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(-) Description

Title :  QUINOLONE(MOXIFLOXACIN)-DNA CLEAVAGE COMPLEX OF GYRASE 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 :  29 Mar 15  (Deposition) - 14 Sep 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.19
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Gyrase, 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 GYRASE SUBUNIT A
    ChainsA, B
    EC Number5.99.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneGYRA, BM52_0349
    Organism ScientificSTREPTOCOCCUS PNEUMONIAE
    Organism Taxid1313
 
Molecule 2 - DNA GYRASE SUBUNIT B
    ChainsC, D
    EC Number5.99.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneGYRB, BM52_1967, DJ38_04430
    Organism ScientificSTREPTOCOCCUS PNEUMONIAE
    Organism Taxid1313
 
Molecule 3 - SYMMETRIZED E-SITE DNA
    ChainsE, G
    EngineeredYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SyntheticYES
 
Molecule 4 - SYMMETRIZED E-SITE DNA
    ChainsF, H
    EngineeredYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
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
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:81 , GLU C:475 , DG F:1 , DT G:15 , MG G:101 , DC H:4 , DA H:5binding site for residue MFX F 101
2AC2SOFTWARESER A:81 , ARG D:456 , GLU D:475 , DT E:15 , DC F:4 , DA F:5 , DG H:1 , MG H:102binding site for residue MFX H 101
3AC3SOFTWAREMFX H:101binding site for residue MG H 102
4AC4SOFTWAREMFX F:101 , DT G:15binding site for residue MG G 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z2C)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:170 -Gly A:171
2Thr B:170 -Gly B:171

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z2C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z2C)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z2C)

(-) 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:485
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeehhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.......eehhhhhhhhhhhh...hhhhhhhhhhhh..........eeee.................eeee..hhhhhhh........eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...hhhhhhh...........eee.hhhhhhhhhhheeeeeee.eeeeee.....eeeeeee.....hhhhhhhhhhhhhh......eeeeee........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z2c A   2 QDKNLVNVNLTKEMKASFIDYAMSVIVARALPDVRDGLKPVHRRILYGMNELGVTPDKPHKKSARITGDVMGKYHPHGDSSIYEAMVRMAQWWSYRYMLVDGHGNFGSMDGDSAAAQRYTEARMSKIALEMLRDINKNTVDFVDNYDANEREPLVLPARFPNLLVNGATGIAVGMATNIPPHNLGETIDAVKLVMDNPEVTTKDLMEVLPGPDFPTGALVMGKSGIHKAYETGKGSIVLRSRTEIETTKTGRERIVVTEFPYMVNKTKVHEHIVRLVQEKRIEGITAVRDESNREGVRFVIEVKRDASANVILNNLFKMTQMQTNFGFNMLAIQNGIPKILSLRQILDAYIEHQKEVVVRRTRFDKEKAEARAHILEGLLIALDHIDEVIRIIRASETDAEAQAELMSKFKLSERQSQAILDMRLRRLTGLERDKIQSEYDDLLALIADLADILAKPERVSQIIKDELDEVKRKFSDKRRTELMV 486
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481     

Chain B from PDB  Type:PROTEIN  Length:482
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh.......eehhhhhhhhhhhh...hhhhhhhhhhhh..........eeee.................eeee..hhhhhh.hhhhh...eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...hhhhhhhhh.........eee.hhhhhhhhhhheeeeeee.eeeeee.....eeeeeee.....hhhhhhhhhhhhhh......eeeee.........eeee....hhhhhhhhhhhh.eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z2c B   2 QDKNLVNVNLTKEMKASFIDYAMSVIVARALPDVRDGLKPVHRRILYGMNELGVTPDKPHKKSARITGDVMGKYHPHGDSSIYEAMVRMAQWWSYRYMLVDGHGNFGSMDGDSAAAQRYTEARMSKIALEMLRDINKNTVDFVDNYDANEREPLVLPARFPNLLVNGATGIAVGMATNIPPHNLGETIDAVKLVMDNPEVTTKDLMEVLPGPDFPTGALVMGKSGIHKAYETGKGSIVLRSRTEIETTKTGRERIVVTEFPYMVNKTKVHEHIVRLVQEKRIEGITAVRDESNREGVFVIEVKRDSANVILNNLFKMTMQTNFGFNMLAIQNGIPKILSLRQILDAYIEHQKEVVVRRTRFDKEKAEARAHILEGLLIALDHIDEVIRIIRASETDAEAQAELMSKFKLSERQSQAILDMRLRRLTGLERDKIQSEYDDLLALIADLADILAKPERVSQIIKDELDEVKRKFSDKRRTELMV 486
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291      |302    || 313       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484  
                                                                                                                                                                                                                                                                                                                                  298|    307|         321|                                                                                                                                                                   
                                                                                                                                                                                                                                                                                                                                   300     309          323                                                                                                                                                                   

Chain C from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........................eeeeeehhhhhhhhhh......eeeeee.....hhhhhhhhhhh.hhhhhhhhhhhh.......hhhhh....eeee...hhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.......hhhhhhhhhh.....eeeeee..hhhhhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4z2c C 401 KHMKSGLEISNLPGKLADCSSNNPAETELFIVEGDSAGGSAKSGRNREFQAILPIRGKILNVEKASMDKILANEEIRSLFTAMGTGFGAEFDVSKARYQKLVLMTDADVDGAHIRTLLLTLIYRYMKPILEAGYVYIAQPPLGEMDDHQLWETTMDPEHRLMARVSVDDAAEADKIFDMLMGDRVEPRREFIEENAVY 643
                                   410       420       430       440       450       460       470       480       490       500       510       520       530       540||     595       605       615       625       635        
                                                                                                                                                                      541|                                                        
                                                                                                                                                                       587                                                        

Chain D from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................eeeeehhhhhhhhhhhh.....eeeee...........hhhhhh.hhhhhhhhhhhh.......hhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhh.......eeeee..hhhhhhhhhhhhh...hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z2c D 403 MKSGLEIPGKLADCSSNNPAETELFIVEGDSAGGSAKSGRNREFQAILPIRGKILNVEKASMDKILANEEIRSLFTAMGTGFGAEFDVSKARYQKLVLMTDADVDGAHIRTLLLTLIYRYMKPILEAGYVYIAQPPLGEMDDHQLWETTMDPEHRLMARVSVDDAAEADKIFDMLMGDRVEPRREFIEENAVYS 644
                                  |415       425       435       445       455       465       475       485       495       505       515       525       535     ||590       600       610       620       630       640    
                                409|                                                                                                                             541|                                                         
                                 413                                                                                                                              587                                                         

Chain E from PDB  Type:DNA  Length:9
                                         
                 4z2c E   7 ACGTTGTAT  15

Chain F from PDB  Type:DNA  Length:13
                                             
                 4z2c F   1 GATCATACAACGT  13
                                    10   

Chain G from PDB  Type:DNA  Length:7
                                       
                 4z2c G   9 GTTGTAT  15

Chain H from PDB  Type:DNA  Length:11
                                           
                 4z2c H   1 GATCATACAAC  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 4Z2C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z2C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z2C)

(-) Gene Ontology  (13, 23)

Asymmetric/Biological Unit(hide GO term definitions)

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    Thr A:170 - Gly A:171   [ RasMol ]  
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 Related Entries

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

UniProtKB/TrEMBL
        Q59957_STREE | Q599574z2d 4z2e
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(-) 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