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(-) Description

Title :  STAPHYLOCOCCUS AUREUS GYRASE B CO-COMPLEX WITH METHYL ({5-[4-(4-HYDROXYPIPERIDIN-1-YL)-2-PHENYL-1,3-THIAZOL-5-YL]-1H-PYRAZOL-3-YL}METHYL)CARBAMATE INHIBITOR
 
Authors :  Y. Wei, P. Charisfon
Date :  09 Feb 09  (Deposition) - 09 Feb 10  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Antibiotic Resistance, Isomerase, Isomerase-Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Ronkin, M. Badia, S. Bellon, A. L. Grillot, C. H. Gross, T. H. Grossman, N. Mani, J. D. Parsons, D. Stamos, M. Trudeau, Y. Wei, P. S. Charifson
Discovery Of Pyrazolthiazoles As Novel And Potent Inhibitor Of Bacterial Gyrase.
Bioorg. Med. Chem. Lett. V. 20 2828 2010
PubMed-ID: 20356737  |  Reference-DOI: 10.1016/J.BMCL.2010.03.052

(-) 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: RESIDUES 24-230
    Gene: GYRB
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 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
1B472Ligand/IonMETHYL ({5-[4-(4-HYDROXYPIPERIDIN-1-YL)-2-PHENYL-1,3-THIAZOL-5-YL]-1H-PYRAZOL-3-YL}METHYL)CARBAMATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1B471Ligand/IonMETHYL ({5-[4-(4-HYDROXYPIPERIDIN-1-YL)-2-PHENYL-1,3-THIAZOL-5-YL]-1H-PYRAZOL-3-YL}METHYL)CARBAMATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1B471Ligand/IonMETHYL ({5-[4-(4-HYDROXYPIPERIDIN-1-YL)-2-PHENYL-1,3-THIAZOL-5-YL]-1H-PYRAZOL-3-YL}METHYL)CARBAMATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:51 , ASN A:54 , SER A:55 , GLU A:58 , ASP A:81 , ARG A:84 , ILE A:102 , ARG A:144 , THR A:173 , ILE A:175 , HOH A:232 , HOH A:235 , HOH A:245BINDING SITE FOR RESIDUE B47 A 1
2AC2SOFTWAREHOH B:7 , ILE B:51 , ASN B:54 , SER B:55 , GLU B:58 , ASP B:81 , ARG B:84 , GLY B:85 , ARG B:144 , THR B:173 , ILE B:175 , HOH B:240BINDING SITE FOR RESIDUE B47 B 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G7B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3G7B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G7B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G7B)

(-) Exons   (0, 0)

(no "Exon" information available for 3G7B)

(-) 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:184
 aligned with GYRB_STAAU | P0A0K8 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:207
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       
           GYRB_STAAU    24 GLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
               SCOP domains d3g7ba_ A: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains 3g7bA00 A:24-230  [code=3.30.565.10, no name defined]                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhh.eeeee...............hhhhhhhh-----------------------.hhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g7b A  24 GLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILT-----------------------SSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
                                    33        43        53        63        73        83        93       103|        -         -    |  133       143       153       163       173       183       193       203       213       223       
                                                                                                          104                     128                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:184
 aligned with GYRB_STAAU | P0A0K8 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:207
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       
           GYRB_STAAU    24 GLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
               SCOP domains d3g7bb_ B: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains 3g7bB00 B:24-230  [code=3.30.565.10, no name defined]                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhh.eeeee...............hhhhhhhh-----------------------.hhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g7b B  24 GLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILT-----------------------SSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
                                    33        43        53        63        73        83        93       103|        -         -    |  133       143       153       163       173       183       193       203       213       223       
                                                                                                          104                     128
   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 3G7B)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GYRB_STAAU | P0A0K8)
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.
    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: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_STAAU | P0A0K8: 3g75 3ttz 3u2d 3u2k 4plb 4urm 4uro 5bs3 5cph 5ctu 5ctw 5ctx 5cty 5d6p 5d6q 5d7c 5d7d 5d7r 5iwi 5iwm

(-) Related Entries Specified in the PDB File

3g75 CRYSTAL STRUCTUTURE OF STAPHYLOCOCCUS AUREUS GYRASE B CO- COMPLEXED WITH INHIBITOR
3g7e CRYSTAL STRUCTURE OF E. COLI GYRASE B CO-COMPLEXED WITH INHIBITOR