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(-) Description

Title :  CRYSTAL STRUCTURE OF A TOPOISOMERASE II COMPLEX
 
Authors :  T. R. Blower, B. H. Williamson, R. J. Kerns, J. M. Berger
Date :  01 Jun 15  (Deposition) - 02 Mar 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Protein-Dna Complex, Topoisomerase Ii, Isomerase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. R. Blower, B. H. Williamson, R. J. Kerns, J. M. Berger
Crystal Structure And Stability Of Gyrase-Fluoroquinolone Cleaved Complexes From Mycobacterium Tuberculosis.
Proc. Natl. Acad. Sci. Usa V. 113 1706 2016
PubMed-ID: 26792525  |  Reference-DOI: 10.1073/PNAS.1525047113

(-) Compounds

Molecule 1 - DNA GYRASE SUBUNIT A
    Chains: A, C
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28B
    Expression System Strain: ROSETTA 2 PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: GYRA TOWER AND C-GATE DOMAINS
    Gene: GYRA, RV0006, MTCY10H4.04
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / H37RV)
    Organism Taxid: 83332
    Strain: ATCC 25618 / H37RV
 
Molecule 2 - DNA GYRASE SUBUNIT B
    Chains: B, D
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28B
    Expression System Strain: ROSETTA 2 PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: GYRB TOPRIM DOMAIN
    Gene: GYRB, RV0005, MTCY10H4.03
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / H37RV)
    Organism Taxid: 83332
    Strain: ATCC 25618 / H37RV
 
Molecule 3 - DNA SUBSTRATE 24-MER GGTCATGAATGACTATGCACGTAA
    Chains: E, H
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - DNA SUBSTRATE 24-MER TTACGTGCATAGTCATTCATGACC
    Chains: F, G
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
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
3PTR2Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:532 , ASP B:534 , HOH B:804 , HOH B:811 , HOH B:812 , HOH B:816binding site for residue MG B 701
2AC2SOFTWAREASP D:532 , ASP D:534 , HOH D:802 , HOH D:807 , HOH D:809 , HOH D:831binding site for residue MG D 701
3AC3SOFTWAREHOH A:615 , MFX H:101 , HOH H:202 , HOH H:203 , HOH H:209binding site for residue MG E 101
4AC4SOFTWAREMFX G:101 , HOH G:203 , HOH G:205 , HOH G:206 , HOH G:210binding site for residue MG F 101
5AC5SOFTWAREARG A:128 , ALA C:90 , ARG D:482 , GLY D:483 , GLU D:501 , DT E:14 , DA E:15 , DT F:10 , DA F:11 , MG F:101 , DC G:14 , DA G:15 , HOH G:203 , HOH G:205 , HOH G:206 , HOH G:209 , HOH G:210 , DT H:10 , DG H:11binding site for residue MFX G 101
6AC6SOFTWAREALA A:90 , HOH A:615 , ARG B:482 , GLU B:501 , ARG C:128 , PTR C:129 , DT E:10 , DG E:11 , MG E:101 , DC F:14 , DA F:15 , DT G:10 , DA G:11 , DT H:14 , DA H:15 , HOH H:201 , HOH H:202 , HOH H:203binding site for residue MFX H 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5BS8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5BS8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5BS8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5BS8)

(-) Exons   (0, 0)

(no "Exon" information available for 5BS8)

(-) 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:487
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhh..........eeee............hhhh.eeeehhhhhhhh.hhhhh...eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.........eee.hhhhhhhhhhheeeeeee.eeeeee.....eeeeeee.....hhhhhhhhhhhhhhh.....eeeeee.........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bs8 A  15 IEPVDIEQEMQRSYIDYAMSVIVGRALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARSVAETMGNYHPHGDASIYDSLVRMAQPWSLRYPLVDGQGNFGSPGNDPPAAMRyTEARLTPLAMEMLREIDEETVDFIPNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLRELADAVFWALENHDADEEETLAAVMGRVKGPDFPTAGLIVGSQGTADAYKTGRGSIRMRGVVEVEEDSRGRTSLVITELPYQVNHDNFITSIAEQVRDGKLAGISNIEDQSSDRVGLRIVIEIKRDAVAKVVINNLYKHTQLQTSFGANMLAIVDGVPRTLRLDQLIRYYVDHQLDVIVRRTTYRLRKANERAHILRGLVKALDALDEVIALIRASETVDIARAGLIELLDIDEIQAQAILDMQLRRLAALERQRIIDDLAKIEAEIADLEDILAKPERQRGIVRDELAEIVDRHGDDRRTRIIAI 501
                                    24        34        44        54        64        74        84        94       104       114       124    |  134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       
                                                                                                                                            129-PTR                                                                                                                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:245
                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................eeeeeehhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....eee.......eee.hhhhhhhhhhhhhhh.........eee..hhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bs8 B 425 ALVRRKGLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAKDVRFLDV 675
                                 ||440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670     
                               430|                                                                                                                                                                                                                                              
                                437                                                                                                                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:487
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhh..........eeee............hhhh.eeeehhhhhhhh.hhhhh...eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.........eee.hhhhhhhhhhheeeeeee.eeeeee.....eeeeeee.....hhhhhhhhhhhhhhh.....eeeeee.........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bs8 C  15 IEPVDIEQEMQRSYIDYAMSVIVGRALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARSVAETMGNYHPHGDASIYDSLVRMAQPWSLRYPLVDGQGNFGSPGNDPPAAMRyTEARLTPLAMEMLREIDEETVDFIPNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLRELADAVFWALENHDADEEETLAAVMGRVKGPDFPTAGLIVGSQGTADAYKTGRGSIRMRGVVEVEEDSRGRTSLVITELPYQVNHDNFITSIAEQVRDGKLAGISNIEDQSSDRVGLRIVIEIKRDAVAKVVINNLYKHTQLQTSFGANMLAIVDGVPRTLRLDQLIRYYVDHQLDVIVRRTTYRLRKANERAHILRGLVKALDALDEVIALIRASETVDIARAGLIELLDIDEIQAQAILDMQLRRLAALERQRIIDDLAKIEAEIADLEDILAKPERQRGIVRDELAEIVDRHGDDRRTRIIAI 501
                                    24        34        44        54        64        74        84        94       104       114       124    |  134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       
                                                                                                                                            129-PTR                                                                                                                                                                                                                                                                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................eeeeeehhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....eee.......eee.hhhhhhhhhhhhhhh.........eee..hhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bs8 D 424 NALVRRKSGLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAKDVRFLDV 675
                                   438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       
                                 431|                                                                                                                                                                                                                                              
                                  437                                                                                                                                                                                                                                              


Chain E from PDB  Type:DNA  Length:21
                                                     
                 5bs8 E   3 TCATGAATGACTATGCACGTA  23
                                    12        22 


Chain F from PDB  Type:DNA  Length:21
                                                     
                 5bs8 F   3 ACGTGCATAGTCATTCATGAC  23
                                    12        22 


Chain G from PDB  Type:DNA  Length:21
                                                     
                 5bs8 G   3 ACGTGCATAGTCATTCATGAC  23
                                    12        22 


Chain H from PDB  Type:DNA  Length:21
                                                     
                 5bs8 H   3 TCATGAATGACTATGCACGTA  23
                                    12        22
   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 5BS8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5BS8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5BS8)

(-) Gene Ontology  (23, 43)

Asymmetric/Biological Unit(hide GO term definitions)

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  5bs8
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  GYRA_MYCTU | P9WG47
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  GYRB_MYCTU | P9WG45
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  5.99.1.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        GYRA_MYCTU | P9WG47: 3ifz 3ilw 3uc1 4g3n 5bta 5btc 5btd 5btf 5btg 5bti 5btl 5btn
        GYRB_MYCTU | P9WG45: 2zjt 3ig0 3m4i 3zkb 3zkd 3zm7 5bta 5btc 5btd 5btf 5btg 5bti 5btl 5btn

(-) Related Entries Specified in the PDB File

5bta 5btc 5btd 5btf 5btg 5bti 5btl 5btn