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(-) Description

Title :  NOVEL FLUOROQUINOLONES IN COMPLEX WITH TOPOISOMERASE IV FROM S. PNEUMONIAE AND E-SITE G-GATE
 
Authors :  I. Laponogov, X. -S. Pan, D. A. Vesekov, R. T. Cirz, A. S. Wagman, H. E. Mos L. M. Fisher, M. R. Sanderson
Date :  13 May 13  (Deposition) - 26 Nov 14  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.43
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Protein-Dna Cleavage Complex, Isomerase-Dna-Inhibitor Complex, Topoisomerase Iia, Quinolone, Achn-245, Isomerase-Dna-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Laponogov, X. -S. Pan, D. A. Vesekov, R. T. Cirz, A. S. Wagman, H. E. Moser, L. M. Fisher, M. R. Sanderson
Novel Fluoroquinolones In Complex With Topoisomerase Iv Fro S. Pneumoniae And E-Site G-Gate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA TOPOISOMERASE 4 SUBUNIT A
    Chains: A, B
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: PARC55, UNP RESIDUES 1-488
    Gene: PARC, SP_0855
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 170187
    Strain: ATCC BAA-334 / TIGR4
    Synonym: TOPOISOMERASE IV SUBUNIT A
 
Molecule 2 - DNA TOPOISOMERASE 4 SUBUNIT B
    Chains: C, D
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: PARE30, UNP RESIDUES 404-647
    Gene: PARE
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE SEROTYPE 4
    Organism Taxid: 170187
    Strain: ATCC BAA-334 / TIGR4
 
Molecule 3 - E-SITE DNA1
    Chains: E
    Engineered: YES
    Other Details: E-SITE DNA
    Synthetic: YES
 
Molecule 4 - E-SITE DNA2
    Chains: F
    Engineered: YES
    Other Details: E-SITE DNA
    Synthetic: YES
 
Molecule 5 - E-SITE DNA3
    Chains: G
    Engineered: YES
    Other Details: E-SITE DNA
    Synthetic: YES
 
Molecule 6 - E-SITE DNA4
    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  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1AF52Ligand/Ion(7AR,8R)-8-AMINO-4-CYCLOPROPYL-12-FLUORO-1-OXO-4,7,7A,8,9,10-HEXAHYDRO-1H-PYRROLO[1',2':1,7]AZEPINO[2,3-H]QUINOLINE-2-CARBOXYLIC ACID
2MG6Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:316 , LYS A:317 , THR A:319 , GLN A:322BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREAF5 F:101BINDING SITE FOR RESIDUE MG A 502
3AC3SOFTWAREPHE B:316 , LYS B:317 , THR B:319 , GLN B:322BINDING SITE FOR RESIDUE MG B 501
4AC4SOFTWAREAF5 H:101BINDING SITE FOR RESIDUE MG B 502
5AC5SOFTWAREASP C:506 , ASP C:508BINDING SITE FOR RESIDUE MG C 701
6AC6SOFTWAREASP D:506 , ASP D:508 , DT G:15BINDING SITE FOR RESIDUE MG D 701
7AC7SOFTWARESER A:79 , MG A:502 , ARG B:117 , ARG C:456 , GLU C:475 , DT E:15 , DC F:4 , DA F:5 , DG H:1BINDING SITE FOR RESIDUE AF5 F 101
8AC8SOFTWAREARG A:117 , SER B:79 , MG B:502 , ARG D:456 , GLU D:475 , DA F:1 , DT G:15 , DT H:4 , DA H:5BINDING SITE FOR RESIDUE AF5 H 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KPE)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:168 -Gly A:169
2Thr B:168 -Gly B:169

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KPE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KPE)

(-) Exons   (0, 0)

(no "Exon" information available for 4KPE)

(-) 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:482
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhh..........eeee.................eeeehhhhhhhhhhhhhh...eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...hhhhhh...........eeeehhhhhhhhhhhheeeeeee.eeeeee.....eeeeeee.....hhhhhhhhhhhhhhhh....eeeeee........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kpe A   3 NIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVITEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRLSSLED 484
                                    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  


Chain B from PDB  Type:PROTEIN  Length:482
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhh..........eeee.................eeee..hhhhhhhhhhhh...eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...hhhhhh............eeehhhhhhhhhhhheeeeeee.eeeeee.hhh.eeeeeee.....hhhhhhhhhhhhhhh.....eeeeee........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kpe B   3 NIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVITEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRLSSLED 484
                                    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  


Chain C from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeehhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhhhh..........hhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeee..........hhhhhhh.............hhhhhhhhhh......eeeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kpe C 415 KLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVINTAKAKMADILKNEEINTMIYTIGAGVGADFSIEDANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKAYAWTDGELEELRKLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDNVKFT 640
                                   424       434       444       454       464       474       484       494       504       514       524       534       544|      565   ||  582       592       602       612       622       632        
                                                                                                                                                           544|          569|                                                               
                                                                                                                                                            556           577                                                               


Chain D from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeeeehhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhh...eeee...........hhhhhhh.........hhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kpe D 415 KLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVINTAKAKMADILKNEEINTMIYTIGAGVGADFSIEDANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMAYAWTDGELEELRKQLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDNVKFT 640
                                   424       434       444       454       464       474       484       494       504       514       524       534       544||     564     ||580       590       600       610       620       630       640
                                                                                                                                                            545|           570|                                                               
                                                                                                                                                             556            577                                                               


Chain E from PDB  Type:DNA  Length:7
                                       
                 4kpe E   9 CATGAAT  15


Chain F from PDB  Type:DNA  Length:11
                                           
                 4kpe F   1 AGTCATTCATG  11
                                    10 


Chain G from PDB  Type:DNA  Length:7
                                       
                 4kpe G   9 CGTGCAT  15


Chain H from PDB  Type:DNA  Length:11
                                           
                 4kpe H   1 GACTATGCACG  11
                                    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  (0, 0)

(no "SCOP Domain" information available for 4KPE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KPE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KPE)

(-) Gene Ontology  (15, 23)

Asymmetric/Biological Unit(hide GO term definitions)

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  PARE_STRPN | Q59961
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2nov CRYSTAL STRUCTURE OF PARC55 FROM S. PNEUMONIAE
3foe CLINAFLOXACIN-STABILISED CLEAVAGE COMPLEX OF TOPO IV FROM S. PNEUMONIAE
3fof MOXIFLOXACIN-STABILISED CLEAVAGE COMPLEX OF TOPO IV FROM S. PNEUMONIAE
3k9f LEVOFLOXACIN-STABILISED CLEAVAGE COMPLEX OF TOPO IV FROM S. PNEUMONIAE (SOAKED)
3ksa DRUG-FREE CLEAVAGE COMPLEX OF TOPO IV FROM S. PNEUMONIAE (CLEAVED FORM)
3ksb DRUG-FREE CLEAVAGE COMPLEX OF TOPO IV FROM S. PNEUMONIAE (RESEALED FORM)
3ltn PD0305970-STABILISED CLEAVAGE COMPLEX OF TOPO IV FROM S. PNEUMONIAE
3rad QUINOLONE(CLINAFLOXACIN)-DNA CLEAVAGE COMPLEX OF TYPE IV TOPOISOMERASE FROM S. PNEUMONIAE
3rae QUINOLONE(LEVOFLOXACIN)-DNA CLEAVAGE COMPLEX OF TYPE IV TOPOISOMERASE FROM S. PNEUMONIAE
3raf QUINAZOLINEDIONE-DNA CLEAVAGE COMPLEX OF TYPE IV TOPOISOMERASE FROM S. PNEUMONIAE
4koe
4kpf