2033 , HOH G:2034BINDING SITE FOR RESIDUE MG G1114
07AC7SOFTWAREPRO B:114 , HOH B:2045 , DC I:31 , HOH I:2026 , HOH I:2029 , HOH I:2031BINDING SITE FOR RESIDUE MG I1038
08AC8SOFTWAREHOH I:2010 , HOH I:2013 , HOH I:2035 , HOH I:2037 , HOH I:2038 , HOH I:2040BINDING SITE FOR RESIDUE MG I1116
09AC9SOFTWARECYS B:27 , CYS B:117 , DC I:15 , DA I:16 , DT J:5 , HOH J:2007 , HOH J:2008BINDING SITE FOR RESIDUE GOL J1006
10BC1SOFTWAREPRO C:114 , HOH C:2049 , DC K:31 , HOH K:2030 , HOH K:2033 , HOH K:2035BINDING SITE FOR RESIDUE MG K1038
11BC2SOFTWAREHOH K:2003 , HOH K:2004 , HOH K:2039 , HOH K:2040 , HOH K:2043 , HOH K:2045BINDING SITE FOR RESIDUE MG K1039
12BC3SOFTWARECYS C:27 , CYS C:117 , HOH C:2005 , DC K:15 , DA K:16 , DT L:5 , HOH L:2004BINDING SITE FOR RESIDUE GOL L1006
13BC4SOFTWAREPRO D:114 , HOH D:2040 , DC M:31 , HOH M:2018 , HOH M:2019 , HOH M:2023BINDING SITE FOR RESIDUE MG M1038
14BC5SOFTWAREHOH M:2008 , HOH M:2010 , HOH M:2026 , HOH M:2027 , HOH M:2028 , HOH M:2029BINDING SITE FOR RESIDUE MG M1121
15BC6SOFTWAREHOH O:2003 , HOH O:2009 , HOH O:2010 , HOH O:2021 , HOH O:2022 , HOH O:2023BINDING SITE FOR RESIDUE MG O1112
16BC7SOFTWARECYS E:27 , CYS E:117 , HOH E:2011 , TYR F:132 , DC O:15 , DA O:16 , DT P:5BINDING SITE FOR RESIDUE GOL P1007
17BC8SOFTWAREHOH Q:2003 , HOH Q:2004 , HOH Q:2015 , HOH Q:2021 , HOH Q:2023 , HOH Q:2024BINDING SITE FOR RESIDUE MG Q1111

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XM3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XM3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XM3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XM3)

(-) Exons   (0, 0)

(no "Exon" information available for 2XM3)

(-) Sequences/Alignments

Asymmetric 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:126
 aligned with O83028_DEIRD | O83028 from UniProtKB/TrEMBL  Length:140

    Alignment length:126
                                    18        28        38        48        58        68        78        88        98       108       118       128      
         O83028_DEIRD     9 EMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIE 134
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee..eeeeeeeeeeee.hhhh...hhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xm3 A   9 EMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIE 134
                                    18        28        38        48        58        68        78        88        98       108       118       128      


Chain B from PDB  Type:PROTEIN  Length:129
 aligned with O83028_DEIRD | O83028 from UniProtKB/TrEMBL  Length:140

    Alignment length:129
                                    15        25        35        45        55        65        75        85        95       105       115       125         
         O83028_DEIRD     6 LPLEMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIE 134
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eeee.eeeeeee.hhhh...hhhhhhhhhhhhhhhhhhh..eeeeeee...eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xm3 B   6 LPLEMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIE 134
                                    15        25        35        45        55        65        75        85        95       105       115       125         


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

    Alignment length:128
                                    16        26        36        46        56        66        76        86        96       106       116       126        
         O83028_DEIRD     7 PLEMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIE 134
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...eeeeeeeeeeee.hhhh....hhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xm3 C   7 PLEMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIE 134
                                    16        26        36        46        56        66        76        86        96       106       116       126        


Chain D 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..eeee.eeeeeee.hhhh...hhhhhhhhhhhhhhhhhhhh.eeeeeee...eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xm3 D   9 EMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIESQH 137
                                    18        28        38        48        58        68        78        88        98       108       118       128         


Chain E from PDB  Type:PROTEIN  Length:126
 aligned with O83028_DEIRD | O83028 from UniProtKB/TrEMBL  Length:140

    Alignment length:126
                                    18        28        38        48        58        68        78        88        98       108       118       128      
         O83028_DEIRD     9 EMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIE 134
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee..eeee.eeeeeee.hhhh....hhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xm3 E   9 EMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIE 134
                                    18        28        38        48        58        68        78        88        98       108       118       128      


Chain F from PDB  Type:PROTEIN  Length:126
 aligned with O83028_DEIRD | O83028 from UniProtKB/TrEMBL  Length:140

    Alignment length:126
                                    18        28        38        48        58        68        78        88        98       108       118       128      
         O83028_DEIRD     9 EMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIE 134
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee..eeee.eeeeeee.hhhh...hhhhhhhhhhhhhhhhhhh..eeeeeee...eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xm3 F   9 EMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIE 134
                                    18        28        38        48        58        68        78        88        98       108       118       128      


Chain G from PDB  Type:DNA  Length:27
                                                           
                 2xm3 G  11 CGCACACTCGTGACTTCAGTCATGAGT  37
                                    20        30       


Chain H from PDB  Type:DNA  Length:5
                                     
                 2xm3 H   1 TTGAT   5


Chain I from PDB  Type:DNA  Length:27
                                                           
                 2xm3 I  11 CGCACACTCGTGACTTCAGTCATGAGT  37
                                    20        30       


Chain J from PDB  Type:DNA  Length:5
                                     
                 2xm3 J   1 TTGAT   5


Chain K from PDB  Type:DNA  Length:27
                                                           
                 2xm3 K  11 CGCACACTCGTGACTTCAGTCATGAGT  37
                                    20        30       


Chain L from PDB  Type:DNA  Length:5
                                     
                 2xm3 L   1 TTGAT   5


Chain M from PDB  Type:DNA  Length:27
                                                           
                 2xm3 M  11 CGCACACTCGTGACTTCAGTCATGAGT  37
                                    20        30       


Chain N from PDB  Type:DNA  Length:5
                                     
                 2xm3 N   1 TTGAT   5


Chain O from PDB  Type:DNA  Length:27
                                                           
                 2xm3 O  11 CGCACACTCGTGACTTCAGTCATGAGT  37
                                    20        30       


Chain P from PDB  Type:DNA  Length:5
                                     
                 2xm3 P   1 TTGAT   5


Chain Q from PDB  Type:DNA  Length:27
                                                           
                 2xm3 Q  11 CGCACACTCGTGACTTCAGTCATGAGT  37
                                    20        30       


Chain R from PDB  Type:DNA  Length:5
                                     
                 2xm3 R   1 TTGAT   5
   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 2XM3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XM3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2XM3)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,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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  2xm3
    Family and Domain Information: ProDom | SYSTERS
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  O83028_DEIRD | O83028
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2XM3)