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(-) Description

Title :  SMALLPOX VIRUS TOPOISOMERASE-DNA TRANSITION STATE
 
Authors :  K. Perry, Y. Hwang, F. D. Bushman, G. D. Van Duyne
Date :  27 Jul 09  (Deposition) - 02 Mar 10  (Release) - 02 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Topoisomerase, Protein-Dna Complex, Poxvirus, Isomerase, Atp-Binding, Dna-Binding, Late Protein, Nucleotide-Binding, Isomerase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Perry, Y. Hwang, F. D. Bushman, G. D. Van Duyne
Insights From The Structure Of A Smallpox Virus Topoisomerase-Dna Transition State Mimic.
Structure V. 18 127 2010
PubMed-ID: 20152159  |  Reference-DOI: 10.1016/J.STR.2009.10.020

(-) Compounds

Molecule 1 - DNA TOPOISOMERASE 1
    Chains: A
    EC Number: 5.99.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: H6R, I6R, TOP1
    Mutation: YES
    Organism Common: SMALLPOX VIRUS
    Organism Scientific: VARIOLA VIRUS
    Organism Taxid: 10255
    Strain: WESTERN RESERVE
    Synonym: DNA TOPOISOMERASE I
 
Molecule 2 - 5'-D(*GP*TP*GP*TP*CP*GP*CP*CP*CP*TP*T)-3'
    Chains: B
    Engineered: YES
    Other Details: UPSTREAM DNA CLEAVED STRAND
    Other Details - Source: OLIGONUCLEOTIDE SYNTHESIZED BY YALE KECK FACILITY
    Synthetic: YES
 
Molecule 3 - 5'-D(*AP*TP*TP*CP*C)-3'
    Chains: C
    Engineered: YES
    Other Details: DOWNSTREAM DNA CLEAVED STRAND
    Other Details - Source: OLIGONUCLEOTIDE SYNTHESIZED BY YALE KECK FACILITY
    Synthetic: YES
 
Molecule 4 - 5'- D(*CP*GP*GP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP*A)-3'
    Chains: D
    Engineered: YES
    Other Details: UNCLEAVED DNA STRAND
    Other Details - Source: OLIGONUCLEOTIDE SYNTHESIZED BY YALE KECK FACILITY
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1VO41Ligand/IonVANADATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:130 , ARG A:223 , HIS A:265 , TYR A:274 , HOH A:404 , DT B:511 , DA C:512BINDING SITE FOR RESIDUE VO4 A 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IGC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IGC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IGC)

(-) PROSITE Motifs  (1, 1)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3IGC)

(-) 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 A from PDB  Type:PROTEIN  Length:313
 aligned with TOP1_VAR67 | P32989 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:313
                                    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 MRALFYKDGKLFTDNNFLNPVSDNNPAYEVLQHVKIPTHLTDVVVYGQTWEEALTRLIFVGSDSKGRRQYFYGKMHVQNRNAKRDRIFVRVYNVMKRINCFINKNIKKSSTDSNYQLAVFMLMETMFFIRFGKMKYLKENETVGLLTLKNKHIEISPDKIVIKFVGKDKVSHEFVVHKSNRLYKPLLKLTDDSSPEEFLFNKLSERKVYECIKQFGIRIKDLRTYGVNYTFLYNFWTNVKSISPLPSPKKLIALTIKQTAEVVGHTPSISKRAYMATTILEMVKDKNFLDVVSKTTFDEFLSIVVDHVKSSTD 313
               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.hhhhhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TOPOISOMERASE_I_EUK---------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3igc A   1 MRALFYKDGKLFTDNNFLNPVSDNNPAYEVLQHVKIPTHLTDVVVYGQTWEEALTRLIFVGSDSKGRRQYFYGKMHVQNRNAKRDRIFVRVYNVMKRINSFINKNIKKSSTDSNYQLAVFMLMETMFFIRFGKMKYLKENETVGLLTLKNKHIEISPDKIVIKFVGKDKVSHEFVVHKSNRLYKPLLKLTDDSSPEEFLFNKLSERKVYESIKQFGIRIKDLRTYGVNYTFLYNFWTNVKSISPLPSPKKLIALTIKQTAEVVGHTPSISKRAYMATTILEMVKDKNFLDVVSKTTFDEFLSIVVDHVKSSTD 313
                                    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   


Chain B from PDB  Type:DNA  Length:11
                                           
                 3igc B 501 GTGTCGCCCTT 511
                                   510 


Chain C from PDB  Type:DNA  Length:5
                                     
                 3igc C 512 ATTCC 516


Chain D from PDB  Type:DNA  Length:16
                                                
                 3igc D 517 CGGAATAAGGGCGACA 532
                                   526
   Legend:   → Mismatch (orange background)
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  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 3IGC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IGC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IGC)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        TOP1_VAR67 | P32989: 2h7f 2h7g

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