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(-) Description

Title :  TN5 TRANSPOSASE: 20MER OUTSIDE END 2 MN COMPLEX
 
Authors :  V. A. Klenchin, S. Lovell, I. Y. Goryshin, W. R. Reznikoff, I. Rayment
Date :  06 Feb 12  (Deposition) - 22 Feb 12  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Transposase, Ribonuclease H-Like Motif, Protein-Dna Complex, Synaptic Complex, Dna Recombination-Dna Complex, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Lovell, I. Y. Goryshin, W. R. Reznikoff, I. Rayment
Two-Metal Active Site Binding Of A Tn5 Transposase Synaptic Complex
Nat. Struct. Biol. V. 9 278 2002
PubMed-ID: 11896402

(-) Compounds

Molecule 1 - TRANSPOSASE FOR TRANSPOSON TN5
    Chains: A
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTYB1
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TNPA, TNP
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: TNP
 
Molecule 2 - DNA TRANSFERRED STRAND
    Chains: B
    Engineered: YES
    Other Details: THE 21 BP SEQUENCE OCCURS NATURALLY IN THE TN5 TRANSPOSON
    Synthetic: YES
 
Molecule 3 - DNA NON-TRANSFERRED STRAND
    Chains: C
    Engineered: YES
    Other Details: THE 20 BP SEQUENCE OCCURS NATURALLY IN THE TN5 TRANSPOSON
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MN3Ligand/IonMANGANESE (II) ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:97 , GLU A:326 , MN A:502 , HOH A:601 , DA B:121BINDING SITE FOR RESIDUE MN A 501
2AC2SOFTWAREASP A:97 , ASP A:188 , MN A:501 , HOH A:602 , DA B:121 , HOH B:201 , HOH B:202BINDING SITE FOR RESIDUE MN A 502
3AC3SOFTWARESER A:178 , SER A:181 , HOH A:881BINDING SITE FOR RESIDUE MN A 503
4AC4SOFTWAREGLN A:37 , SER A:49 , SER A:50 , GLU A:51 , HOH A:848BINDING SITE FOR RESIDUE EDO A 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DM0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DM0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DM0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DM0)

(-) Exons   (0, 0)

(no "Exon" information available for 4DM0)

(-) 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:460
 aligned with TN5P_ECOLX | Q46731 from UniProtKB/Swiss-Prot  Length:476

    Alignment length:475
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   476 
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472   | 
           TN5P_ECOLX     3 TSALHRAADWAKSVFSSAALGDPRRTARLVNVAAQLAKYSGKSITISSEGSEAMQEGAYRFIRNPNVSAEAIRKAGAMQTVKLAQEFPELLAIEDTTSLSYRHQVAEELGKLGSIQDKSRGWWVHSVLLLEATTFRTVGLLHQEWWMRPDDPADADEKESGKWLAAAATSRLRMGSMMSNVIAVCDREADIHAYLQDKLAHNERFVVRSKHPRKDVESGLYLYDHLKNQPELGGYQISIPQKGVVDKRGKRKNRPARKASLSLRSGRITLKQGNITLNAVLAEEINPPKGETPLKWLLLTSEPVESLAQALRVIDIYTHRWRIEEFHKAWKTGAGAERQRMEEPDNLERMVSILSFVAVRLLQLRESFTLPQALRAQGLLKEAEHVESQSAETVLTPDECQLLGYLDKGKRKRKEKAGSLQWAYMAIARLGGFMDSKRTGIASWGALWEGWEALQSKLDGFLAAKDLMAQGIKI-   -
               SCOP domains d4dm0a_ A: Transposase inhibitor (Tn5 transposase)                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....eeeeeeeeeeee.hhhhhhhee........eeeeeeeeeeee.....eeeeeeeeee....hhhhh..hhhhhhhhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhh..eeeee............hhhhhhhhh...eeeeeee..eeee.....eeee..eeeeeeeeeeeeeehhhheeeeeeeeeee.........eeeeee.....hhhhhhhhhhhhhh.hhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh...---------------....hhhhh.hhhhhhhhhhhhh..........hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dm0 A   3 TSALHRAADWAKSVFSSAALGDPRRTARLVNVAAQLAKYSGKSITISSEGSKAAQEGAYRFIRNPNVSAEAIRKAGAMQTVKLAQEFPELLAIEDTTSLSYRHQVAEELGKLGSIQDKSRGWWVHSVLLLEATTFRTVGLLHQEWWMRPDDPADADEKESGKWLAAAATSRLRMGSMMSNVIAVCDREADIHAYLQDKLAHNERFVVRSKHPRKDVESGLYLYDHLKNQPELGGYQISIPQKGVVDKRGKRKNRPARKASLSLRSGRITLKQGNITLNAVLAEEINPPKGETPLKWLLLTSEPVESLAQALRVIDIYTHRWRIEEFHKAWKTGAGAERQRMEKPDNLERMVSILSFVAVRLLQLRESFTP---------------VESQSAETVLTPDECQLLGYLDKGKRKRKEKAGSLQWAYMAIARLGGFMDSKRTGIASWGALWEGWEALQSKLDGFLAAKDLMAQGIKIG 477
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372         -     | 392       402       412       422       432       442       452       462       472     
                                                                                                                                                                                                                                                                                                                                                                                                           372             388                                                                                         


Chain B from PDB  Type:DNA  Length:21
                                                     
                 4dm0 B 101 GACTTGTGTATAAGAGTCAGA 121
                                   110       120 


Chain C from PDB  Type:DNA  Length:20
                                                    
                 4dm0 C 201 CTGACTCTTATACACAAGTC 220
                                   210       220
   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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0 ; only for superseded entry 1MUR: 3,3)

(no "CATH Domain" information available for 4DM0, only for superseded entry 1MUR replaced by 4DM0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DM0)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (TN5P_ECOLX | Q46731)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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. Interchromosomal 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TN5P_ECOLX | Q46731: 1b7e 1mm8 1muh 1mus 3ecp

(-) Related Entries Specified in the PDB File

1muh 1mus