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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 43K ATPASE DOMAIN OF THERMUS THERMOPHILUS GYRASE B IN COMPLEX WITH NOVOBIOCIN
 
Authors :  V. Lamour, L. Hoermann, J. -M. Jeltsch, P. Oudet, D. Moras
Date :  03 Dec 01  (Deposition) - 03 Jun 02  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Topoisomerase, Gyrase B-Coumarin Complex, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Lamour, L. Hoermann, J. M. Jeltsch, P. Oudet, D. Moras
An Open Conformation Of The Thermus Thermophilus Gyrase B Atp-Binding Domain.
J. Biol. Chem. V. 277 18947 2002
PubMed-ID: 11850422  |  Reference-DOI: 10.1074/JBC.M111740200

(-) Compounds

Molecule 1 - DNA GYRASE SUBUNIT B
    Chains: A, B
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: 43K DOMAIN
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2NOV2Ligand/IonNOVOBIOCIN

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:45 , ASP A:48 , GLU A:49 , ASP A:72 , ARG A:75 , GLY A:76 , ILE A:77 , PRO A:78 , ASP A:80 , ILE A:93 , LYS A:102 , VAL A:117 , ARG A:135 , THR A:166 , HOH A:507 , HOH A:646 , HOH A:732 , HOH A:909BINDING SITE FOR RESIDUE NOV A 400
2AC2SOFTWAREILE A:10 , ASN B:45 , ASP B:48 , GLU B:49 , ASP B:72 , ARG B:75 , ILE B:77 , PRO B:78 , ASP B:80 , ARG B:135 , THR B:166 , HOH B:520 , HOH B:539 , HOH B:591 , HOH B:723 , HOH B:755 , HOH B:894BINDING SITE FOR RESIDUE NOV B 444
3AC3SOFTWAREHOH A:792BINDING SITE FOR RESIDUE FMT A 401
4AC4SOFTWAREASN B:294 , HOH B:821 , HOH B:823 , HOH B:915BINDING SITE FOR RESIDUE FMT B 441

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KIJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KIJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KIJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KIJ)

(-) Exons   (0, 0)

(no "Exon" information available for 1KIJ)

(-) 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:384
 aligned with GYRB_THET8 | Q5SHZ4 from UniProtKB/Swiss-Prot  Length:634

    Alignment length:384
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386    
           GYRB_THET8     7 AIRVLKGLEGVRHRPAMYIGGTGVEGYHHLFKEILDNAVDEALAGYATEILVRLNEDGSLTVEDNGRGIPVDLMPEEGKPAVEVIYTTLHSGGKFEQGAYKVSGGLHGVGASVVNALSEWTVVEVFREGKHHRIAFSRGEVTEPLRVVGEAPRGKTGTRVTFKPDPEIFGNLRFDPSKIRARLREVAYLVAGLKLVFQDRQHGKEEVFLDKGGVASFAKALAEGEDLLYEKPFLIRGTHGEVEVEVGFLHTQGYNAEILTYANMIPTRDGGTHLTAFKSAYSRALNQYAKKAGLNKEKGPQPTGDDLLEGLYAVVSVKLPNPQFEGQTKGKLLNPEAGTAVGQVVYERLLEILEENPRIAKAVYEKALRAAQAREAARKARELV 390
               SCOP domains d1kija2 A:9-220 DNA gyrase B                                                                                                                                                                                        d1kija1 A:221-392 DNA gyrase B                                                                                                                                               SCOP domains
               CATH domains ---1kijA01 A:12-219  [code=3.30.565.10, no name defined]                                                                                                                                                           1kijA02 A:220-392  [code=3.30.230.10, no name defined]                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeee...............hhhhhhhhh..eehhhhhh...........hhhhhhhheeeeeeeeee..eeeeeeee..eeeeeeeeeee.hhhh.eeeeeeeehhhhhh....hhhhhhhhhhhhhhhh...eeeeee.hhheeeee...hhhhhhhhhhh..........eeeeeee..eeeeeeeee......eeeeee..ee....hhhhhhhhhhhhhhhhhhhhhh..................eeeeeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kij A   9 AIRVLKGLEGVRHRPAMYIGGTGVEGYHHLFKEILDNAVDEALAGYATEILVRLNEDGSLTVEDNGRGIPVDLMPEEGKPAVEVIYNTLHSGGKFEQGAYKVSGGLHGVGASVVNALSEWTVVEVFREGKHHRIAFSRGEVTEPLRVVGEAPRGKTGTRVTFKPDPEIFGNLRFDPSKIRARLREVAYLVAGLKLVFQDRQHGKEEVFLDKGGVASFAKALAEGEDLLYEKPFLIRGTHGEVEVEVGFLHTQGYNAEILTYANMIPTRDGGTHLTAFKSAYSRALNQYAKKAGLNKEKGPQPTGDDLLEGLYAVVSVKLPNPQFEGQTKGKLLNPEAGTAVGQVVYERLLEILEENPRIAKAVYEKALRAAQAREAARKARELV 392
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388    


Chain B from PDB  Type:PROTEIN  Length:384
 aligned with GYRB_THET8 | Q5SHZ4 from UniProtKB/Swiss-Prot  Length:634

    Alignment length:384
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386    
           GYRB_THET8     7 AIRVLKGLEGVRHRPAMYIGGTGVEGYHHLFKEILDNAVDEALAGYATEILVRLNEDGSLTVEDNGRGIPVDLMPEEGKPAVEVIYTTLHSGGKFEQGAYKVSGGLHGVGASVVNALSEWTVVEVFREGKHHRIAFSRGEVTEPLRVVGEAPRGKTGTRVTFKPDPEIFGNLRFDPSKIRARLREVAYLVAGLKLVFQDRQHGKEEVFLDKGGVASFAKALAEGEDLLYEKPFLIRGTHGEVEVEVGFLHTQGYNAEILTYANMIPTRDGGTHLTAFKSAYSRALNQYAKKAGLNKEKGPQPTGDDLLEGLYAVVSVKLPNPQFEGQTKGKLLNPEAGTAVGQVVYERLLEILEENPRIAKAVYEKALRAAQAREAARKARELV 390
               SCOP domains d1kijb2 B:9-220 DNA gyrase B                                                                                                                                                                                        d1kijb1 B:221-392 DNA gyrase B                                                                                                                                               SCOP domains
               CATH domains ---1kijB01 B:12-219  [code=3.30.565.10, no name defined]                                                                                                                                                           1kijB02 B:220-392  [code=3.30.230.10, no name defined]                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeee........ee....eehhhhhhhh..eehhhhh............hhhhhhhheeeeeeeeee..eeeeeeee..eeeeeeeeeee......eeeeeeeehhhhhh....hhhhhhhhhhhhhhhh...eeeeee....eeeee...hhhhhhhhhhh..........eeeeeee..eeeeeeeee......eeeeee..ee....hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhh.eeeeeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kij B   9 AIRVLKGLEGVRHRPAMYIGGTGVEGYHHLFKEILDNAVDEALAGYATEILVRLNEDGSLTVEDNGRGIPVDLMPEEGKPAVEVIYNTLHSGGKFEQGAYKVSGGLHGVGASVVNALSEWTVVEVFREGKHHRIAFSRGEVTEPLRVVGEAPRGKTGTRVTFKPDPEIFGNLRFDPSKIRARLREVAYLVAGLKLVFQDRQHGKEEVFLDKGGVASFAKALAEGEDLLYEKPFLIRGTHGEVEVEVGFLHTQGYNAEILTYANMIPTRDGGTHLTAFKSAYSRALNQYAKKAGLNKEKGPQPTGDDLLEGLYAVVSVKLPNPQFEGQTKGKLLNPEAGTAVGQVVYERLLEILEENPRIAKAVYEKALRAAQAREAARKARELV 392
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1KIJ)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GYRB_THET8 | Q5SHZ4)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0034335    DNA supercoiling activity    Catalytic introduction of supercoils in a DNA molecule or region thereof. In bacteria, negative supercoils are only introduced by DNA gyrase, a type II topoisomerase, but not all DNA gyrases are capable of introducing supercoils. In bacteria, the level of supercoiling varies widely between species and has been characterized properly in only a handful of organisms. The best characterized enzyme, from E.coli, is exceptionally proficient at supercoiling and this ability is not representative of all bacteria.
    GO:0003916    DNA topoisomerase activity    Catalysis of the transient cleavage and passage of individual DNA strands or double helices through one another, resulting a topological transformation in double-stranded DNA.
    GO:0003918    DNA topoisomerase type II (ATP-hydrolyzing) activity    Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0006265    DNA topological change    The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.
    GO:0006261    DNA-dependent DNA replication    A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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