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(-) Description

Title :  TOPOISOMERASE VI-B BOUND TO RADICICOL
 
Authors :  K. D. Corbett, J. M. Berger
Date :  04 Jul 06  (Deposition) - 29 Aug 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Topoisomerase, Ghkl, Drug Complex, Radicicol, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. D. Corbett, J. M. Berger
Structural Basis For Topoisomerase Vi Inhibition By The Anti-Hsp90 Drug Radicicol
Nucleic Acids Res. V. 34 4269 2006
PubMed-ID: 16920739  |  Reference-DOI: 10.1093/NAR/GKL567

(-) Compounds

Molecule 1 - TYPE II DNA TOPOISOMERASE VI SUBUNIT B
    Chains: A
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: RESIDUES 2-470
    Gene: TOP6B
    Organism Scientific: SULFOLOBUS SHIBATAE
    Organism Taxid: 2286
    Synonym: TOPOVI-B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE
2MG1Ligand/IonMAGNESIUM ION
3RDC1Ligand/IonRADICICOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:105 , GLY A:106 , HOH A:502 , HOH A:553 , HOH A:582 , HOH A:658 , HOH A:688BINDING SITE FOR RESIDUE MG A 471
2AC2SOFTWAREPRO A:309 , ALA A:344 , TYR A:345 , GLN A:346 , GLY A:347 , HIS A:348BINDING SITE FOR RESIDUE DMS A 472
3AC3SOFTWARELEU A:39 , ASN A:42 , ASP A:45 , ALA A:46 , ASP A:76 , GLY A:80 , ILE A:81 , ALA A:89 , PHE A:90 , VAL A:112 , THR A:170 , VAL A:172 , HOH A:506 , HOH A:508 , HOH A:560 , HOH A:578BINDING SITE FOR RESIDUE RDC A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2HKJ)

(-) 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:461
 aligned with TOP6B_SULSH | O05207 from UniProtKB/Swiss-Prot  Length:530

    Alignment length:461
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469 
          TOP6B_SULSH    10 LSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIEIETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIYEYIKRTYIITPYAEFIFKDPEGNVTYYPRLTNKIPKPPQEVKPHPYGVDREEIKILINNLKRDYTIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKDEDFRSPSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAFGGSIPVGEEPIVLRYANKIPLIYDEKSDVIWKVVEELDWKRYGIESDQYQMVVMVHLCSTKIPYKSAGKESIAEVENIEKEIKNALMEVARKLKQYLSEKRKEQEAKKKLLA 470
               SCOP domains d2hkja3 A:10-228 Topoisomerase VI-B subunit                                                                                                                                                                                d2hkja1 A:229-306 Topoisomerase VI-B subunit middle domain                    d2hkja2 A:307-470 Topoisomerase VI-B subunit                                                                                                                         SCOP domains
               CATH domains 2hkjA01 A:10-220  [code=3.30.565.10, no name defined]                                                                                                                                                              ---------2hkjA02 A:230-307  [code=1.10.8.50, no name defined]                          -------2hkjA03 A:315-470  [code=3.30.230.10, no name defined]                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee....eeeeeeee.....hhhhhhhhhhh..................hhhhhhhhhhhhh...eeeeee.....eeeeeeeeee....eeeeeeeeeee......eeeeeeeee.hhhhhhhhhhhhhhhhhhhh...eeeee.....eeee................hhhhhhhhhhhhhhhh.....hhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh......hhhhh...hhhhhhhhhhhhhh..eeeeee...eee..eeeeeeeeeee..........eeeeee..eee..hhhhhhhhhhhhhhhhhhhh.......eeeeeeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hkj A  10 LSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIEIETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIYEYIKRTYIITPYAEFIFKDPEGNVTYYPRLTNKIPKPPQEVKPHPYGVDREEIKILINNLKRDYTIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKYEDFRSPSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAFGGSIPVGEEPIVLRYANKIPLIYDEKSDVIWKVVEELDWKRYGIESDQYQMVVMVHLCSTKIPYKSAGKESIAEVEDIEKEIKNALMEVARKLKQYLSEKRKEQEAKKKLLA 470
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TOP6B_SULSH | O05207)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
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.
    GO:0006268    DNA unwinding involved in DNA replication    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.

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  5.99.1.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        TOP6B_SULSH | O05207: 1mu5 1mx0 1z59 1z5a 1z5b 1z5c 2zbk

(-) Related Entries Specified in the PDB File

1mu5 THE SAME PROTEIN IN THE APO STATE
1mx0 THE SAME PROTEIN IN A DIMER FORM COMPLEXED WITH AMP-PNP