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(-) Description

Title :  CRYSTAL STRUCTURE OF HETERODIMERIC L. DONOVANI TOPOISOMERASE I-VANADATE-DNA COMPLEX
 
Authors :  D. R. Davies, W. G. J. Hol
Date :  12 Oct 05  (Deposition) - 17 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Topoisomerase I, Vanadate Complex, Isomerase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. R. Davies, A. Mushtaq, H. Interthal, J. J. Champoux, W. G. Hol
The Structure Of The Transition State Of The Heterodimeric Topoisomerase I Of Leishmania Donovani As A Vanadate Complex With Nicked Dna.
J. Mol. Biol. V. 357 1202 2006
PubMed-ID: 16487540  |  Reference-DOI: 10.1016/J.JMB.2006.01.022
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'- D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*AP*AP*GP*TP*CP*TP*TP *TP*TP*T)-3'
    Chains: E
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - TOPOISOMERASE I-LIKE PROTEIN
    Chains: A
    EC Number: 5.99.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PLYSS
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TOPOISOMERASE I, LARGE SUBUNIT (LDTOP1L)
    Organism Scientific: LEISHMANIA DONOVANI
    Organism Taxid: 5661
 
Molecule 5 - DNA TOPOISOMERASE I-LIKE PROTEIN
    Chains: B
    EC Number: 5.99.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PLYSS
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TOPOISOMERASE I, SMALL SUBUNIT (LDTOP1S)
    Organism Scientific: LEISHMANIA DONOVANI
    Organism Taxid: 5661

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

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:314 , ARG A:410 , HIS A:453 , TYR B:222 , HOH B:303 , DT C:10 , DA D:11BINDING SITE FOR RESIDUE VO4 B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B9S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2B9S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B9S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B9S)

(-) Exons   (0, 0)

(no "Exon" information available for 2B9S)

(-) 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:426
 aligned with Q9GPZ9_LEIIN | Q9GPZ9 from UniProtKB/TrEMBL  Length:635

    Alignment length:430
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456
         Q9GPZ9_LEIIN    27 DLNWWEQENLRIAMKGERRWETLAHNGVLFPPEYEPHGIPIFYDGREFKMTPEEEEVATMFAVMKEHDYYRMEVFRRNFFESWREILDKRQHPIRRLELCDFEPIYQWHLVQREKKLSRTKEEKKAIKEKQDAEAEPYRYCVWDGRREQVANFRVEPPGLFRGRGKHPLMGKLKVRVQPEDITINIGETAEVPVPPAGHKWAAVQHDHTVTWLAMWRDSVAGNMKYVMLAPSSSVKGQSDMVKFEKARKLKDKVDDIRASYMEDFKSNDLHVAQRAVAMYFIDRLALRVGNEKGEDEADTVGCCSLRVEHIQLMPDNIVRFDFLGKDSIRYQNDVAVLPEVYALLQRFTRRKSPGMDIFDQLNPTQLNDHLKSFMDGLSAKVFRTYNASITLDRWFKEKPVDPKWSTADKLAYFNKANTEVAILCNHQKS 456
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................ee................eee..eee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eeee..eeee.........ee............ee...hhhh.eee.................eee........eeee......eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...............hhhhhhhh.eee....eeeeeee.hhh.eeeeeee.hhhhhhhhhhhhh............hhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.----...hhhhhhhhhhhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b9s A  27 DLNWWEQENLRIAMKGERRWETLAHNGVLFPPEYEPHGIPIFYDGREFKMTPEEEEVATMFAVMKEHDYYRMEVFRRNFFESWREILDKRQHPIRRLELCDFEPIYQWHLVQREKKLSRTKEEKKAIKEKQDAEAEPYRYCVWDGRREQVANFRVEPPGLFRGRGKHPLMGKLKVRVQPEDITINIGETAEVPVPPAGHKWAAVQHDHTVTWLAMWRDSVAGNMKYVMLAPSSSVKGQSDMVKFEKARKLKDKVDDIRASYMEDFKSNDLHVAQRAVAMYFIDRLALRVGNEKGEDEADTVGCCSLRVEHIQLMPDNIVRFDFLGKDSIRYQNDVAVLPEVYALLQRFTRRKSPGMDIFDQLNPTQLNDHLKSFMDGLSAKVFRTYNASITLDRWFKEKP----WSTADKLAYFNKANTEVAILCNHQKS 456
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426    |  436       446       456
                                                                                                                                                                                                                                                                                                                                                                                                                                         426  431                         


Chain B from PDB  Type:PROTEIN  Length:52
 aligned with Q8WQM6_LEIDO | Q8WQM6 from UniProtKB/TrEMBL  Length:262

    Alignment length:52
                                   220       230       240       250       260  
         Q8WQM6_LEIDO   211 KAVSLGTSKINYIDPRIICSWAKAQDVPINKIFSATIQKKFPWAMNAENFDF 262
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhhh.hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                 2b9s B 211 KAVSLGTSKINYIDPRIICSWAKAQDVPINKIFSATIQKKFPWAMNAENFDF 262
                                   220       230       240       250       260  


Chain C from PDB  Type:DNA  Length:10
                                          
                 2b9s C   1 AAAAAGACTT  10
                                    10


Chain D from PDB  Type:DNA  Length:12
                                            
                 2b9s D  11 AGAAAAATTTTT  22
                                    20  


Chain E from PDB  Type:DNA  Length:22
                                                      
                 2b9s E 101 AAAAATTTTTCTAAGTCTTTTT 122
                                   110       120
   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  (0, 0)

(no "SCOP Domain" information available for 2B9S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2B9S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B9S)

(-) Gene Ontology  (6, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9GPZ9_LEIIN | Q9GPZ9)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.

Chain B   (Q8WQM6_LEIDO | Q8WQM6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.

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