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(-) Description

Title :  QUINOLONE(MOXIFLOXACIN)-DNA CLEAVAGE COMPLEX OF TOPOISOMERASE IV FROM S. PNEUMONIAE
 
Authors :  I. Laponogov, D. A. Veselkov, X. -S. Pan, J. Selvarajah, I. M. -T. Crevel L. M. Fisher, M. R. Sanderson
Date :  31 Mar 15  (Deposition) - 14 Sep 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.44
Chains :  Asym./Biol. Unit :  A,B,E,F,G,H
Keywords :  Topo Iv, Cleavage Complex, Dna, Quinolone, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Laponogov, D. A. Veselkov, X. -S. Pan, J. Selvarajah, I. M. -T. Crevel, L. M. Fisher, M. R. Sanderson
Structural Studies Of The Drug-Stabilized Cleavage Complexe Of Topoisomerase Iv And Gyrase From Streptococcus Pneumonia
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA TOPOISOMERASE 4 SUBUNIT B,PARE30-PARC55 FUSED TOPO IV FROM S. PNEUMONIAE
    Chains: A, B
    EC Number: 5.99.1.3, 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PARE, SP_0852, Z67739
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Synonym: TOPOISOMERASE IV SUBUNIT B
 
Molecule 2 - E-SITE DNA
    Chains: E
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synthetic: YES
 
Molecule 3 - E-SITE DNA
    Chains: F
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synthetic: YES
 
Molecule 4 - E-SITE DNA
    Chains: G
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synthetic: YES
 
Molecule 5 - E-SITE DNA
    Chains: H
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MFX2Ligand/Ion1-CYCLOPROPYL-6-FLUORO-8-METHOXY-7-[(4AS,7AS)-OCTAHYDRO-6H-PYRROLO[3,4-B]PYRIDIN-6-YL]-4-OXO-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID
2MG4Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:506 , ASP A:508binding site for residue MG A 1501
2AC2SOFTWAREMFX H:101binding site for residue MG A 1502
3AC3SOFTWAREASP B:506 , ASP B:508binding site for residue MG B 1501
4AC4SOFTWAREMFX F:101binding site for residue MG B 1502
5AC5SOFTWAREARG A:1117 , ARG B:456 , GLU B:475 , SER B:1079 , MG B:1502 , DT E:15 , DC F:4 , DA F:5 , DG H:1binding site for residue MFX F 101
6AC6SOFTWAREARG A:456 , SER A:1079 , MG A:1502 , DA F:1 , DT G:15 , DT H:4 , DA H:5binding site for residue MFX H 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z3O)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:1168 -Gly A:1169
2Thr B:1168 -Gly B:1169

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z3O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z3O)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z3O)

(-) 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:689
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeehhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhhhhhhh.......hhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhh.....hhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhh...hhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhh..........eeee.................eeeehhhhhhhh.hhhhh...eee......eee.......hhhhhh................hhhhhhhhhhhhhhh...hhhhhh............eeehhhhhhhhhhhheeeeeee.eeeeeee...eeeeeeee.....hhhhhhhhhhhhhhhh....eeeeee........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4z3o A  415 KLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVINTAKAKMADILKNEEINTMIYTIGAGVGADFSIEDANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKYAWTDGELEELRKLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDNVKFTNIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVITEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRLSSLED 1484
                                   424       434       444       454       464       474       484       494       504       514       524       534       544|      566  ||   583       593       603       613       623       633      1005      1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175      1185      1195      1205      1215      1225      1235      1245      1255      1265      1275      1285      1295      1305      1315      1325      1335      1345      1355      1365      1375      1385      1395      1405      1415      1425      1435      1445      1455      1465      1475         
                                                                                                                                                           544|         569|                                                            640|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                                            557          577                                                            1003                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:689
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeehhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhhhhhhh...............eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeee...........hhhhhhhhh..........hhhhhhhhhh......eeeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhh..........eeee.................eeeehhhhhhhhhhhhhh...eee......eee.......hhhhhhh...............hhhhhhhhhhhhhhh...hhhhhh............eeehhhhhhhhhhhheeeeeee.eeeeee.hhh.eeeeeee.....hhhhhhhhhhhhhhh.....eeeeee........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4z3o B  415 KLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVINTAKAKMADILKNEEINTMIYTIGAGVGADFSIEDANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMAYAWTDGELEELRKQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDNVKFTIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVITEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRLSSLED 1484
                                   424       434       444       454       464       474       484       494       504       514       524       534       544||     564    || 582       592       602       612       622       632      1005      1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175      1185      1195      1205      1215      1225      1235      1245      1255      1265      1275      1285      1295      1305      1315      1325      1335      1345      1355      1365      1375      1385      1395      1405      1415      1425      1435      1445      1455      1465      1475         
                                                                                                                                                            545|          569|                                                           640|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
                                                                                                                                                             556           578                                                           1004                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                


Chain E from PDB  Type:DNA  Length:7
                                        
                4z3o E    9 CATGAAT   15


Chain F from PDB  Type:DNA  Length:11
                                            
                4z3o F    1 AGTCATTCATG   11
                                    10 


Chain G from PDB  Type:DNA  Length:7
                                        
                4z3o G    9 CGTGCAT   15


Chain H from PDB  Type:DNA  Length:11
                                            
                4z3o 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 4Z3O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z3O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z3O)

(-) Gene Ontology  (15, 23)

Asymmetric/Biological Unit(hide GO term definitions)

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    Thr A:1168 - Gly A:1169   [ RasMol ]  
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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 4kpe 4kpf 4z4q 4z53
        PARE_STRPN | Q59961: 3foe 3fof 3k9f 3ksa 3ksb 3ltn 3rad 3rae 3raf 4juo 4koe 4kpe 4kpf 4z4q 4z53

(-) Related Entries Specified in the PDB File

3ksa DETAILED STRUCTURAL INSIGHT INTO THE DNA CLEAVAGE COMPLEX OF TYPE IIA TOPOISOMERASES (CLEAVED FORM)
3ksb DETAILED STRUCTURAL INSIGHT INTO THE DNA CLEAVAGE COMPLEX OF TYPE IIA TOPOISOMERASES (RE-SEALED FORM)
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
4i3h A THREE-GATE STRUCTURE OF TOPOISOMERASE IV FROM STREPTOCOCCUS PNEUMONIAE
4koe QUINOLONE(TROVAFLOXACIN)-DNA CLEAVAGE COMPLEX OF TYPE IV TOPOISOMERASE FROM S. PNEUMONIAE
4pxp QUINOLONE-STABILIZED CLEAVAGE COMPLEX OF TOPOISOMERASE IV FROM KLEBSIELLA PNEUMONIAE