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(-) Description

Title :  CRYSTAL STRUCTURE OF STAPH GYRASEB 24KDA IN COMPLEX WITH KIBDELOMYCIN
 
Authors :  J. Lu, S. Patel, N. Sharma, S. Soisson, R. Kishii, M. Takei, Y. Fukuda, K. S. B. Singh
Date :  30 Jun 14  (Deposition) - 30 Jul 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.94
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, Gyrase, 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 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
1XAM4Ligand/Ion(1R,4AS,5S,6S,8AR)-5-{[(5S)-1-(3-O-ACETYL-4-O-CARBAMOYL-6-DEOXY-2-O-METHYL-ALPHA-L-TALOPYRANOSYL)-4-HYDROXY-2-OXO-5-(PROPAN-2-YL)-2,5-DIHYDRO-1H-PYRROL-3-YL]CARBONYL}-6-METHYL-4-METHYLIDENE-1,2,3,4,4A,5,6,8A-OCTAHYDRONAPHTHALEN-1-YL 2,6-DIDEOXY-3-C-[(1S)-1-{[(3,DICHLORO-5-METHYL-1H-PYRROL-2-YL)CARBONYL]AMINO}ETHYL]-BETA-D-RIBO-HEXOPYRANOSIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1XAM1Ligand/Ion(1R,4AS,5S,6S,8AR)-5-{[(5S)-1-(3-O-ACETYL-4-O-CARBAMOYL-6-DEOXY-2-O-METHYL-ALPHA-L-TALOPYRANOSYL)-4-HYDROXY-2-OXO-5-(PROPAN-2-YL)-2,5-DIHYDRO-1H-PYRROL-3-YL]CARBONYL}-6-METHYL-4-METHYLIDENE-1,2,3,4,4A,5,6,8A-OCTAHYDRONAPHTHALEN-1-YL 2,6-DIDEOXY-3-C-[(1S)-1-{[(3,DICHLORO-5-METHYL-1H-PYRROL-2-YL)CARBONYL]AMINO}ETHYL]-BETA-D-RIBO-HEXOPYRANOSIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1XAM1Ligand/Ion(1R,4AS,5S,6S,8AR)-5-{[(5S)-1-(3-O-ACETYL-4-O-CARBAMOYL-6-DEOXY-2-O-METHYL-ALPHA-L-TALOPYRANOSYL)-4-HYDROXY-2-OXO-5-(PROPAN-2-YL)-2,5-DIHYDRO-1H-PYRROL-3-YL]CARBONYL}-6-METHYL-4-METHYLIDENE-1,2,3,4,4A,5,6,8A-OCTAHYDRONAPHTHALEN-1-YL 2,6-DIDEOXY-3-C-[(1S)-1-{[(3,DICHLORO-5-METHYL-1H-PYRROL-2-YL)CARBONYL]AMINO}ETHYL]-BETA-D-RIBO-HEXOPYRANOSIDE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1XAM1Ligand/Ion(1R,4AS,5S,6S,8AR)-5-{[(5S)-1-(3-O-ACETYL-4-O-CARBAMOYL-6-DEOXY-2-O-METHYL-ALPHA-L-TALOPYRANOSYL)-4-HYDROXY-2-OXO-5-(PROPAN-2-YL)-2,5-DIHYDRO-1H-PYRROL-3-YL]CARBONYL}-6-METHYL-4-METHYLIDENE-1,2,3,4,4A,5,6,8A-OCTAHYDRONAPHTHALEN-1-YL 2,6-DIDEOXY-3-C-[(1S)-1-{[(3,DICHLORO-5-METHYL-1H-PYRROL-2-YL)CARBONYL]AMINO}ETHYL]-BETA-D-RIBO-HEXOPYRANOSIDE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1XAM1Ligand/Ion(1R,4AS,5S,6S,8AR)-5-{[(5S)-1-(3-O-ACETYL-4-O-CARBAMOYL-6-DEOXY-2-O-METHYL-ALPHA-L-TALOPYRANOSYL)-4-HYDROXY-2-OXO-5-(PROPAN-2-YL)-2,5-DIHYDRO-1H-PYRROL-3-YL]CARBONYL}-6-METHYL-4-METHYLIDENE-1,2,3,4,4A,5,6,8A-OCTAHYDRONAPHTHALEN-1-YL 2,6-DIDEOXY-3-C-[(1S)-1-{[(3,DICHLORO-5-METHYL-1H-PYRROL-2-YL)CARBONYL]AMINO}ETHYL]-BETA-D-RIBO-HEXOPYRANOSIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:54 , SER A:55 , GLU A:58 , ASP A:81 , ARG A:84 , ILE A:86 , GLN A:91 , LYS A:93 , MET A:94 , ILE A:102 , LEU A:106 , HIS A:107 , ALA A:108 , GLY A:109 , GLY A:110 , LYS A:111 , THR A:173 , ILE A:175 , HOH A:2003BINDING SITE FOR RESIDUE XAM A2000
2AC2SOFTWAREASN B:54 , SER B:55 , GLU B:58 , ASP B:81 , ARG B:84 , ILE B:86 , GLN B:91 , LYS B:93 , ILE B:102 , HIS B:107 , ALA B:108 , GLY B:109 , GLY B:110 , LYS B:111 , PHE B:112 , HOH B:2001 , ARG C:200 , GLU C:201BINDING SITE FOR RESIDUE XAM B2000
3AC3SOFTWAREASN C:54 , SER C:55 , GLU C:58 , ASP C:81 , GLY C:85 , ILE C:86 , PRO C:87 , VAL C:101 , ILE C:102 , VAL C:105 , HIS C:107 , ALA C:108 , GLY C:109 , THR C:173 , ILE C:175BINDING SITE FOR RESIDUE XAM 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 , ALA D:98 , VAL D:101 , ILE D:102 , VAL D:105 , HIS D:107 , ALA D:108 , GLY D:109 , THR D:173 , ILE D:175BINDING SITE FOR RESIDUE XAM D2000

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4URM)

(-) 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:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...................................hhhhhhhhh........hhhhhhhh............eeeeeeee..ee....eeeee.......................hhhhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4urm A  25 LEAARKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGGKGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEG 231
                                    34        44        54        64        74        84        94       104      |127       137       147       157       167       177       187       197       207       217       227    
                                                                                                                111|                                                                                                          
                                                                                                                 125                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhh.eeeee...............hhhhhhhhh.........hhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee.....eeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4urm B  25 LEAARKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGGKFGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEG 231
                                    34        44        54        64        74        84        94       104       126       136       146       156       166       176       186       196       206       216       226     
                                                                                                                 112|                                                                                                          
                                                                                                                  125                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:191
                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...................................hhhhhhh.......hhhhhhhh............eeeeeeee..ee....eeeee.......................hhhhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4urm C  25 LEAARKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEG 231
                                    34        44        54        64        74        84        94       104    || 130       140       150       160       170       180       190       200       210       220       230 
                                                                                                              109|                                                                                                         
                                                                                                               126                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhh.eeeee...............hhhhhhhhh.....hhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4urm D  26 EAARKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEG 231
                                    35        45        55        65        75        85        95       105   ||  131       141       151       161       171       181       191       201       211       221       231
                                                                                                             109|                                                                                                         
                                                                                                              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 4URM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

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  GYRB_STAAU | P0A0K8
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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
        GYRB_STAAU | P0A0K8: 3g75 3g7b 3ttz 3u2d 3u2k 4plb 4uro 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
4urn CRYSTAL STRUCTURE OF STAPH PARE 24KDA IN COMPLEX WITH NOVOBIOCIN
4uro CRYSTAL STRUCTURE OF STAPH GYRASEB 24KDA IN COMPLEX WITH NOVOBIOCIN