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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 :  03 Jun 15  (Deposition) - 02 Mar 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
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 2-500 WITH IGSG C-TERMINAL TAG
    Gene: GYRA, RV0006, MTCY10H4.04
    Mutation: YES
    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: 83332
    Expression System Vector Type: PLASMID
    Fragment: GYRB 426-675 WITH N-TERMINAL SNA TAG
    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
    Expression System: SYNTHETIC CONSTRUCT
    Expression System Taxid: 32630
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
 
Molecule 4 - DNA SUBSTRATE 24-MER TTACGTGCATAGTCATTCATGACC
    Chains: F, G
    Engineered: YES
    Expression System: SYNTHETIC CONSTRUCT
    Expression System Taxid: 32630
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630

 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
18MX2Ligand/Ion1-CYCLOPROPYL-6-FLUORO-8-METHYL-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:801 , HOH B:802 , HOH B:803 , HOH B:810binding site for residue MG B 701
2AC2SOFTWARE8MX G:101 , HOH G:201 , HOH G:202 , HOH G:203binding site for residue MG C 601
3AC3SOFTWAREASP D:532 , ASP D:534 , HOH D:801 , HOH D:802 , HOH D:805 , HOH D:808binding site for residue MG D 701
4AC4SOFTWARE8MX H:101 , HOH H:201 , HOH H:203 , HOH H:204binding site for residue MG E 101
5AC5SOFTWAREARG A:128 , SER C:90 , MG C:601 , THR D:500 , GLU D:501 , DT E:14 , DA E:15 , DT F:10 , DA F:11 , DC G:14 , DA G:15 , HOH G:201 , HOH G:202 , HOH G:203 , HOH G:204 , DT H:10 , DG H:11binding site for residue 8MX G 101
6AC6SOFTWARESER A:90 , 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:203 , HOH H:204 , HOH H:206 , HOH H:207binding site for residue 8MX H 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BTN)

(-) 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
                 5btn A  15 IEPVDIEQEMQRSYIDYAMSVIVGRALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARSVAETMGNYHPHGDSSIYDSLVRMAQPWSLRYPLVDGQGNFGSPGNDPPAAMRyTEARLTPLAMEMLREIDEETVDFIPNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLRELADAVFWALENHDADEEETLAAVMGRVKGPDFPTAGLIVGSQGTADAYKTGRGSIRMRGVVEVEEDSRGRTSLVITELPYQVNHDNFITSIAEQVRDGKLAGISNIEDQSSDRVGLRIVIEIKRDAVAKVVINNLYKHTQLQTSFGANMLAIVDGVPRTLRLDQLIRYYVDHQLDVIVRRTTYRLRKANERAHILRGLVKALDALDEVIALIRASETVDIARAGLIELLDIDEIQAQAILDMQLRRLAALERQRIIDDLAKIEAEIADLEDILAKPERQRGIVRDELAEIVDRHGDDRRTRIIAI 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
                 5btn 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.........hhhhhhhhhhhhhhh.......eehhhhhhhhhhhh...hhhhhhhhhhhh..........eeee.................eeeehhhhhhhh.hhhhh...eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.........eee.hhhhhhhhhhheeeeeee.eeeeee.....eeeeeee.....hhhhhhhhhhhhhhh.....eeeeee.........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5btn C  15 IEPVDIEQEMQRSYIDYAMSVIVGRALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARSVAETMGNYHPHGDSSIYDSLVRMAQPWSLRYPLVDGQGNFGSPGNDPPAAMRyTEARLTPLAMEMLREIDEETVDFIPNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLRELADAVFWALENHDADEEETLAAVMGRVKGPDFPTAGLIVGSQGTADAYKTGRGSIRMRGVVEVEEDSRGRTSLVITELPYQVNHDNFITSIAEQVRDGKLAGISNIEDQSSDRVGLRIVIEIKRDAVAKVVINNLYKHTQLQTSFGANMLAIVDGVPRTLRLDQLIRYYVDHQLDVIVRRTTYRLRKANERAHILRGLVKALDALDEVIALIRASETVDIARAGLIELLDIDEIQAQAILDMQLRRLAALERQRIIDDLAKIEAEIADLEDILAKPERQRGIVRDELAEIVDRHGDDRRTRIIAI 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
                 5btn 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
                                                     
                 5btn E   3 TCATGAATGACTATGCACGTA  23
                                    12        22 


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


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


Chain H from PDB  Type:DNA  Length:21
                                                     
                 5btn 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 5BTN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 43)

Asymmetric/Biological Unit(hide GO term definitions)

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  5btn
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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 5bs8 5bta 5btc 5btd 5btf 5btg 5bti 5btl
        GYRB_MYCTU | P9WG45: 2zjt 3ig0 3m4i 3zkb 3zkd 3zm7 5bs8 5bta 5btc 5btd 5btf 5btg 5bti 5btl

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5BTN)