Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  DETAILED STRUCTURAL INSIGHT INTO THE DNA CLEAVAGE COMPLEX OF TYPE IIA TOPOISOMERASES (RE-SEALED FORM)
 
Authors :  I. Laponogov, X. -S. Pan, D. A. Veselkov, K. E. Mcauley, L. M. Fisher, M. R. Sanderson
Date :  21 Nov 09  (Deposition) - 05 May 10  (Release) - 14 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Topoisomerase, Protein-Dna Cleavage Complex, Streptococcus Pneumoniae, Dna-Binding, Nucleotide-Binding, Quinolone, Sealed Dna Form, Isomerase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Laponogov, X. -S. Pan, D. A. Veselkov, K. E. Mcauley, L. M. Fisher, M. R. Sanderson
Structural Basis Of Gate-Dna Breakage And Resealing By Type Ii Topoisomerases
Plos One V. 5 E1133 2010
PubMed-ID: 20596531  |  Reference-DOI: 10.1371/JOURNAL.PONE.0011338
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA TOPOISOMERASE 4 SUBUNIT A
    Chains: A, B
    EC Number: 5.99.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-488
    Gene: PARC
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Strain: 7785
    Synonym: PARC55, TOPOISOMERASE IV SUBUNIT A
 
Molecule 2 - DNA TOPOISOMERASE 4 SUBUNIT B
    Chains: C, D
    EC Number: 5.99.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET19B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 404-647
    Gene: PARE
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Strain: 7785
    Synonym: PARE30, TOPOISOMERASE IV SUBUNIT B
 
Molecule 3 - 5'-D(*AP*CP*CP*AP*AP*GP*GP*T*CP*AP*TP*GP*AP*AP*TP*GP*AP*CP* TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G)-3'
    Chains: E
    Engineered: YES
    Other Details: E-SITE
    Synthetic: YES
 
Molecule 4 - 5'-D(*CP*TP*GP*TP*TP*TP*TP*A*CP*GP*TP*GP*CP*AP*TP*AP*GP*TP* CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*GP*T)-3'
    Chains: F
    Engineered: YES
    Other Details: E-SITE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU C:433 , ASP C:506 , DT E:15 , DG E:16BINDING SITE FOR RESIDUE MG C 742
2AC2SOFTWAREGLU D:433 , ASP D:506 , DT F:15 , DA F:16BINDING SITE FOR RESIDUE MG D 742

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Thr A:168 -Gly A:169
2Thr B:168 -Gly B:169
3Ala C:496 -Asn C:497
4Ala D:496 -Asn D:497

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TOPRIMPS50880 Toprim domain profile.PARE_STRPN427-541
 		  2C:427-541
D:427-541
2TOPOISOMERASE_IIPS00177 DNA topoisomerase II signature.PARE_STRPN431-439
 		  2C:431-439
D:431-439

(-) Exons   (0, 0)

(no "Exon" information available for 3KSB)

(-) 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:471
 aligned with PARC_STRPN | P72525 from UniProtKB/Swiss-Prot  Length:823

    Alignment length:481
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482 
           PARC_STRPN     3 NIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVIIEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRLSSLE 483
               SCOP domains d3ksba_ A: DNA Gyrase A                                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhh..........eeee.................eeeehhhhhhhhhhhhhh...eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...hhhhhhhhh.........eeehhhhhhhhhhhheeeeeee..eee..------.eee.......hhhhhhhhhhhhhhh.......-.ee........eee---...hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ksb A   3 NIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEK------QIVITEIPYEINKANLVKKIDDVRVNNKVAGIA-VRDESDRDGLRIAI---KDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRLSSLE 483
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242   |     -|      262       272       282  | |  292       | - |     312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482 
                                                                                                                                                                                                                                                                             246    253                             285 |          300 304                                                                                                                                                                                   
                                                                                                                                                                                                                                                                                                                      287                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:471
 aligned with PARC_STRPN | P72525 from UniProtKB/Swiss-Prot  Length:823

    Alignment length:481
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482 
           PARC_STRPN     3 NIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVIIEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRLSSLE 483
               SCOP domains d3ksbb_ B: DNA Gyrase A                                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------DNA_topoisoIV-3ksbB01 B:28-468                                                                                                                                                                                                                                                                                                                                                                                                                           --------------- Pfam domains (1)
           Pfam domains (2) -------------------------DNA_topoisoIV-3ksbB02 B:28-468                                                                                                                                                                                                                                                                                                                                                                                                                           --------------- Pfam domains (2)
         Sec.struct. author .eeeeehhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhh..........eeee.................eeeehhhhhhhhhhhhhh...eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...hhhhhhhhh.........eeehhhhhhhhhhhheeeeeee..eee..------.eee.......hhhhhhhhhhhhhhh.......-.ee........eee---...hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ksb B   3 NIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEK------QIVITEIPYEINKANLVKKIDDVRVNNKVAGIA-VRDESDRDGLRIAI---KDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRLSSLE 483
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242   |     -|      262       272       282  | |  292       | - |     312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482 
                                                                                                                                                                                                                                                                             246    253                             285 |          300 304                                                                                                                                                                                   
                                                                                                                                                                                                                                                                                                                      287                                                                                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:217
 aligned with PARE_STRPN | Q59961 from UniProtKB/Swiss-Prot  Length:647

    Alignment length:226
                                   424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634      
           PARE_STRPN   415 KLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVVNTAKAKMADILKNEEINTMIYTIGAGVGADFSIEDANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGELEELRKQFGKGATLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDNVKFT 640
               SCOP domains d3ksbc_ C: DNA gyrase beta-prime domain                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.hhhhhhhhhhh.....eeeee..........---.....hhhhhhhhhhhh...--.....-....eeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....eeee.---....eeee.hhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhh...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------TOPRIM  PDB: C:427-541 UniProt: 427-541                                                                            --------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------TOPOISOME--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ksb C 415 KLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVINTAK---ADILKNEEINTMIYTIGAGV--DFSIE-ANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMSK---KKEEVAYAWTDGELEELRKQFGKGATLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDNVKFT 640
                                   424       434       444       454       464   |   474       484  |  | 494 |     504       514       524       534       544  |   |554       564       574       584       594       604       614       624       634      
                                                                           464 468                487  | 494 |                                                547 551                                                                                         
                                                                                                     490   496                                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:214
 aligned with PARE_STRPN | Q59961 from UniProtKB/Swiss-Prot  Length:647

    Alignment length:226
                                   424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634      
           PARE_STRPN   415 KLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVVNTAKAKMADILKNEEINTMIYTIGAGVGADFSIEDANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGELEELRKQFGKGATLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDNVKFT 640
               SCOP domains d3ksbd_ D: DNA gyrase beta-prime domain                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------Toprim-3ksbD01 D:428-540                                                                                         -------   -------------------DN   A_gyraseB_C-3ksbD03 D:570-634                               ------ Pfam domains (1)
           Pfam domains (2) -------------Toprim-3ksbD02 D:428-540                                                                                         -------   -------------------DN   A_gyraseB_C-3ksbD04 D:570-634                               ------ Pfam domains (2)
         Sec.struct. author .............eeeee.hhhhhhhhhhh.....eeeee..........---.....hhhhhhhhhhhh...--.....-....eeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....eeee.---....eeee.hhhhhhhhhhhh---.eeee..hhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhh...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------TOPRIM  PDB: D:427-541 UniProt: 427-541                                                                            --------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------TOPOISOME--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ksb D 415 KLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVINTAK---ADILKNEEINTMIYTIGAGV--DFSIE-ANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMSK---KKEEVAYAWTDGELEELRKQF---ATLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDNVKFT 640
                                   424       434       444       454       464   |   474       484  |  | 494 |     504       514       524       534       544  |   |554       564      |  -|      584       594       604       614       624       634      
                                                                           464 468                487  | 494 |                                                547 551                 571 575                                                                 
                                                                                                     490   496                                                                                                                                                


Chain E from PDB  Type:DNA  Length:18
                                                  
                 3ksb E   9 CATGAATGACTATGCACG  26
                                    18        


Chain F from PDB  Type:DNA  Length:18
                                                  
                 3ksb F   9 CGTGCATAGTCATTCATG  26
                                    18
   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  (2, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: Toprim-like (19)
(-)
Clan: no clan defined [family: DNA_gyraseB_C] (7)
(-)
Clan: no clan defined [family: DNA_topoisoIV] (19)

(-) Gene Ontology  (15, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PARC_STRPN | P72525)
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.
biological process
    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:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
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.
    GO:0019897    extrinsic component of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain C,D   (PARE_STRPN | Q59961)
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: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: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:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala C:496 - Asn C:497   [ RasMol ]  
    Ala D:496 - Asn D:497   [ RasMol ]  
    Thr A:168 - Gly A:169   [ RasMol ]  
    Thr B:168 - Gly B:169   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3ksb
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PARC_STRPN | P72525
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  PARE_STRPN | Q59961
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  5.99.1.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PARC_STRPN | P72525
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PARE_STRPN | Q59961
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PARC_STRPN | P72525: 2nov 3foe 3fof 3k9f 3ksa 3ltn 3rad 3rae 3raf 4juo 4koe 4kpe 4kpf 4z3o 4z4q 4z53
        PARE_STRPN | Q59961: 3foe 3fof 3k9f 3ksa 3ltn 3rad 3rae 3raf 4juo 4koe 4kpe 4kpf 4z3o 4z4q 4z53

(-) Related Entries Specified in the PDB File

2nov PARC55 DOMAIN OF TYPE IV TOPOISOMERASE FROM S. PNEUMONIAE
3foe CLINAFLOXACIN-DNA CLEAVAGE COMPLEX OF TYPE IV TOPOISOMERASE FROM S. PNEUMONIAE
3fof MOXIFLOXACIN-DNA CLEAVAGE COMPLEX OF TYPE IV TOPOISOMERASE FROM S. PNEUMONIAE
3k9f LEVOFLOXACIN-DNA CLEAVAGE COMPLEX OF TYPE IV TOPOISOMERASE FROM S. PNEUMONIAE
3ksa DNA CLEAVAGE COMPLEX OF TYPE IIA TOPOISOMERASES (CLEAVED FORM)