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(-) Description

Title :  QUINOLONE(TROVAFLOXACIN)-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 :  3.26
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,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), STREPTOCOCCUS PNEUMONIAE TIGR4
    Organism Taxid170187
    StrainATCC BAA-334 / TIGR4
    SynonymTOPOISOMERASE IV SUBUNIT B,TOPOISOMERASE IV SUBUNIT A
 
Molecule 2 - E-SITE DNA
    ChainsE
    EngineeredYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SyntheticYES
 
Molecule 3 - E-SITE DNA
    ChainsF
    EngineeredYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SyntheticYES
 
Molecule 4 - E-SITE DNA
    ChainsG
    EngineeredYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SyntheticYES
 
Molecule 5 - E-SITE DNA
    ChainsH
    EngineeredYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    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
2TR62Ligand/IonTROVAFLOXACIN

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETR6 F:101binding site for residue MG A 1501
2AC2SOFTWAREGLU A:433 , ASP A:506 , ASP A:508binding site for residue MG A 1502
3AC3SOFTWARETR6 H:101binding site for residue MG B 1501
4AC4SOFTWAREGLU B:433 , ASP B:506 , ASP B:508binding site for residue MG B 1502
5AC5SOFTWAREARG A:456 , SER A:1079 , MG A:1501 , ARG B:1117 , DT E:15 , DC F:4 , DA F:5 , DG H:1binding site for residue TR6 F 101
6AC6SOFTWAREARG A:1117 , GLY B:434 , ARG B:456 , GLY B:457 , GLU B:475 , SER B:1079 , MG B:1501 , DA F:1 , DT G:15 , DT H:4 , DA H:5binding site for residue TR6 H 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z53)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Thr A:1168 -Gly A:1169
2Met B:545 -Ala B:556
3Thr B:1168 -Gly B:1169

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z53)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z53)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z53)

(-) 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..........hhhhhhhhhhhhhhhhhhh.......hhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eee.....ee....hhhhhhhhhh.ee.......hhhhhhhhhh......eeeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhh..........eeee.................eeeehhhhhhhhhhhhhh...eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...hhhhhh............eeehhhhhhhhhhhheeeeeee.............eeee.......hhhhhhhhhhhhhhhh....eeeeee........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4z53 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:695
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeehhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhhhhhh...hhhhh........eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eee............hhhhhhhhhhh..........hhhhhhhhh..........ee..hhhhhhhhhhhhhh.hhhhhhhhhhhhh..........eehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhh..........eeee.................eeee..hhhhhhhhhhhh...eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...hhhhhh............eeehhhhhhhhhhhheeeeeee....eee.hhh.eeeee.......hhhhhhhhhhhhhhhh....eeeeee........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4z53 B  415 KLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVINTAKAKMADILKNEEINTMIYTIGAGVGADFSIEDANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMAYAWTDGELEELRKQLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDNVKFTLEENIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVITEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRLSSLED 1484
                                   424       434       444       454       464       474       484       494       504       514       524       534       544||     564     ||580       590       600       610       620       630       640  ||  1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289      1299      1309      1319      1329      1339      1349      1359      1369      1379      1389      1399      1409      1419      1429      1439      1449      1459      1469      1479     
                                                                                                                                                            545|           570|                                                               643|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                                             556            577                                                               1003                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 

Chain E from PDB  Type:DNA  Length:7
                                        
                4z53 E    9 CATGAAT   15

Chain F from PDB  Type:DNA  Length:11
                                            
                4z53 F    1 AGTCATTCATG   11
                                    10 

Chain G from PDB  Type:DNA  Length:7
                                        
                4z53 G    9 CGTGCAT   15

Chain H from PDB  Type:DNA  Length:11
                                            
                4z53 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 4Z53)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z53)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z53)

(-) Gene Ontology  (15, 23)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Met B:545 - Ala B:556   [ 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 4z4q
        PARE_STRPN | Q599613foe 3fof 3k9f 3ksa 3ksb 3ltn 3rad 3rae 3raf 4juo 4koe 4kpe 4kpf 4z3o 4z4q

(-) 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