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(-) Description

Title :  STRUCTURE OF THE DNA TOPOISOMERASE VI A SUBUNIT
 
Authors :  M. D. Nichols, K. A. Deangelis, J. L. Keck, J. M. Berger
Date :  01 Oct 99  (Deposition) - 05 Nov 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Topoisomerase Vi, Dna Binding Protein, Spo11 Homolog (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. D. Nichols, K. Deangelis, J. L. Keck, J. M. Berger
Structure And Function Of An Archaeal Topoisomerase Vi Subunit With Homology To The Meiotic Recombination Factor Spo11.
Embo J. V. 18 6177 1999
PubMed-ID: 10545127  |  Reference-DOI: 10.1093/EMBOJ/18.21.6177
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA TOPOISOMERASE VI A SUBUNIT
    Chains: A, B
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING CORE
    Mutation: YES
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2NA2Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:74 , GLN A:78 , ASP A:114BINDING SITE FOR RESIDUE NA A 370
2AC2SOFTWAREGLU A:197 , ASP A:249 , HOH A:381 , HOH A:399 , HOH A:463 , HOH A:511BINDING SITE FOR RESIDUE MG A 371
3AC3SOFTWAREHOH A:394 , HOH A:426 , HOH A:490 , HOH B:376 , HOH B:379 , HOH B:451BINDING SITE FOR RESIDUE MG A 372
4AC4SOFTWARELYS B:74 , GLN B:78 , ASP B:114BINDING SITE FOR RESIDUE NA B 373
5AC5SOFTWAREGLU B:197 , ASP B:249 , HOH B:413 , HOH B:417 , HOH B:426 , HOH B:501BINDING SITE FOR RESIDUE MG B 374

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1D3Y)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:285 -Val A:286
2Gly B:285 -Val B:286

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1D3Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1D3Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1D3Y)

(-) 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:289
 aligned with TOP6A_METJA | Q57815 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:298
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361        
          TOP6A_METJA    72 QAKIFAQTTKMLEFAKQLLETDDFSTLREAYYVSKNWGEARFDDQQASNNVIEDLEAALGVLREHLGFIPEEDGSSVVGPLKIIEETPEGELVVDCTKLGTGAYNIPNDVTKLNLETDADFILAIETSGMFARLNAERFWDKHNCILVSLKGVPARATRRFIKRLHEEHDLPVLVFTDGDPYGYLNIYRTLKVGSGKAIHLADKLSIPAARLIGVTPQDIIDYDLPTHPLKEQDIKRIKDGLKNDDFVRSFPEWQKALKQMLDMGVRAEQQSLAKYGLKYVVNTYLPEKIKDESTWLP 369
               SCOP domains d1d3ya_ A: DNA topoisomerase IV, alpha subunit                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1d3yA01 A:72-142 'winged helix' repressor DNA binding domain           1d3yA02 A:143-369  [code=3.40.1360.10, no name defined]                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhh.ee......eee...eeeeee..eeeeee.......eee........eee....eeeee.hhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh---------........eeee.hhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee.hhhhhhhhh.hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d3y A  72 QAKIFAQTTKMLEFAKQLLETDDFSTLREAYYVSKNWGEARFDDQQASNNVIEDLEAALGVLREHLGFIPEEDGSSVVGPLKIIEETPEGELVVDCTKLGTGAYNIPNDVTKLNLETDADFILAIETSGMFARLNAERFWDKHNCILVSLKGVPARATRRFIKRLHEEHDLPVLVFTDGDPYGYLNIYRTLKV---------DKLSIPAARLIGVTPQDIIDYDLPTHPLKEQDIKRIKDGLKNDDFVRSFPEWQKALKQMLDMGVRAEQQSLAKYGLKYVVNTYLPEKIKDESTWLP 369
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261  |      -  |    281       291       301       311       321       331       341       351       361        
                                                                                                                                                                                                                          264       274                                                                                               


Chain B from PDB  Type:PROTEIN  Length:290
 aligned with TOP6A_METJA | Q57815 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:299
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360         
          TOP6A_METJA    71 NQAKIFAQTTKMLEFAKQLLETDDFSTLREAYYVSKNWGEARFDDQQASNNVIEDLEAALGVLREHLGFIPEEDGSSVVGPLKIIEETPEGELVVDCTKLGTGAYNIPNDVTKLNLETDADFILAIETSGMFARLNAERFWDKHNCILVSLKGVPARATRRFIKRLHEEHDLPVLVFTDGDPYGYLNIYRTLKVGSGKAIHLADKLSIPAARLIGVTPQDIIDYDLPTHPLKEQDIKRIKDGLKNDDFVRSFPEWQKALKQMLDMGVRAEQQSLAKYGLKYVVNTYLPEKIKDESTWLP 369
               SCOP domains d1d3yb_ B: DNA topoisomerase IV, alpha subunit                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -1d3yB01 B:72-142 'winged helix' repressor DNA binding domain           1d3yB02 B:143-368  [code=3.40.1360.10, no name defined]                                                                                                                                                                           - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................................................................................................................................................................................................---------............................................................................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d3y B  71 NQAKIFAQTTKMLEFAKQLLETDDFSTLREAYYVSKNWGEARFDDQQASNNVIEDLEAALGVLREHLGFIPEEDGSSVVGPLKIIEETPEGELVVDCTKLGTGAYNIPNDVTKLNLETDADFILAIETSGMFARLNAERFWDKHNCILVSLKGVPARATRRFIKRLHEEHDLPVLVFTDGDPYGYLNIYRTLKVG---------KLSIPAARLIGVTPQDIIDYDLPTHPLKEQDIKRIKDGLKNDDFVRSFPEWQKALKQMLDMGVRAEQQSLAKYGLKYVVNTYLPEKIKDESTWLP 369
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    |    -    |  280       290       300       310       320       330       340       350       360         
                                                                                                                                                                                                                            265       275
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1D3Y)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TOP6A_METJA | Q57815)
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:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0000737    DNA catabolic process, endonucleolytic    The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides.
    GO:0006259    DNA metabolic process    Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
    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.
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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