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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI TOPOISOMERASE IV CO-COMPLEXED WITH INHIBITOR
 
Authors :  Y. Wei, P. Charifson, A. Letiran
Date :  15 Jan 09  (Deposition) - 26 Jan 10  (Release) - 26 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Topoisomerase Iv B Subunit Complex, Antibiotic Resistance, Atp-Binding, Nucleotide-Binding, Topoisomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Wei, A. Letiran
Design And Syntheses Of Novel C7-Derived-Aminobenzimidazole Ureas: Bacterial Gyrase/Topoisomerase Iv Inhibitors With Potent Gram-Positve Antibacterial Activity
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA TOPOISOMERASE 4 SUBUNIT B
    Chains: A, B
    EC Number: 5.99.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: TOPOISOMERASE IV SUBUNIT B
    Gene: PARE, NFXD, B3030, JW2998
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: TOPOISOMERASE IV SUBUNIT B

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
11EU2Ligand/Ion1-(4-ACETYL-6-PYRIDIN-3-YL-1H-BENZIMIDAZOL-2-YL)-3-ETHYLUREA
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
11EU1Ligand/Ion1-(4-ACETYL-6-PYRIDIN-3-YL-1H-BENZIMIDAZOL-2-YL)-3-ETHYLUREA
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
11EU1Ligand/Ion1-(4-ACETYL-6-PYRIDIN-3-YL-1H-BENZIMIDAZOL-2-YL)-3-ETHYLUREA

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:9 , VAL A:39 , ASN A:42 , SER A:43 , GLU A:46 , VAL A:67 , ASP A:69 , ARG A:72 , GLY A:73 , MET A:74 , PRO A:75 , ILE A:90 , ARG A:132 , THR A:163 , VAL A:165 , HOH A:333BINDING SITE FOR RESIDUE 1EU A 2
2AC2SOFTWAREASN B:42 , SER B:43 , GLU B:46 , VAL B:67 , ASP B:69 , ARG B:72 , GLY B:73 , MET B:74 , PRO B:75 , ILE B:90 , ARG B:132 , THR B:163 , VAL B:165 , HOH B:219 , HOH B:302BINDING SITE FOR RESIDUE 1EU B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FV5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FV5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FV5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FV5)

(-) Exons   (0, 0)

(no "Exon" information available for 3FV5)

(-) Sequences/Alignments

Asymmetric 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:180
 aligned with PARE_ECOLI | P20083 from UniProtKB/Swiss-Prot  Length:630

    Alignment length:201
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214 
           PARE_ECOLI    15 GLEPVRRRPGMYTDTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSKRVEVNVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSPRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQRWCY 215
               SCOP domains d3fv5a_ A: automated matches                                                                                                                                                                              SCOP domains
               CATH domains 3fv5A00 A:15-215  [code=3.30.565.10, no name defined]                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....eeeeee.....eeeee...............hhhhhhhhh.---------------------hhhhhhheeeeeeeeee..eeeeeeee..eeeeeeeeeee......eeeeeeee.hhhh.....hhhhhhhhhhhhhhhh...eeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fv5 A  15 GLEPVRRRPGMYTDTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPEEGVPAVELILCRL---------------------ISVVNALSKRVEVNVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSPRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQRWCY 215
                                    24        34        44        54        64        74        84        94         -         - |     124       134       144       154       164       174       184       194       204       214 
                                                                                                          94                   116                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:181
 aligned with PARE_ECOLI | P20083 from UniProtKB/Swiss-Prot  Length:630

    Alignment length:201
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214 
           PARE_ECOLI    15 GLEPVRRRPGMYTDTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSKRVEVNVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSPRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQRWCY 215
               SCOP domains d3fv5b_ B: automated matches                                                                                                                                                                              SCOP domains
               CATH domains 3fv5B00 B:15-215  [code=3.30.565.10, no name defined]                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....eeeeee.....eeeee........ee....eehhhhhhhh.--------------------hhhhhhhheeeeeeeeee..eeeeeeee..eeeeeeeeeee......eeeeeeee.hhhh.....hhhhhhhhhhhhhhhh...eeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fv5 B  15 GLEPVRRRPGMYTDTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPEEGVPAVELILCRL--------------------GISVVNALSKRVEVNVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSPRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQRWCY 215
                                    24        34        44        54        64        74        84        94         -         -|      124       134       144       154       164       174       184       194       204       214 
                                                                                                          94                  115
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FV5)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PARE_ECOLI | P20083)
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: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:0051276    chromosome organization    A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
    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:0030541    plasmid partitioning    Any process in which plasmids are segregated or distributed into daughter cells upon cell division.
    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.
    GO:0007062    sister chromatid cohesion    The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
cellular component
    GO:0009330    DNA topoisomerase complex (ATP-hydrolyzing)    Complex that possesses DNA topoisomerase (ATP-hydrolyzing) activity.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0009295    nucleoid    The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined.

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 Related Entries

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        PARE_ECOLI | P20083: 1s14 1s16 4hz0

(-) Related Entries Specified in the PDB File

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