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(-) Description

Title :  CRYSTAL STRUCTURE OF 24 KDA DOMAIN OF E. COLI DNA GYRASE B IN COMPLEX WITH SMALL MOLECULE INHIBITOR
 
Authors :  M. Brvar, M. Renko, A. Perdih, T. Solmajer, D. Turk
Date :  22 Feb 12  (Deposition) - 01 Aug 12  (Release) - 08 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structure-Based Drug Design, Antibacterial, Dna Gyrase B, Gyrase, Isomerase-Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Brvar, A. Perdih, M. Renko, G. Anderluh, D. Turk, T. Solmajer
Structure-Based Discovery Of Substituted 4, 5'-Bithiazoles A Novel Dna Gyrase Inhibitors.
J. Med. Chem. V. 55 6413 2012
PubMed-ID: 22731783  |  Reference-DOI: 10.1021/JM300395D

(-) Compounds

Molecule 1 - DNA GYRASE SUBUNIT B
    Chains: A, B
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASIMD
    Fragment: N-TERMINAL DOMAIN
    Gene: GYRB, ACRB, HIMB, HISU, NALC, PARA, PCBA, B3699, JW5625
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 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
1RLI2Ligand/Ion4-{[4'-METHYL-2'-(PROPANOYLAMINO)-4,5'-BI-1,3-THIAZOL-2-YL]AMINO}BENZOIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1RLI1Ligand/Ion4-{[4'-METHYL-2'-(PROPANOYLAMINO)-4,5'-BI-1,3-THIAZOL-2-YL]AMINO}BENZOIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1RLI1Ligand/Ion4-{[4'-METHYL-2'-(PROPANOYLAMINO)-4,5'-BI-1,3-THIAZOL-2-YL]AMINO}BENZOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:43 , ASN A:46 , GLU A:50 , ASP A:73 , ARG A:76 , ILE A:78 , PRO A:79 , GLY A:101 , LYS A:103 , ARG A:136 , THR A:165 , HOH A:614 , HOH A:702BINDING SITE FOR RESIDUE RLI A 301
2AC2SOFTWAREVAL B:43 , ASN B:46 , GLU B:50 , VAL B:71 , ASP B:73 , ARG B:76 , ILE B:78 , PRO B:79 , ILE B:94 , GLY B:101 , ARG B:136 , THR B:165 , HOH B:451BINDING SITE FOR RESIDUE RLI B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DUH)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:216 -His A:217

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DUH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DUH)

(-) Exons   (0, 0)

(no "Exon" information available for 4DUH)

(-) 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:195
 aligned with GYRB_ECOLI | P0AES6 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:203
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214   
           GYRB_ECOLI    15 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFH 217
               SCOP domains d4duha_ A: automated matches                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...eeeeee.....eeeee........ee....eehhhhhhhh...........--------..hhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.....eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4duh A  15 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNS--------GVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFH 217
                                    24        34        44        54        64        74        84        94       104   |     -  |    124       134       144       154       164       174       184       194       204       214   
                                                                                                                       108      117                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:194
 aligned with GYRB_ECOLI | P0AES6 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:206
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
           GYRB_ECOLI    12 VLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFH 217
               SCOP domains d4duhb_ B: automated matches                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeee...............hhhhhhhhh.......------------..hhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4duh B  12 VLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKF------------GVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFH 217
                                    21        31        41        51        61        71        81        91       101  |      -     | 121       131       141       151       161       171       181       191       201       211      
                                                                                                                      104          117
   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  (0, 0)

(no "CATH Domain" information available for 4DUH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DUH)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GYRB_ECOLI | P0AES6)
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:0008094    DNA-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.
    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: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:0042493    response to drug    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 a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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

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

UniProtKB/Swiss-Prot
        GYRB_ECOLI | P0AES6: 1aj6 1ei1 1kzn 3g7e 3nuh 4hyp 4kfg 4prv 4prx 4pu9 4wub 4wuc 4wud 4xtj 4zvi 5l3j

(-) Related Entries Specified in the PDB File

1aj6 SAME PROTEIN IN COMPLEX WITH NOVOBIOCIN
1kzn SAME PROTEIN IN COMPLEX WITH CLOROBIOCIN