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(-) Description

Title :  THE TWINNED 3.35A STRUCTURE OF S. AUREUS GYRASE COMPLEX WITH CIPROFLOXACIN AND DNA
 
Authors :  B. D. Bax, P. 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. Jo K. K. Brown, C. J. Lewis, E. May, O. Singh, C. Spitzfaden, C. Shen, A. Shi A. Theobald, A. Wohlkonig, N. D. Pearson, M. N. Gwynn
Date :  25 Apr 10  (Deposition) - 25 Aug 10  (Release) - 25 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.35
Chains :  Asym. Unit :  B,D,E,F,G,H,S,U,V,W,X,Y
Biol. Unit 1:  B,D,E,F,G,H  (1x)
Biol. Unit 2:  S,U,V,W,X,Y  (1x)
Keywords :  Isomerase-Dna-Antibiotic Complex (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: GYRB- C-TERMINAL 27KDA DOMAIN, RESIDUES 410-543 AND 580- 644, GYRA- N-TERMINAL 56KDA DOMAIN, RESIDUES 2-491
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 158879
    Other Details: C-TERMINUS GYRB (644) FUSED TO N-TERMINUS GYRA (1002). GREEK KEY DOMAIN (544-579) DELETED AND REPLACED WITH TWO RESIDUES, TG
    Strain: N315
 
Molecule 2 - 5'-D(TP*GP*TP*GP*CP*GP*GP*T)-3'
    Chains: E, V
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - 5'-D(AP*GP*CP*CP*GP*TP*AP*G)-3'
    Chains: F, W
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - 5'-D(GP*TP*AP*CP*CP*CP*AP*CP*GP*GP*CP*T)-3'
    Chains: G, X
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 5 - 5'-D(GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3'
    Chains: H, Y
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : BDEFGHSUVWXY
Biological Unit 1 (1x): BDEFGH      
Biological Unit 2 (1x):       SUVWXY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1CPF4Ligand/Ion1-CYCLOPROPYL-6-FLUORO-4-OXO-7-PIPERAZIN-1-YL-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID
2MN8Ligand/IonMANGANESE (II) ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CPF2Ligand/Ion1-CYCLOPROPYL-6-FLUORO-4-OXO-7-PIPERAZIN-1-YL-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID
2MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CPF2Ligand/Ion1-CYCLOPROPYL-6-FLUORO-4-OXO-7-PIPERAZIN-1-YL-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID
2MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP B:508 , ASP B:510BINDING SITE FOR RESIDUE MN B2492
02AC2SOFTWAREASP D:508 , ASP D:510BINDING SITE FOR RESIDUE MN D2492
03AC3SOFTWAREARG B:458 , SER B:1084 , DT E:8 , DG G:9 , MN G:2000 , DC H:12 , DA H:13BINDING SITE FOR RESIDUE CPF G1020
04AC4SOFTWAREARG D:458 , GLU D:477 , SER D:1084 , DG F:8 , MN F:2000 , DC G:12 , DC G:13 , DG H:9BINDING SITE FOR RESIDUE CPF H1020
05AC5SOFTWARECPF G:1020BINDING SITE FOR RESIDUE MN G2000
06AC6SOFTWARECPF H:1020BINDING SITE FOR RESIDUE MN F2000
07AC7SOFTWARECPF X:1020 , DG Y:9BINDING SITE FOR RESIDUE MN W2000
08AC8SOFTWARECPF Y:1020BINDING SITE FOR RESIDUE MN W2001
09AC9SOFTWAREASP S:508 , ASP S:510BINDING SITE FOR RESIDUE MN S2492
10BC1SOFTWAREASP U:508 , ASP U:510BINDING SITE FOR RESIDUE MN U2492
11BC2SOFTWAREARG S:458 , GLY S:459 , DG W:8 , MN W:2000 , DC X:12 , DC X:13 , DG Y:9BINDING SITE FOR RESIDUE CPF X1020
12BC3SOFTWARESER S:1084 , ARG U:458 , DT V:8 , MN W:2001 , DG X:9 , DC Y:12 , DA Y:13BINDING SITE FOR RESIDUE CPF Y1020

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XCT)

(-) 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:669
 aligned with GYRA_STAAN | Q99XG5 from UniProtKB/Swiss-Prot  Length:889

    Alignment length:670
                                                                                                                                                                                                       1      8        9                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         - |      |-       |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      - ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------MAELPQSR--------INERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRYTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG  491
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhh.eeeee..hhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhh..hhhhh........eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhh-.eeehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.......eehhhhhhhhhhhh...hhhhhhhhhhhh...........eee.................eee.hhhhhhhh.........eee......eee.......hhhhhhh...............hhhhhhhhhhhhhhh...hhhhh............eeeehhhhhhhhhhhheeeeeee..eeeee.....eeeee.......hhhhhhhhhhhhhh......eeeeee.........eeeee....hhhhhhhhhhhhh...eeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2xct B  417 KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNA-NERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG 1491
                                   426       436       446       456       466       476       486       496       506       516       526       536       580       590       600       610       620       630      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
                                                                                                                                                          545|                                                      637 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                                           580                                                       1010                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:669
 aligned with GYRA_STAAN | Q99XG5 from UniProtKB/Swiss-Prot  Length:889

    Alignment length:670
                                                                                                                                                                                                     1      8          9                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         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      - -------------------------------------------------------------------------------------------------------------------------------------------------------------------------MAELPQSR----------INERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRYTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG  491
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh.eeee.......hhhhhh.....eeee...........hhhhhh.hhhhhhhhhhhh..hhhhh.........eeee...hhhhhhhhhhhhhhhhh.hhhhhhhh.ee.............hhhhhhhhh........eee..hhhhhhhhhhhhhh.hhhhhhhhhhhh...-.eeehhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhh..........................hhhh.ee..hhhhhhhhh........eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhh....hhhhhh............eeehhhhhhhhhhhh...eeee.eeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhh.....eeeeee.........eeeee....hhhhhhhhhhhhh..eeee....eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2xct D  417 KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPTKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVY-NERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG 1491
                                   426       436       446       456       466       476       486       496       506       516       526       536       582       592       602       612       622       632      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
                                                                                                                                                         544|                                                       639 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                                          581                                                        1010                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 


Chain E from PDB  Type:DNA  Length:7
                                        
                2xct E    2 GTGCGGT    8


Chain F from PDB  Type:DNA  Length:7
                                        
                2xct F    2 GCCGTAG    8


Chain G from PDB  Type:DNA  Length:11
                                            
                2xct G    9 GTACCCACGGC   19
                                    18 


Chain H from PDB  Type:DNA  Length:12
                                             
                2xct H    9 GTACACCGCACA   20
                                    18  


Chain S from PDB  Type:PROTEIN  Length:667
 aligned with GYRA_STAAN | Q99XG5 from UniProtKB/Swiss-Prot  Length:889

    Alignment length:667
                                                                                                                                                                                                                11                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                                                                                                                                                                                                    1      8   9 |    12                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                                     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -        |2     |   9 |     |14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       
          GYRA_STAAN      - ------------------------------------------------------------------------------------------------------------------------------------------------------------------------MAELPQSR---INE-----RNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRYTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG  491
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee..hhhhhhhhh......eeee.......hhhhhhhhhhh.hhhhhhhh......hhhhh........eeeee.....hhhhhhhhhhhhhhhhhhhhhhh..eee...........hhhhhhhhh.......ee....hhhhhhhhhhhhh...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh.........eehhhhhhhhhhh....hhhhhhhhhhh............ee..................eee....hhhhhh........eee......eee.......hhhhhhh...............hhhhhhhhhhhhh.....hhhhhhhhh........eee..hhhhhhhhhh.eeeeeee.....eeee..eeeeee.......hhhhhhhhhhhhhhhh...................eeeee....hhhhhhhh.......eeeeeee...ee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2xct S  417 KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPTGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYARNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG 1491
                                   426       436       446       456       466       476       486       496       506       516       526       536       583       593       603       613       623       633      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      1234      1244      1254      1264      1274      1284      1294      1304      1314      1324      1334      1344      1354      1364      1374      1384      1394      1404      1414      1424      1434      1444      1454      1464      1474      1484       
                                                                                                                                                         544|                                                       640|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                                                                                                                                                          582                                                       1012                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               


Chain U from PDB  Type:PROTEIN  Length:665
 aligned with GYRA_STAAN | Q99XG5 from UniProtKB/Swiss-Prot  Length:889

    Alignment length:666
                                                                                                                                                                                                                11                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                                                                                                                                                                                    1      8   9 |   12                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                                     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -        |2     |   9 |    | 15        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---INE----RNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRYTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG  491
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_topoisoIV-2xctU01 U:1033-1474                                                                                                                                                                                                                                                                                                                                                                                                                         ----------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_topoisoIV-2xctU02 U:1033-1474                                                                                                                                                                                                                                                                                                                                                                                                                         ----------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_topoisoIV-2xctU03 U:1033-1474                                                                                                                                                                                                                                                                                                                                                                                                                         ----------------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_topoisoIV-2xctU04 U:1033-1474                                                                                                                                                                                                                                                                                                                                                                                                                         ----------------- Pfam domains (4)
         Sec.struct. author ............eeeee..hhhhhhhhhh.....eeeee...........hhhhhh.hhhhhhhhhhhh..hhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.eee...........hhhhhhhhhhh......ee.....hhhhhhhhhhh...hhhhhhhhhhhh...-..hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhh.............eee.................eee.hhhhhhhhh........eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhh.....hhhhhhhhh........ee...hhhhhhhhhhh........eeeee.......eeeeee.....hhhhhhhhhhhhhhh.....eeeeee.........eeeee....hhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2xct U  418 LADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPTKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVY-NITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG 1491
                                   427       437       447       457       467       477       487       497       507       517       527       537      |583       593       603       613       623       633     |1015      1025      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      
                                                                                                                                                        544|                                                       639 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                                         581                                                        1013                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              


Chain V from PDB  Type:DNA  Length:7
                                        
                2xct V    2 GTGCGGT    8


Chain W from PDB  Type:DNA  Length:6
                                       
                2xct W    3 CCGTAG    8


Chain X from PDB  Type:DNA  Length:11
                                            
                2xct X    9 GTACCCACGGC   19
                                    18 


Chain Y from PDB  Type:DNA  Length:11
                                            
                2xct Y    9 GTACACCGCAC   19
                                    18
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        GYRA_STAAN | Q99XG5: 2xco 2xcq 2xcr 2xcs 4bul 5cdm 5cdn 5cdo 5cdp 5cdq 5cdr 5iwi 5iwm 5npk 5npp
        GYRB_STAAN | P66937: 2xco 2xcq 2xcr 2xcs 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
2xcr THE 3.5A CRYSTAL STRUCTURE OF THE CATALYTIC CORE (B'A' REGION) OF STAPHYLOCOCCUS AUREUS DNA GYRASE COMPLEXED
2xcs THE 2.1A CRYSTAL STRUCTURE OF S. AUREUS GYRASE COMPLEX WITH GSK299423 AND DNA