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(-) Description

Title :  THE 2.98A CRYSTAL STRUCTURE OF THE CATALYTIC CORE (B'A' REGION) OF STAPHYLOCOCCUS AUREUS DNA GYRASE
 
Authors :  B. D. Bax, P. F. Chan, D. S. Eggleston, A. Fosberry, D. R. Gentry, F. Gorre I. Giordano, M. M. Hann, A. Hennessy, M. Hibbs, J. Huang, E. Jones, J. Jo K. K. Brown, C. J. Lewis, E. W. May, O. Singh, C. Spitzfaden, C. Shen, A. S A. F. Theobald, A. Wohlkonig, N. D. Pearson, M. N. Gwynn
Date :  24 Apr 10  (Deposition) - 04 Aug 10  (Release) - 25 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.98
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. D. Bax, P. F. Chan, D. S. Eggleston, A. Fosberry, D. R. Gentry, F. Gorrec, I. Giordano, M. M. Hann, A. Hennessy, M. Hibbs, J. Huang, E. Jones, J. Jones, K. K. Brown, C. J. Lewis, E. W. May, M. R. Saunders, O. Singh, C. Spitzfaden, C. Shen, A. Shillings, A. F. Theobald, A. Wohlkonig, N. D. Pearson, M. N. Gwynn
Type Iia Topoisomerase Inhibition By A New Class Of Antibacterial Agents.
Nature V. 466 935 2010
PubMed-ID: 20686482  |  Reference-DOI: 10.1038/NATURE09197

(-) Compounds

Molecule 1 - DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
    ChainsA
    EC Number5.99.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentC-TERMINAL 27KDA DOMAIN, RESIDUES 410-644, N-TERMINAL 56KDA DOMAIN, RESIDUES 2-491
    Organism ScientificSTAPHYLOCOCCUS AUREUS
    Organism Taxid158879
    Other DetailsC-TERMINUS GYRB (A644) FUSED TO N-TERMINUS GYRA (A1002)
    StrainN315

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2XCQ)

(-) Sites  (0, 0)

(no "Site" information available for 2XCQ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XCQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XCQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XCQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XCQ)

(-) Exons   (0, 0)

(no "Exon" information available for 2XCQ)

(-) 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:653
 aligned with GYRA_STAAN | Q99XG5 from UniProtKB/Swiss-Prot  Length:889

    Alignment length:656
                                                                                                                                                          1      8     9 12  13      21                              22                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                                     -         -         -         -         -         -         -         -         -         -         -         -      |  4   |     9  |   | 16    |    -         -         -      | 25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485      
          GYRA_STAAN      - ------------------------------------------------------------------------------------------------------------------------------MAELPQSR-----INER---NITSEMRES-------------------------------FLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRYTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG  491
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_topoisoIV-2xcqA01 A:1033-1474                                                                                                                                                                                                                                                                                                                                                                                                                         ----------------- Pfam domains
         Sec.struct. author ..............hhhh.eeeeeehhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhh...............eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eee......eee.hhhhhhhhhh......eee..hhhhhhhhhhhhhhh.......ee.......hhhhhh.........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhh..........eeee.................eeeehhhhhhhhh........eee......eee.......hhhhhhh.....---.......hhhhhhhhhhhhh.....hhhhhhhhh.........ee.hhhhhhhhhhh.eeeeeee.eeeeee.....eeeeeee.....hhhhhhhhhhhhhhhh....eeeeee...hhh...eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2xcq A  411 VASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPLYKLTQGKQKYYVYNDRELDKLKSELNPTSIARYKGLGEMNADQLWETTMNPEHRALLQVKLEDAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRYTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIA---ATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG 1491
                                   420       430       440       450       460   ||  477       487       497       507       517       527       537       547       557       567    || 580       590       600       610||    1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175|   | 1185      1195      1205      1215      1225      1235      1245      1255      1265      1275      1285      1295      1305      1315      1325      1335      1345      1355      1365      1375      1385      1395      1405      1415      1425      1435      1445      1455      1465      1475      1485      
                                                                               464|                                                                                                 572|                                611|                                                                                                                                                 1176   |                                                                                                                                                                                                                                                                                                                       
                                                                                472                                                                                                  576                                1027                                                                                                                                                     1180                                                                                                                                                                                                                                                                                                                       

   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "SCOP Domain" information available for 2XCQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XCQ)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (14, 24)

Asymmetric Unit(hide GO term definitions)
Chain A   (GYRA_STAAN | Q99XG5)
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: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:0006259    DNA metabolic process    Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
    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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  GYRB_STAAN | P66937
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 Related Entries

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

UniProtKB/Swiss-Prot
        GYRA_STAAN | Q99XG52xco 2xcr 2xcs 2xct 4bul 5cdm 5cdn 5cdo 5cdp 5cdq 5cdr 5iwi 5iwm 5npk 5npp
        GYRB_STAAN | P669372xco 2xcr 2xcs 2xct 4bul 5cdm 5cdn 5cdo 5cdp 5cdq 5cdr 5iwi 5iwm 5npk 5npp

(-) Related Entries Specified in the PDB File

2xco THE 3.1A CRYSTAL STRUCTURE OF THE CATALYTIC CORE (B'A' REGION) OF STAPHYLOCOCCUS AUREUS DNA GYRASE
2xcr THE 3.5A CRYSTAL STRUCTURE OF THE CATALYTIC CORE (B'A' REGION) OF STAPHYLOCOCCUS AUREUS DNA GYRASE COMPLEXED WITH GSK299423 AND DNA
2xcs THE 2.1A CRYSTAL STRUCTURE OF S. AUREUS GYRASE COMPLEX WITH GSK299423 AND DNA
2xct THE TWINNED 3.35A STRUCTURE OF S. AUREUS GYRASE COMPLEX WITH CIPROFLOXACIN AND DNA