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(-) Description

Title :  QUINAZOLINEDIONE(PD 0305970)-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 :  02 Apr 15  (Deposition) - 14 Sep 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.04
Chains :  Asym./Biol. Unit :  A,B,E,F,G,H
Keywords :  Topoisomerase 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,DNA TOPOISOMERASE 4 SUBUNIT A
    ChainsA, B
    EC Number5.99.1.3, 5.99.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GenePARE, SP_0852, PARC, SP_0855
    Organism ScientificSTREPTOCOCCUS PNEUMONIAE SEROTYPE 4 (STRAIN ATCC BAA-334 / TIGR4)
    Organism Taxid170187
    StrainATCC BAA-334 / TIGR4
    SynonymTOPOISOMERASE IV SUBUNIT B,TOPOISOMERASE IV SUBUNIT A
 
Molecule 2 - V-SITE DNA
    ChainsE
    EngineeredYES
    Organism ScientificPBR322 BASED IG-LAMBDA EXPRESSION VECTOR
    Organism Taxid588180
    SyntheticYES
 
Molecule 3 - V-SITE DNA
    ChainsF
    EngineeredYES
    Organism ScientificPBR322 BASED IG-LAMBDA EXPRESSION VECTOR
    Organism Taxid588180
    SyntheticYES
 
Molecule 4 - V-SITE DNA
    ChainsG
    EngineeredYES
    Organism ScientificPBR322 BASED IG-LAMBDA EXPRESSION VECTOR
    Organism Taxid588180
    SyntheticYES
 
Molecule 5 - V-SITE DNA
    ChainsH
    EngineeredYES
    Organism ScientificPBR322 BASED IG-LAMBDA EXPRESSION VECTOR
    Organism Taxid588180
    SyntheticYES

 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
1MG4Ligand/IonMAGNESIUM ION
2PDQ2Ligand/Ion3-AMINO-7-{(3R)-3-[(1S)-1-AMINOETHYL]PYRROLIDIN-1-YL}-1-CYCLOPROPYL-6-FLUORO-8-METHYLQUINAZOLINE-2,4(1H,3H)-DIONE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:1316 , LYS A:1317 , THR A:1319 , GLN A:1322binding site for residue MG A 1501
2AC2SOFTWAREASP A:506 , ASP A:508binding site for residue MG A 1502
3AC3SOFTWAREPHE B:1316 , THR B:1319 , GLN B:1322binding site for residue MG B 1501
4AC4SOFTWAREASP B:506 , ASP B:508binding site for residue MG B 1502
5AC5SOFTWAREARG A:456 , GLU A:475 , SER A:1079 , ARG B:1117 , DC E:15 , DC F:4 , DG F:5 , DG H:1binding site for residue PDQ F 101
6AC6SOFTWAREARG A:1117 , ARG B:456 , GLY B:457 , GLU B:475 , SER B:1079 , DA F:1 , DT G:15 , DT H:4 , DA H:5binding site for residue PDQ H 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z4Q)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Thr A:1168 -Gly A:1169
2Ser B:546 -Lys B:547
3Lys B:573 -Gly B:574
4Thr B:1168 -Gly B:1169

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z4Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z4Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z4Q)

(-) 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:690
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeeeehhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhhhhhh...hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeee............hhhhhhh......hhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhh..........eeee.................eeeehhhhhhhhhhhhhh...eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...hhhhhhhhh.........eeehhhhhhhhhhhheeeeeee....eeee...eeeeee.......hhhhhhhhhhhhhhhh....eeeeee........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4z4q A  415 KLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVINTAKAKMADILKNEEINTMIYTIGAGVGADFSIEDANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKAYAWTDGELEELRKLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDNVKFTNIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVITEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRLSSLED 1484
                                   424       434       444       454       464       474       484       494       504       514       524       534       544|      565   ||  582       592       602       612       622       632      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      1234      1244      1254      1264      1274      1284      1294      1304      1314      1324      1334      1344      1354      1364      1374      1384      1394      1404      1414      1424      1434      1444      1454      1464      1474      1484
                                                                                                                                                           544|          569|                                                            640|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                                            556           577                                                            1003                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:708
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeeeehhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhhhh.....hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....eee...hhhhh..eee.hhhhhhhhhhh......eee..hhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh.........hhhhhhhhhhhhh...hhhhhhhhhhhh..........eeee.................eeeehhhhhhhh.hhhhh...eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...hhhhhhhhh.........eeehhhhhhhhhhhheeeeeee.eeeeeee...eeeeeeee.....hhhhhhhhhhhhhhh.....eeeeee........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4z4q B  415 KLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVINTAKAKMADILKNEEINTMIYTIGAGVGADFSIEDANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGELEELRKQFGKGATLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDNVKFTNIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVITEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRLSSLED 1484
                                   424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634     |1006      1016      1026      1036      1046      1056      1066      1076      1086      1096      1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286      1296      1306      1316      1326      1336      1346      1356      1366      1376      1386      1396      1406      1416      1426      1436      1446      1456      1466      1476        
                                                                                                                                                                                                                                                           640|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                                                                                                                                           1003                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 

Chain E from PDB  Type:DNA  Length:7
                                        
                4z4q E    9 GTAATAC   15

Chain F from PDB  Type:DNA  Length:11
                                            
                4z4q F    1 AACCGTATTAC   11
                                    10 

Chain G from PDB  Type:DNA  Length:7
                                        
                4z4q G    9 TGTGGAT   15

Chain H from PDB  Type:DNA  Length:11
                                            
                4z4q H    1 GGTTATCCACA   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 4Z4Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z4Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z4Q)

(-) Gene Ontology  (15, 23)

Asymmetric/Biological Unit(hide GO term definitions)

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    Lys B:573 - Gly B:574   [ RasMol ]  
    Ser B:546 - Lys B:547   [ RasMol ]  
    Thr A:1168 - Gly A:1169   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        PARC_STRPN | P725252nov 3foe 3fof 3k9f 3ksa 3ksb 3ltn 3rad 3rae 3raf 4juo 4koe 4kpe 4kpf 4z3o 4z53
        PARE_STRPN | Q599613foe 3fof 3k9f 3ksa 3ksb 3ltn 3rad 3rae 3raf 4juo 4koe 4kpe 4kpf 4z3o 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