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(-) Description

Title :  STRUCTURE OF VARIOLA TOPOISOMERASE COVALENTLY BOUND TO DNA
 
Authors :  K. Perry, Y. Hwang, F. D. Bushman, G. D. Van Duyne
Date :  02 Jun 06  (Deposition) - 15 Aug 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  X,Y,Z
Keywords :  Type Ib Topoisomerase, Dna Binding, Protein-Dna Complex, Isomerase, Isomerase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Perry, Y. Hwang, F. D. Bushman, G. D. Van Duyne
Structural Basis For Specificity In The Poxvirus Topoisomerase.
Mol. Cell V. 23 343 2006
PubMed-ID: 16885024  |  Reference-DOI: 10.1016/J.MOLCEL.2006.06.015

(-) Compounds

Molecule 1 - 5'-D(*TP*TP*GP*TP*CP*GP*CP*CP*CP*TP*T)-3'
    Chains: Y
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*TP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP*A)-3'
    Chains: Z
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA TOPOISOMERASE 1
    Chains: X
    EC Number: 5.99.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TOP1
    Mutation: YES
    Organism Scientific: VARIOLA VIRUS
    Organism Taxid: 10255
    Synonym: DNA TOPOISOMERASE I

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : XYZ

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (0, 0)

(no "Site" information available for 2H7F)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2H7F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2H7F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H7F)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TOPOISOMERASE_I_EUKPS00176 Eukaryotic DNA topoisomerase I active site.TOP1_VAR67261-279  1X:261-279

(-) Exons   (0, 0)

(no "Exon" information available for 2H7F)

(-) 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 X from PDB  Type:PROTEIN  Length:314
 aligned with TOP1_VAR67 | P32989 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:314
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310    
           TOP1_VAR67     1 MRALFYKDGKLFTDNNFLNPVSDNNPAYEVLQHVKIPTHLTDVVVYGQTWEEALTRLIFVGSDSKGRRQYFYGKMHVQNRNAKRDRIFVRVYNVMKRINCFINKNIKKSSTDSNYQLAVFMLMETMFFIRFGKMKYLKENETVGLLTLKNKHIEISPDKIVIKFVGKDKVSHEFVVHKSNRLYKPLLKLTDDSSPEEFLFNKLSERKVYECIKQFGIRIKDLRTYGVNYTFLYNFWTNVKSISPLPSPKKLIALTIKQTAEVVGHTPSISKRAYMATTILEMVKDKNFLDVVSKTTFDEFLSIVVDHVKSSTDG 314
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.............hhhhhhhhh......eeeeee..hhhhhh..eeeeee.....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhhhh.......hhh.eee...eeeeeee.hhh.eeeeeee....hhhhhhhhh.............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TOPOISOMERASE_I_EUK----------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h7f X   1 MRALFYKDGKLFTDNNFLNPVSDNNPAYEVLQHVKIPTHLTDVVVYGQTWEEALTRLIFVGSDSKGRRQYFYGKMHVQNRNAKRDRIFVRVYNVMKRINSFINKNIKKSSTDSNYQLAVFMLMETMFFIRFGKMKYLKENETVGLLTLKNKHIEISPDKIVIKFVGKDKVSHEFVVHKSNRLYKPLLKLTDDSSPEEFLFNKLSERKVYESIKQFGIRIKDLRTYGVNYTFLYNFWTNVKSISPLPSPKKLIALTIKQTAEVVGHTPSISKRAyMATTILEMVKDKNFLDVVSKTTFDEFLSIVVDHVKSSTDG 314
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   |   280       290       300       310    
                                                                                                                                                                                                                                                                                                           274-PTR                                    


Chain Y from PDB  Type:DNA  Length:11
                                           
                 2h7f Y 501 TTGTCGCCCTT 511
                                   510 


Chain Z from PDB  Type:DNA  Length:14
                                              
                 2h7f Z 515 TAATAAGGGCGACA 528
                                   524
   Legend:   → Mismatch (orange background)
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    → 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 2H7F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2H7F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H7F)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (TOP1_VAR67 | P32989)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003916    DNA topoisomerase activity    Catalysis of the transient cleavage and passage of individual DNA strands or double helices through one another, resulting a topological transformation in double-stranded DNA.
    GO:0003917    DNA topoisomerase type I activity    Catalysis of a DNA topological transformation by transiently cleaving one DNA strand at a time to allow passage of another strand; changes the linking number by +1 per catalytic cycle.
    GO:0003918    DNA topoisomerase type II (ATP-hydrolyzing) activity    Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
    GO:0006265    DNA topological change    The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.

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  2h7f
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 Related Entries

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

UniProtKB/Swiss-Prot
        TOP1_VAR67 | P32989: 2h7g 3igc

(-) Related Entries Specified in the PDB File

2h7g