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(-) Description

Title :  THE 3.5A CRYSTAL STRUCTURE OF THE CATALYTIC CORE (B'A' REGION) OF STAPHYLOCOCCUS AUREUS DNA GYRASE COMPLEXED WITH GSK299423 AND DNA
 
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 :  25 Apr 10  (Deposition) - 04 Aug 10  (Release) - 25 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  B,D,E,F,S,U,V,W
Biol. Unit 1:  B,D,E,F  (1x)
Biol. Unit 2:  S,U,V,W  (1x)
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
    Chains: B, D, S, U
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: C-TERMINAL 27KDA DOMAIN, RESIDUES 410-644, N-TERMINAL 56KDA DOMAIN, RESIDUES 2-491
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Other Details: C-TERMINUS GYRB (B644) FUSED TO N-TERMINUS GYRA (A2)
 
Molecule 2 - 5'-D(*5UA*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP *GP*CP*TP)-3'
    Chains: E, F
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - 5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP *GP*CP*TP)-3'
    Chains: V, W
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : BDEFSUVW
Biological Unit 1 (1x): BDEF    
Biological Unit 2 (1x):     SUVW

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
15UA2Mod. Nucleotide5'-O-CARBOXY-2'-DEOXYADENOSINE
2RXV2Ligand/Ion6-METHOXY-4-(2-{4-[([1,3]OXATHIOLO[5,4-C]PYRIDIN-6-YLMETHYL)AMINO]PIPERIDIN-1-YL}ETHYL)QUINOLINE-3-CARBONITRILE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
15UA2Mod. Nucleotide5'-O-CARBOXY-2'-DEOXYADENOSINE
2RXV1Ligand/Ion6-METHOXY-4-(2-{4-[([1,3]OXATHIOLO[5,4-C]PYRIDIN-6-YLMETHYL)AMINO]PIPERIDIN-1-YL}ETHYL)QUINOLINE-3-CARBONITRILE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
15UA-1Mod. Nucleotide5'-O-CARBOXY-2'-DEOXYADENOSINE
2RXV1Ligand/Ion6-METHOXY-4-(2-{4-[([1,3]OXATHIOLO[5,4-C]PYRIDIN-6-YLMETHYL)AMINO]PIPERIDIN-1-YL}ETHYL)QUINOLINE-3-CARBONITRILE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA B:1068 , ASP B:1083 , ALA D:1068 , GLY D:1072 , ASP D:1083 , MET D:1121 , DG E:10 , DC E:11 , DG F:10 , DC F:11BINDING SITE FOR RESIDUE RXV E1021
2AC2SOFTWAREALA S:1068 , GLY S:1072 , MET S:1075 , ASP S:1083 , ALA U:1068 , ASP U:1083 , DG V:10 , DC V:11 , DG W:10 , DC W:11BINDING SITE FOR RESIDUE RXV W1020

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Glu B:1003 -Leu B:1004
2Ala D:640 -Asn D:641
3Leu D:1004 -Pro D:1005
4Gly D:1253 -Gly D:1254
5Ala S:1002 -Glu S:1003
6Glu S:1003 -Leu S:1004
7Pro S:1005 -Gln S:1006
8Ala U:1002 -Glu U:1003
9Pro U:1005 -Gln U:1006
10Gly U:1253 -Gly U:1254

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XCR)

(-) 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 B from PDB  Type:PROTEIN  Length:718
 aligned with GYRA_STAAN | Q99XG5 from UniProtKB/Swiss-Prot  Length:889

    Alignment length:719
                                                                                                                                                                                                                                                                1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
                                     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482         
          GYRA_STAAN      - ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MAELPQSRINERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRYTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG  491
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee...hhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhh.......hhhhh....eeee...hhhhhhhhhhhhhhhhhhhhhhhhh...ee.......ee....ee...hhhhhhhhh.....................................eeee..hhhhhhhhhhhhh..hhhhhhhhhhhhh.......-.........eeehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.......eehhhhhhhhhh.....hhhhhhhhhhhh..........eeee.................eeee.hhhh............eee......eee.......hhhhhhh...............hhhhhhhhhhhhhhh...hhhhhh............eee.hhhhhhhhhh.eeeeeee.eeeeee.....eeeeeee.....hhhhhhhhhhhhhhh.....eeeeee.........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh...hhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2xcr B  417 KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPLYKLTQGKQKYYVYNDRELDKLKSELNPTPKWSIARYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDF-AELPQSRINERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG 1491
                                   426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292      1302      1312      1322      1332      1342      1352      1362      1372      1382      1392      1402      1412      1422      1432      1442      1452      1462      1472      1482         
                                                                                                                                                                                                                                                             644 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
                                                                                                                                                                                                                                                              1002                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:719
 aligned with GYRA_STAAN | Q99XG5 from UniProtKB/Swiss-Prot  Length:889

    Alignment length:720
                                                                                                                                                                                                                                                                 1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
                                     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491
          GYRA_STAAN      - -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MAELPQSRINERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRYTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG  491
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhh.eeeee.................eeeee...........hhhhhh.hhhhhhhhhhhh..hhhhh........eeee.....hhhhhhhhhhhhhhhhhhhhhhhh..eee.......eee..eee...hhhhhhhhhh....................hhhhhhhhhh......eeee..hhhhhhhhhhhhh..hhhhhhhhhhhh........-.........eeehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhh..........eeee.................eeee..hhhhhh.........eee......eee.......hhhhhhh...............hhhhhhhhhhhhhhh...hhhhhh............eee...hhhhhhhh.eeeeeee.eeeeee.....eeeeeee.....hhhhhhhhhhhhhhh.....eeeeee.........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhh..hhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2xcr D  416 GKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPLYKLTQGKQKYYVYNDRELDKLKSELNPTPKWSIARYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDF-AELPQSRINERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG 1491
                                   425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635        |-|     1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381      1391      1401      1411      1421      1431      1441      1451      1461      1471      1481      1491
                                                                                                                                                                                                                                                              644 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
                                                                                                                                                                                                                                                               1002                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         


Chain E from PDB  Type:DNA  Length:20
                                                     
                2xcr E    1 aGCCGTAGGGCCCTACGGCT   20
                            |       10        20
                            1-5UA               


Chain F from PDB  Type:DNA  Length:20
                                                     
                2xcr F    1 aGCCGTAGGGCCCTACGGCT   20
                            |       10        20
                            1-5UA               


Chain S from PDB  Type:PROTEIN  Length:718
 aligned with GYRA_STAAN | Q99XG5 from UniProtKB/Swiss-Prot  Length:889

    Alignment length:719
                                                                                                                                                                                                                                                                 1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481         
          GYRA_STAAN      - -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MAELPQSRINERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRYTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQL  490
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhheee.....hhhhhhhhhh....eee.............hhhhhhhhhhhhhhhhhhh..hhhhh.........ee.....hhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eeeee..eeeee.hhhhhhhhh.........eeee..hhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhh.......-.........eeehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh.........eehhhhhhhhh......hhhhhhhhhhhh..........eeee.................eeee...hhhhhh........eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhh....hhhhh.............eee...hhhhhhhhh.ee..ee....eee.....eeeee.......hhhhhhhhhhhhhhh.....eeeeee.........eeeee......hhhhhhhhhhh......ee..eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2xcr S  416 GKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPLYKLTQGKQKYYVYNDRELDKLKSELNPTPKWSIARYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDF-AELPQSRINERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQL 1490
                                   425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635        |-|     1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381      1391      1401      1411      1421      1431      1441      1451      1461      1471      1481         
                                                                                                                                                                                                                                                              644 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                                                                                                                                                                                                                                                               1002                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        


Chain U from PDB  Type:PROTEIN  Length:717
 aligned with GYRA_STAAN | Q99XG5 from UniProtKB/Swiss-Prot  Length:889

    Alignment length:718
                                                                                                                                                                                                                                                                1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482        
          GYRA_STAAN      - ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MAELPQSRINERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRYTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQL  490
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_topoisoIV-2xcrU01 U:1033-1474                                                                                                                                                                                                                                                                                                                                                                                                                         ---------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_topoisoIV-2xcrU02 U:1033-1474                                                                                                                                                                                                                                                                                                                                                                                                                         ---------------- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_topoisoIV-2xcrU03 U:1033-1474                                                                                                                                                                                                                                                                                                                                                                                                                         ---------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_topoisoIV-2xcrU04 U:1033-1474                                                                                                                                                                                                                                                                                                                                                                                                                         ---------------- Pfam domains (4)
         Sec.struct. author .............eeeee.hhhhhhhhhhhh....eeeee...........hhhhhh.hhhhhhhhhhhh................eee....hhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eee......eee.hhhhhhhhh...........ee.......hhhhhhh..........eeee.........hhhhhh...hhhhhhhhhhh........-.........eeehhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.......eehhhhhhhhhhh....hhhhhhhhhhhh..........eeee.................eeee..hhhhh..........eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh....................eeee.hhhhhh.....eeeeeee..eeeee.....eeeee........hhhhhhhhhhhhh........eeee.........eeee.....hhhhhhhhhhhhh....eeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhh..hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2xcr U  417 KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPLYKLTQGKQKYYVYNDRELDKLKSELNPTPKWSIARYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDF-AELPQSRINERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQL 1490
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Chain V from PDB  Type:DNA  Length:20
                                                     
                2xcr V    1 AGCCGTAGGGCCCTACGGCT   20
                                    10        20


Chain W from PDB  Type:DNA  Length:18
                                                   
                2xcr W    2 GCCGTAGGGCCCTACGGC   19
                                    11
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: DNA_topoisoIV] (19)

(-) Gene Ontology  (14, 24)

Asymmetric Unit(hide GO term definitions)
Chain B,D,S,U   (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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  5.99.1.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        GYRA_STAAN | Q99XG5: 2xco 2xcq 2xcs 2xct 4bul 5cdm 5cdn 5cdo 5cdp 5cdq 5cdr 5iwi 5iwm 5npk 5npp
        GYRB_STAAN | P66937: 2xco 2xcq 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
2xcq THE 2.98A CRYSTAL STRUCTURE OF THE CATALYTIC CORE (B'A' REGION) OF STAPHYLOCOCCUS AUREUS DNA GYRASE
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