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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SECOND PART OF THE MYCOBACTERIUM TUBERCULOSIS DNA GYRASE REACTION CORE: THE TOPRIM DOMAIN AT 2.1 A RESOLUTION
 
Authors :  J. Piton, A. Aubry, M. Delarue, C. Mayer
Date :  27 Jul 09  (Deposition) - 28 Jul 10  (Release) - 27 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Dna Gyrase, Gyrb, Toprim, Type Ii Topoisomerase, Tuberculosis, Quinolone Binding Site, Dna Binding Site, Atp-Binding, Isomerase, Nucleotide-Binding, Topoisomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Piton, S. Petrella, M. Delarue, G. Andre-Leroux, V. Jarlier, A. Aubry, C. Mayer
Structural Insights Into The Quinolone Resistance Mechanism Of Mycobacterium Tuberculosis Dna Gyrase.
Plos One V. 5 E1224 2010
PubMed-ID: 20805881  |  Reference-DOI: 10.1371/JOURNAL.PONE.0012245

(-) Compounds

Molecule 1 - DNA GYRASE SUBUNIT B
    ChainsA
    EC Number5.99.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRSF-2 EK/LIC
    Expression System StrainBL21 ROSETTA 2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentTOPRIM DOMAIN (C-TERMINAL DOMAIN)
    GeneGYRB, MT0005, MTCY10H4.03, RV0005
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid83332
    StrainHR37RV

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3IG0)

(-) Sites  (0, 0)

(no "Site" information available for 3IG0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IG0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IG0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IG0)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TOPRIMPS50880 Toprim domain profile.GYRB_MYCTO453-567  1A:453-567
GYRB_MYCTU453-567  1A:453-567
2TOPOISOMERASE_IIPS00177 DNA topoisomerase II signature.GYRB_MYCTO457-465  1A:457-460
GYRB_MYCTU457-465  1A:457-460

(-) Exons   (0, 0)

(no "Exon" information available for 3IG0)

(-) 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:185
 aligned with GYRB_MYCTO | P9WG44 from UniProtKB/Swiss-Prot  Length:675

    Alignment length:207
                                   457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       
           GYRB_MYCTO   448 TDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGE 654
               SCOP domains d3ig0a_ A: DN             A gyrase b         eta-prime domain                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh.eeeeeeee-------------.eeeeeeee.---------..hhhhhhhhhhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....eee.......eee.hhhhhhhhhhhhhhhh........eee..hhhhhhhhhhhhhhh......eee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----TOPRIM  PDB: A:453-567 UniProt: 453-567                                                                            --------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ---------TOPOISOME--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ig0 A 448 TDPRKSELYVVEG-------------MFQAILPLRG---------IDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGE 654
                                   457  |      -      |477     |   -     | 497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       
                                      460           474      483       493                                                                                                                                                                 

Chain A from PDB  Type:PROTEIN  Length:185
 aligned with GYRB_MYCTU | P9WG45 from UniProtKB/Swiss-Prot  Length:675

    Alignment length:207
                                   457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       
           GYRB_MYCTU   448 TDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGE 654
               SCOP domains d3ig0a_ A: DN             A gyrase b         eta-prime domain                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh.eeeeeeee-------------.eeeeeeee.---------..hhhhhhhhhhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....eee.......eee.hhhhhhhhhhhhhhhh........eee..hhhhhhhhhhhhhhh......eee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----TOPRIM  PDB: A:453-567 UniProt: 453-567                                                                            --------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------TOPOISOME--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ig0 A 448 TDPRKSELYVVEG-------------MFQAILPLRG---------IDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGE 654
                                   457  |      -      |477     |   -     | 497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       
                                      460           474      483       493                                                                                                                                                                 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IG0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IG0)

(-) Gene Ontology  (22, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GYRB_MYCTU | P9WG45)
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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0006268    DNA unwinding involved in DNA replication    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.
    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.
    GO:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
cellular component
    GO:0009330    DNA topoisomerase complex (ATP-hydrolyzing)    Complex that possesses DNA topoisomerase (ATP-hydrolyzing) activity.
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    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.
    GO:0009295    nucleoid    The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A   (GYRB_MYCTO | P9WG44)
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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        GYRB_MYCTO | P9WG442zjt 3m4i 5btl
        GYRB_MYCTU | P9WG452zjt 3m4i 3zkb 3zkd 3zm7 5bs8 5bta 5btc 5btd 5btf 5btg 5bti 5btl 5btn

(-) Related Entries Specified in the PDB File

2zjt CRYSTAL STRUCTURE OF GYRB TOPRIM DOMAIN AT 2.8 A RESOLUTION