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(-) Description

Title :  CRYSTAL STRUCTURE OF TN5 TRANSPOSASE COMPLEXED WITH ME DNA
 
Authors :  M. Steiniger-White, A. Bhasin, S. Lovell, I. Rayment, W. S. Reznikoff
Date :  03 Sep 02  (Deposition) - 13 Dec 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Protein-Dna Complex, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Steiniger-White, A. Bhasin, S. Lovell, I. Rayment, W. S. Reznikoff
Evidence For "Unseen" Transposase--Dna Contacts
J. Mol. Biol. V. 322 971 2002
PubMed-ID: 12367522  |  Reference-DOI: 10.1016/S0022-2836(02)00877-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ME DNA TRANSFERRED STRAND
    Chains: B
    Engineered: YES
    Other Details: DNA SYNTHESIZED BY IDT
    Synthetic: YES
 
Molecule 2 - ME DNA NON-TRANSFERRED STRAND
    Chains: C
    Engineered: YES
    Other Details: DNA SYNTHESIZED BY IDT
    Synthetic: YES
 
Molecule 3 - TN5 TRANSPOSASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTYB4
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TN5 TRANSPOSASES
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:97 , THR A:98 , GLU A:326 , HOH A:714 , DG B:120BINDING SITE FOR RESIDUE MN A 500
2AC2SOFTWAREASP A:97 , ASP A:188 , HOH A:692 , HOH A:714BINDING SITE FOR RESIDUE MN A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1MM8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MM8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MM8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MM8)

(-) Exons   (0, 0)

(no "Exon" information available for 1MM8)

(-) 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:455
 aligned with TN5P_ECOLX | Q46731 from UniProtKB/Swiss-Prot  Length:476

    Alignment length:473
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 476 
                                    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       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474 | 
           TN5P_ECOLX     5 ALHRAADWAKSVFSSAALGDPRRTARLVNVAAQLAKYSGKSITISSEGSEAMQEGAYRFIRNPNVSAEAIRKAGAMQTVKLAQEFPELLAIEDTTSLSYRHQVAEELGKLGSIQDKSRGWWVHSVLLLEATTFRTVGLLHQEWWMRPDDPADADEKESGKWLAAAATSRLRMGSMMSNVIAVCDREADIHAYLQDKLAHNERFVVRSKHPRKDVESGLYLYDHLKNQPELGGYQISIPQKGVVDKRGKRKNRPARKASLSLRSGRITLKQGNITLNAVLAEEINPPKGETPLKWLLLTSEPVESLAQALRVIDIYTHRWRIEEFHKAWKTGAGAERQRMEEPDNLERMVSILSFVAVRLLQLRESFTLPQALRAQGLLKEAEHVESQSAETVLTPDECQLLGYLDKGKRKRKEKAGSLQWAYMAIARLGGFMDSKRTGIASWGALWEGWEALQSKLDGFLAAKDLMAQGIKI-   -
               SCOP domains d1mm8a_ A: Transposase inhibitor (Tn5 transposase)                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1mm8A01 A:5-69 Tn5 transposase; domain 1                         1mm8A02 A:70-345 Transposase Inhibitor Protein From Tn5; Chain A, domain 1                                                                                                                                                                                                          1mm8A03 A:346-471 Transfera                  se Inhibitor Protein From Tn5; Chain                                             ------ CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------DDE_Tnp_1-1mm8A01 A:124-363                                                                                                                                                                                                                     ----Dimer                  _Tnp_Tn5-1mm8A02 A:368-476                                                            - Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeeeeeeeeee.hhhhhhhee........eeeeeeeeeeee.....eeeeeeeeee....hhhhh..hhhhhhhhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhh..eeeee............hhhhhhh.....eeeeeee..eee.......eee..eeeeeeeeeeeee.hhhh.eeeeeeeeee.........eeeeee.....hhhhhhhhhhhhhh.hhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..------------------.hhhhh.hhhhhhhhhhhh.............hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mm8 A   5 ALHRAADWAKSVFSSAALGDPRRTARLVNVAAQLAKYSGKSITISSEGSKAAQEGAYRFIRNPNVSAEAIRKAGAMQTVKLAQEFPELLAIEDTTSLSYRHQVAEELGKLGSIQDKSRGWWVHSVLLLEATTFRTVGLLHQEWWMRPDDPADADEKESGKWLAAAATSRLRMGSMMSNVIAVCDREADIHAYLQDKLAHNERFVVRSKHPRKDVESGLYLYDHLKNQPELGGYQISIPQKGVVDKRGKRKNRPARKASLSLRSGRITLKQGNITLNAVLAEEINPPKGETPLKWLLLTSEPVESLAQALRVIDIYTHRWRIEEFHKAWKTGAGAERQRMEKPDNLERMVSILSFVAVRLLQLRESFTP------------------QSAETVLTPDECQLLGYLDKGKRKRKEKAGSLQWAYMAIARLGGFMDSKRTGIASWGALWEGWEALQSKLDGFLAAKDLMAQGIKIG 477
                                    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       274       284       294       304       314       324       334       344       354       364       | -         -      |394       404       414       424       434       444       454       464       474   
                                                                                                                                                                                                                                                                                                                                                                                                         372                391                                                                                      


Chain B from PDB  Type:DNA  Length:20
                                                    
                 1mm8 B 101 GAGATGTGTATAAGAGACAG 120
                                   110       120


Chain C from PDB  Type:DNA  Length:20
                                                    
                 1mm8 C 201 CTGTCTCTTATACACATCTC 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  (3, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: RNase_H (288)
(-)
Clan: no clan defined [family: Dimer_Tnp_Tn5] (2)

(-) 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 1muh 1mus 3ecp 4dm0

(-) Related Entries Specified in the PDB File

1f3i CRYSTAL STRUCTURE OF TN5 TRANSPOSASE COMPLEXED WITH TRANSPOSON END DNA
1l1a TN5 TRANSPOSASE: 20MER OUTSIDE END 2 MN COMPLEX