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(-) Description

Title :  STRUCTURAL INSIGHT INTO THE QUINOLONE-DNA CLEAVAGE COMPLEX OF TYPE IIA TOPOISOMERASES
 
Authors :  I. Laponogov, M. K. Sohi, D. A. Veselkov, X. -S. Pan, R. Sawhney, A. W. Thompson, K. E. Mcauley, L. M. Fisher, M. R. Sanderson
Date :  30 Dec 08  (Deposition) - 24 Feb 09  (Release) - 23 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Quinolone, Topoisomerase, Dna, Protein-Dna Cleavage Complex, Streptococcus Pneumoniae, Clinafloxacin, Cell Membrane, Dna-Binding, Isomerase, Membrane, Atp-Binding, Nucleotide- Binding, Isomerase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Laponogov, M. K. Sohi, D. A. Veselkov, X. -S. Pan, R. Sawhney, A. W. Thompson, K. E. Mcauley, L. M. Fisher, M. R. Sanderson
Structural Insight Into The Quinolone-Dna Cleavage Complex Of Type Iia Topoisomerases
Nat. Struct. Mol. Biol. V. 16 667 2009
PubMed-ID: 19448616  |  Reference-DOI: 10.1038/NSMB.1604
(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 Taxid: 562
    Fragment: RESIDUES 1-488
    Gene: PARC, SP_0855
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    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 Taxid: 562
    Fragment: RESIDUES 404-647
    Gene: PARE, SP_0852
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Synonym: PARE30, TOPOISOMERASE IV SUBUNIT B
 
Molecule 3 - DNA (5'- D(P*AP*CP*CP*AP*AP*GP*GP*TP*CP*AP*TP*GP*AP*AP*T)-3')
    Chains: E
    Engineered: YES
    Other Details: E-SITE DNA
    Synthetic: YES
 
Molecule 4 - DNA (5'- D(P*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 DNA
    Synthetic: YES
 
Molecule 5 - DNA (5'- D(P*CP*TP*GP*TP*TP*TP*TP*AP*CP*GP*TP*GP*CP*AP*T)-3')
    Chains: G
    Engineered: YES
    Other Details: E-SITE DNA
    Synthetic: YES
 
Molecule 6 - DNA (5'- D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G )-3')
    Chains: H
    Engineered: YES
    Other Details: E-SITE DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NFX2Ligand/Ion7-[(3R)-3-AMINOPYRROLIDIN-1-YL]-8-CHLORO-1-CYCLOPROPYL-6-FLUORO-4-OXO-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:77 , ASP B:78 , SER B:79 , DA F:1 , DT H:4 , DA H:5BINDING SITE FOR RESIDUE NFX F 0
2AC2SOFTWARESER A:79 , SER A:80 , DC F:4 , DA F:5 , DG H:1BINDING SITE FOR RESIDUE NFX H 0

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:103 -Asn A:104
2Asn A:324 -Tyr A:325

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 3FOE)

(-) 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:432
 aligned with PARC_STRPN | P72525 from UniProtKB/Swiss-Prot  Length:823

    Alignment length:475
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474     
           PARC_STRPN     5 QNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVIIEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRL 479
               SCOP domains d3foea_ A: DNA Gyrase A                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh..--......hhhhhhhhh......hhhhhhhhhhhhhh........eee...................eeehhhhhhhh.........eee......eee.......hhhhhh----------......hhhhhhhhhhhhhhh..-hhhhhh..........--...hhhhhhhhhhhh-...........eee...eee....----..hhhhhhhhhhhhhhhh..------------------...-----.hhhhhhhhh............eee....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3foe A   5 QNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSN--DKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVN----------TDIPPHNLAEVIDAAVYMIDHPT-KIDKLMEFLPGPDFPT--IIQGRDEIKKAYETG-GRVVVRSKTEIEKLKGGKEQIVIT----EINKANLVKKIDDVRVNNKV------------------IEL-----TELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRL 479
                                    14        24        34        44        |- |      64        74        84        94       104       114       124       134       144       154       164|        - |     184       194   | | 204       214|  |   224       234       244       254  |    264       274      |  -         -     | | -   |   314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474     
                                                                           53 56                                                                                                          165        176                   198 |            215  |           232 |                    257  262                281                300 |   308                                                                                                                                                                           
                                                                                                                                                                                                                             200               218             234                                                                 302                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:433
 aligned with PARC_STRPN | P72525 from UniProtKB/Swiss-Prot  Length:823

    Alignment length:475
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474     
           PARC_STRPN     5 QNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVIIEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRL 479
               SCOP domains d3foeb_ B: DNA Gyrase A                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh..........hhhhhhhhh......hhhhhhhhhhhhhh........eeee.................eeeehhhhhhhhh........eee......eee.......hhhhhh----------......hhhhhhhhhhhhhhh...hhhhhh..........--...hhhhhhhhhhhh........--..eee...eee....----..hhhhhhhhhhhhhhhh..------------------...----..hhhhhhhhh......--....eee....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3foe B   5 QNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVN----------TDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPT--IIQGRDEIKKAYETGKGRVVVRS--EIEKLKGGKEQIVIT----EINKANLVKKIDDVRVNNKV------------------IEL----NTELVLNYLFKYTDLQI--NFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRL 479
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164|        - |     184       194       204       214|  |   224       234     | 244       254  |    264       274      |  -         -     | | -  |    314        |- |     334       344       354       364       374       384       394       404       414       424       434       444       454       464       474     
                                                                                                                                                                                          165        176                                    215  |                   240  |           257  262                281                300 |  307             323  |                                                                                                                                                         
                                                                                                                                                                                                                                               218                      243                                                        302                     326                                                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:196
 aligned with PARE_STRPN | Q59961 from UniProtKB/Swiss-Prot  Length:647

    Alignment length:220
                                   426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636
           PARE_STRPN   417 TPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVVNTAKAKMADILKNEEINTMIYTIGAGVGADFSIEDANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGELEELRKQFGKGATLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDN 636
               SCOP domains d3foec_ C: DNA gyrase beta-prime   domai  n                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeehhhhhhhhhhh.....--.eee.--.......hhhhhhhhhhhhhhhhh......-----------........hhhhhhhhhhhhhhh...hhhhhhhh...ee...............--......hhhhhh-----..............--hhhhhh.......ee.........hhhhhh.........hhhhhh... 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
                 3foe C 417 TPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKF--ILPLR--VINTAKAKMADILKNEEINTMIYTIGAGVG-----------KIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMSKGKGKKE--AYAWTDGELEEL-----KGATLQRYKGLGEM--DQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDN 636
                                   426       436       446  |  | 456  |    466       476       486 |       -   |   506       516       526       536       546      |556       566|     |576       586  |    596       606       616       626       636
                                                          449  | 456  |                          488         500                                                  553  |        567   573          586  |                                               
                                                             452    459                                                                                              556                              589                                               


Chain D from PDB  Type:PROTEIN  Length:198
 aligned with PARE_STRPN | Q59961 from UniProtKB/Swiss-Prot  Length:647

    Alignment length:220
                                   426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636
           PARE_STRPN   417 TPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVVNTAKAKMADILKNEEINTMIYTIGAGVGADFSIEDANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGELEELRKQFGKGATLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDN 636
               SCOP domains d3foed_ D: DNA gyrase beta-prime   domai  n                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeehhhhhhhhhh......--.eee.--.......hhhhhhhhhhhhhhhhh......-----------........hhhhhhhhhhhhhhh...hhhhhhhh...ee.......................hhhhhh-----..............--hhhhhh.......ee.........hhhhhh.........hhhhhh... 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
                 3foe D 417 TPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKF--ILPLR--VINTAKAKMADILKNEEINTMIYTIGAGVG-----------KIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGELEEL-----KGATLQRYKGLGEM--DQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDN 636
                                   426       436       446  |  | 456  |    466       476       486 |       -   |   506       516       526       536       546       556       566|     |576       586  |    596       606       616       626       636
                                                          449  | 456  |                          488         500                                                                567   573          586  |                                               
                                                             452    459                                                                                                                               589                                               


Chain E from PDB  Type:DNA  Length:15
                                               
                 3foe E   1 ACCAAGGTCATGAAT  15
                                    10     


Chain F from PDB  Type:DNA  Length:19
                                                   
                 3foe F   1 AGTCATTCATGACCTTGGT  19
                                    10         


Chain G from PDB  Type:DNA  Length:15
                                               
                 3foe G   1 CTGTTTTACGTGCAT  15
                                    10     


Chain H from PDB  Type:DNA  Length:19
                                                   
                 3foe H   1 GACTATGCACGTAAAACAG  19
                                    10
   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 3FOE)

(-) Pfam Domains  (0, 0)

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

(-) 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.

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 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3foe
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
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    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
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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
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    Genomic Information: Ensembl
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    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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  5.99.1.-
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  (no 'MIM ID' available)
    Disease Information: OMIM
 
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    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
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  PARC_STRPN | P72525
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  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 3fof 3k9f 3ksa 3ksb 3ltn 3rad 3rae 3raf 4juo 4koe 4kpe 4kpf 4z3o 4z4q 4z53
        PARE_STRPN | Q59961: 3fof 3k9f 3ksa 3ksb 3ltn 3rad 3rae 3raf 4juo 4koe 4kpe 4kpf 4z3o 4z4q 4z53

(-) Related Entries Specified in the PDB File

2nov CRYSTAL STRUCTURE OF PARC55 FROM S. PNEUMONIAE
3fof QUINOLONE: MOXIFLOXACIN