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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TNSA/TNSC(504-555) COMPLEX
 
Authors :  D. R. Ronning, Y. Li, Z. N. Perez, P. D. Ross, A. B. Hickman, N. L. Craig, F.
Date :  08 Apr 04  (Deposition) - 09 Nov 04  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Protein-Protein Complex, Mixed Alpha-Beta, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. R. Ronning, Y. Li, Z. N. Perez, P. D. Ross, A. B. Hickman, N. L. Craig, F. Dyda
The Carboxy-Terminal Portion Of Tnsc Activates The Tn7 Transposase Through A Specific Interaction With Tnsa.
Embo J. V. 23 2972 2004
PubMed-ID: 15257292  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600311
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSPOSON TN7 TRANSPOSITION PROTEIN TNSA
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET30
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneTNSA
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
 
Molecule 2 - TRANSPOSON TN7 TRANSPOSITION PROTEIN TNSC
    ChainsC, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET32
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 504-555
    GeneTNSC
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymPROTEIN E

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D
Biological Unit 3 (1x)ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2MLA3Ligand/IonMALONIC ACID
3MPD5Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MLA1Ligand/IonMALONIC ACID
3MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MLA2Ligand/IonMALONIC ACID
3MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 3 (2, 8)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MLA3Ligand/IonMALONIC ACID
3MPD5Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP B:114 , GLN B:130 , VAL B:131 , HOH B:2030 , HOH B:2178 , HOH B:2223BINDING SITE FOR RESIDUE MG B 1009
02AC2SOFTWAREASP A:114 , GLN A:130 , VAL A:131 , HOH A:2120 , HOH A:2211 , HOH A:2216BINDING SITE FOR RESIDUE MG A 1010
03AC3SOFTWAREPRO A:102 , VAL A:103 , ILE A:104 , ARG A:141 , LYS A:145 , HOH A:2269 , HOH A:2344 , ARG B:105BINDING SITE FOR RESIDUE MLA A 1001
04AC4SOFTWAREVAL A:182 , HOH A:2318 , GLN B:138 , TYR D:525 , ARG D:528 , HOH D:2153BINDING SITE FOR RESIDUE MLA D 1002
05AC5SOFTWAREARG A:105 , PRO B:102 , VAL B:103 , ILE B:104 , ARG B:141 , LYS B:145 , HOH B:2019 , HOH B:2061BINDING SITE FOR RESIDUE MLA B 1003
06AC6SOFTWAREASP A:61 , ILE A:168 , LYS A:173 , GLU A:177BINDING SITE FOR RESIDUE MPD A 1004
07AC7SOFTWAREARG B:21 , GLY B:22 , GLN B:23 , PRO B:84 , LEU B:86 , PRO B:87 , VAL B:110BINDING SITE FOR RESIDUE MPD B 1005
08AC8SOFTWAREGLN A:194 , PRO A:197 , TYR A:221 , HOH A:2111 , HOH A:2288BINDING SITE FOR RESIDUE MPD A 1006
09AC9SOFTWAREGLN B:194BINDING SITE FOR RESIDUE MPD B 1007
10BC1SOFTWAREARG A:21 , GLN A:23 , PRO A:84 , LEU A:86 , PRO A:87BINDING SITE FOR RESIDUE MPD A 1008

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T0F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1T0F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T0F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T0F)

(-) Exons   (0, 0)

(no "Exon" information available for 1T0F)

(-) 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:264
 aligned with TNSA_ECOLX | P13988 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:264
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264    
           TNSA_ECOLX     5 NSSFSEVQIARRIKEGRGQGHGKDYIPWLTVQEVPSSGRSHRIYSHKTGRVHHLLSDLELAVFLSLEWESSVLDIREQFPLLPSDTRQIAIDSGIKHPVIRGVDQVMSTDFLVDCKDGPFEQFAIQVKPAAALQDERTLEKLELERRYWQQKQIPWFIFTDKEINPVVKENIEWLYSVKTEEVSAELLAQLSPLAHILQEKGDENIINVCKQVDIAYDLELGKTLSEIRALTANGFIKFNIYKSFRANKCADLCISQVVNMEEL 268
               SCOP domains --d1t0fa2 A:7-168 TnsA endonuclease, N-terminal domain                                                                                                              d1t0fa1 A:169-268 TnsA endonuclease, C-terminal domain                                               SCOP domains
               CATH domains --1t0fA01 A:7-168  [code=3.40.1350.10, no name defined]                                                                                                             1t0fA02 A:169-267 'winged helix' repressor DNA binding domain                                      - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhh.....hhhhh....hhhhh......eeee......eeee.hhhhhhhhhhhhhh..eeeeeeeee.hhhhhhhhhhhhh....ee..ee...eeeeeeee......eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhh..ee.....hhhhhhhhhhee..eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1t0f A   5 NSSFSEVQIARRIKEGRGQGHGKDYIPWLTVQEVPSSGRSHRIYSHKTGRVHHLLSDLELAVFLSLEWESSVLDIREQFPLLPSDTRQIAIDSGIKHPVIRGVDQVMSTDFLVDCKDGPFEQFAIQVKPAAALQDERTLEKLELERRYWQQKQIPWFIFTDKEINPVVKENIEWLYSVKTEEVSAELLAQLSPLAHILQEKGDENIINVCKQVDIAYDLELGKTLSEIRALTANGFIKFNIYKSFRANKCADLCISQVVNMEEL 268
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264    

Chain B from PDB  Type:PROTEIN  Length:262
 aligned with TNSA_ECOLX | P13988 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:262
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266  
           TNSA_ECOLX     7 SFSEVQIARRIKEGRGQGHGKDYIPWLTVQEVPSSGRSHRIYSHKTGRVHHLLSDLELAVFLSLEWESSVLDIREQFPLLPSDTRQIAIDSGIKHPVIRGVDQVMSTDFLVDCKDGPFEQFAIQVKPAAALQDERTLEKLELERRYWQQKQIPWFIFTDKEINPVVKENIEWLYSVKTEEVSAELLAQLSPLAHILQEKGDENIINVCKQVDIAYDLELGKTLSEIRALTANGFIKFNIYKSFRANKCADLCISQVVNMEEL 268
               SCOP domains d1t0fb2 B:7-168 TnsA endonuclease, N-terminal domain                                                                                                              d1t0fb1 B:169-268 TnsA endonuclease, C-terminal domain                                               SCOP domains
               CATH domains 1t0fB01 B:7-168  [code=3.40.1350.10, no name defined]                                                                                                             1t0fB02 B:169-267 'winged helix' repressor DNA binding domain                                      - CATH domains
           Pfam domains (1) -------------------------------------------------------------------Tn7_Tnp_TnsA_N-1t0fB03 B:74-165                                                             -Tn7_Tnp_TnsA_C-1t0fB01 B:167-245                                               ----------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------Tn7_Tnp_TnsA_N-1t0fB04 B:74-165                                                             -Tn7_Tnp_TnsA_C-1t0fB02 B:167-245                                               ----------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhh.....hhhhh....hhhhh......eeee......eeee.hhhhhhhhhhhhhh..eeeeeeeee.hhhhhhhhhhhhh....ee..ee...eeeeeeee......eeeeee.hhhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhh..ee.....hhhhhhhhhhee.eeehhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t0f B   7 SFSEVQIARRIKEGRGQGHGKDYIPWLTVQEVPSSGRSHRIYSHKTGRVHHLLSDLELAVFLSLEWESSVLDIREQFPLLPSDTRQIAIDSGIKHPVIRGVDQVMSTDFLVDCKDGPFEQFAIQVKPAAALQDERTLEKLELERRYWQQKQIPWFIFTDKEINPVVKENIEWLYSVKTEEVSAELLAQLSPLAHILQEKGDENIINVCKQVDIAYDLELGKTLSEIRALTANGFIKFNIYKSFRANKCADLCISQVVNMEEL 268
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266  

Chain C from PDB  Type:PROTEIN  Length:49
 aligned with TNSC_ECOLX | P05846 from UniProtKB/Swiss-Prot  Length:555

    Alignment length:49
                                   514       524       534       544         
           TNSC_ECOLX   505 IKVVKPSDWDSLPDTDLRYIYSQRQPEKTMHERLKGKGVIVDMASLFKQ 553
               SCOP domains ------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh...hhhhhhhh.....hhhhhhhhh....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------- Transcript
                 1t0f C 505 IKVVKPSDWDSLPDTDLRYIYSQRQPEKTMHERLKGKGVIVDMASLFKQ 553
                                   514       524       534       544         

Chain D from PDB  Type:PROTEIN  Length:47
 aligned with TNSC_ECOLX | P05846 from UniProtKB/Swiss-Prot  Length:555

    Alignment length:47
                                   515       525       535       545       
           TNSC_ECOLX   506 KVVKPSDWDSLPDTDLRYIYSQRQPEKTMHERLKGKGVIVDMASLFK 552
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------- CATH domains
           Pfam domains (1) --Tn7_TnsC_Int-1t0fD01 D:508-552                Pfam domains (1)
           Pfam domains (2) --Tn7_TnsC_Int-1t0fD02 D:508-552                Pfam domains (2)
         Sec.struct. author ...hhhhhhhh...hhhhhhhh.....hhhhhhhhh....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                 1t0f D 506 KVVKPSDWDSLPDTDLRYIYSQRQPEKTMHERLKGKGVIVDMASLFK 552
                                   515       525       535       545       

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (3, 6)

Asymmetric Unit

(-) Gene Ontology  (11, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TNSA_ECOLX | P13988)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic 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:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0032196    transposition    Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites.
    GO:0006313    transposition, DNA-mediated    Any process involved in a type of transpositional recombination which occurs via a DNA intermediate.
cellular component
    GO:0000229    cytoplasmic chromosome    A chromosome found in the cytoplasm.

Chain C,D   (TNSC_ECOLX | P05846)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0032196    transposition    Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TNSA_ECOLX | P139881f1z

(-) Related Entries Specified in the PDB File

1f1z TNSA, A CATALYTIC COMPONENT OF THE TN7 TRANSPOSITION SYSTEM