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(-) Description

Title :  CRYSTAL STRUCTURE OF STAPH GYRASEB 24KDA IN COMPLEX WITH NOVOBIOCIN
 
Authors :  J. Lu, S. Patel, N. Sharma, S. Soisson, R. Kishii, M. Takei, Y. Fukuda, K. S. B. Singh
Date :  01 Jul 14  (Deposition) - 30 Jul 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Isomerase, Antibiotics, Topoisomerase Iv, Natural Product (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Lu, S. Patel, N. Sharma, S. M. Soisson, R. Kishii, M. Takei, Y. Fukuda K. J. Lumb, S. B. Singh
Structures Of Kibdelomycin Bound To Staphylococcus Aureus Gyrb And Pare Showed A Novel U-Shaped Binding Mode.
Acs Chem. Biol. V. 9 2023 2014
PubMed-ID: 24992706  |  Reference-DOI: 10.1021/CB5001197

(-) Compounds

Molecule 1 - DNA GYRASE SUBUNIT B
    Chains: A, B, C, D
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PGEX-4T3
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN, RESIDUES 1-231
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: GYRASEB

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1NOV4Ligand/IonNOVOBIOCIN
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NOV1Ligand/IonNOVOBIOCIN
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NOV1Ligand/IonNOVOBIOCIN
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1NOV1Ligand/IonNOVOBIOCIN
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1NOV1Ligand/IonNOVOBIOCIN

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:54 , SER A:55 , ASP A:57 , GLU A:58 , ASP A:81 , ARG A:84 , GLY A:85 , ILE A:86 , PRO A:87 , ASP A:89 , GLN A:91 , ILE A:102 , SER A:128 , ARG A:144 , HOH A:2002 , HOH A:2005 , HOH A:2013 , ARG D:200BINDING SITE FOR RESIDUE NOV A2000
2AC2SOFTWAREASN B:54 , ASP B:57 , GLU B:58 , ASP B:81 , ARG B:84 , GLY B:85 , ILE B:86 , PRO B:87 , ASP B:89 , GLN B:91 , ILE B:102 , ARG B:144 , HOH B:2001 , HOH B:2009BINDING SITE FOR RESIDUE NOV B2000
3AC3SOFTWAREASN C:54 , ASP C:57 , GLU C:58 , ASP C:81 , ARG C:84 , GLY C:85 , ILE C:86 , PRO C:87 , ASP C:89 , GLN C:91 , ILE C:102 , SER C:128 , ARG C:144BINDING SITE FOR RESIDUE NOV C2000
4AC4SOFTWAREASN D:54 , SER D:55 , GLU D:58 , ASP D:81 , ARG D:84 , GLY D:85 , ILE D:86 , PRO D:87 , ASP D:89 , ILE D:102 , SER D:128 , ARG D:144 , HOH D:2002BINDING SITE FOR RESIDUE NOV D2000

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4URO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4URO)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:187
                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhh.eeeee........ee....eehhhhhhh.hhhhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uro A  26 EAARKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEG 231
                                    35        45        55        65        75        85        95       105|      134       144       154       164       174       184       194       204       214       224       
                                                                                                         105|                                                                                                          
                                                                                                          125                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...................................hhhhhhhh.hhhhhhhhh............eeeeeeee..ee....eeeee.......................hhhhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4uro B  26 EAARKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEG 231
                                    35        45        55        65        75        85        95       105|      135       145       155       165       175       185       195       205       215       225      
                                                                                                         105|                                                                                                         
                                                                                                          126                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...................................hhhhhhhhhhhhhhhhh............eeeeeeee..ee....eeeee.......................hhhhhhhhhhhhhhhh........................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uro C  25 LEAARKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
                                    34        44        54        64        74        84        94       104||     135       145       155       165       175       185       195       205       215       225     
                                                                                                          105|                                                                                                       
                                                                                                           127                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:180
                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhh.eeeee.........hhhhhhhhhhhhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4uro D  25 LEAARKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIPAVEVILTVVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
                                    34        44        54        64        74        84     ||100    || 130       140       150       160       170       180       190       200       210       220       230
                                                                                            90|     105|                                                                                                        
                                                                                             97      126
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4URO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

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  GYRB_STAAU | P0A0K8
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 Related Entries

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

UniProtKB/Swiss-Prot
        GYRB_STAAU | P0A0K8: 3g75 3g7b 3ttz 3u2d 3u2k 4plb 4urm 5bs3 5cph 5ctu 5ctw 5ctx 5cty 5d6p 5d6q 5d7c 5d7d 5d7r 5iwi 5iwm

(-) Related Entries Specified in the PDB File

4url CRYSTAL STRUCTURE OF STAPH PARE43KDA IN COMPLEX WITH KBD
4urm CRYSTAL STRUCTURE OF STAPH GYRASEB 24KDA IN COMPLEX WITH KIBDELOMYCIN
4urn CRYSTAL STRUCTURE OF STAPH PARE 24KDA IN COMPLEX WITH NOVOBIOCIN