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(-) Description

Title :  CRYSTAL STRUCTURE OF STAPH PARE43KDA IN COMPLEX WITH KBD
 
Authors :  J. Lu, S. Patel, N. Sharma, S. Soisson, R. Kishii, M. Takei, Y. Fukuda, K. S. B. Singh
Date :  30 Jun 14  (Deposition) - 16 Jul 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Isomerase, Antibiotics, Natural Product, Kibdelomycin, Gyrase, Topoisomerase Iv (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 TOPOISOMERASE IV, B SUBUNIT
    Chains: A, B
    EC Number: 5.99.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PGEX-4T3
    Expression System Vector Type: PLASMID
    Fragment: 43KDA N-TERMINAL DOMAIN, RESIDUES 1-406
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Other Details: KIBDELOMYCIN
    Synonym: TOPOISOMERASE IV PARE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1XAM2Ligand/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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:49 , SER A:50 , GLU A:53 , ASP A:76 , ARG A:79 , MET A:81 , PRO A:82 , HIS A:86 , THR A:92 , ILE A:96 , LEU A:100 , HIS A:101 , ALA A:102 , GLY A:103 , THR A:168 , HOH A:2004 , HOH A:2008 , HOH A:2009BINDING SITE FOR RESIDUE XAM A2000
2AC2SOFTWAREASN B:49 , SER B:50 , GLU B:53 , ASP B:76 , ARG B:79 , MET B:81 , HIS B:86 , LYS B:87 , THR B:92 , LEU B:100 , HIS B:101 , ALA B:102 , GLY B:103 , GLY B:104 , THR B:168 , HOH B:2003 , HOH B:2007 , HOH B:2008BINDING SITE FOR RESIDUE XAM B2000

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4URL)

(-) 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:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeee..............hhhhhhhhh.......hhhhhhhheeeeeeeeee..eeeeeeee...ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee......eeeeee...hhhhhhhhhh.........eeeeeee..eeeeeeeee......eeeeee..ee....hhhhhhhhhhhhhhhhhhhhhh.........hhhhhh..eeeeeeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4url A  18 EGLEAVRKRPGMYIGSTDKRGLHHLVYEIVDNSVDEVLNGYGNEIDVTINKDGSISIEDNGRGMPTGIHKSGKPTVEVIFTVLHAGHGVGASVVNALSEWLEVEIHRDGNIYHQSFKNGGSPSSGLVKKGKTKKTGTKVTFKPDDTIFKASTSFNFDVLSERLQESAFLLKNLKITLNDLRSGKERQEHYHYEEGIKEFVSYVNEGKEVLHDVATFSGEANGIEVDVAFQYNDQYSESILSFVNNVRTKDGGTHEVGFKTAMTRVFNDYARRINELKTDKNLDGNDIREGLTAVVSVRIPEELLQFKSKLGTSEARSAVDSVVADKLPFYLEEKGQLSKSLVKKAIKAQQAREAARKAREDARS 400
                                    27        37        47        57        67        77        87        97     ||121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       312       322       332     ||346       356       366       376       386       396    
                                                                                                               103|                                                                                                                                                                                            309|                        338|                                                         
                                                                                                                118                                                                                                                                                                                             311                         343                                                         


Chain B from PDB  Type:PROTEIN  Length:363
                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeee..............hhhhhhhhh.......hhhhhhhheeeeeeeeee..eeeeeeee...ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee......eeeeee...hhhhhhhhhh.........eeeeeee..eeeeeeeee......eeeeee..ee....hhhhhhhhhhhhhhhhhhhhhh..........hhhhhh..eeeeeeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4url B  20 LEAVRKRPGMYIGSTDKRGLHHLVYEIVDNSVDEVLNGYGNEIDVTINKDGSISIEDNGRGMPTGIHKSGKPTVEVIFTVLHAGGGVGASVVNALSEWLEVEIHRDGNIYHQSFKNGGSPSSGLVKKGKTKKTGTKVTFKPDDTIFKASTSFNFDVLSERLQESAFLLKNLKITLNDLRSGKERQEHYHYEEGIKEFVSYVNEGKEVLHDVATFSGEANGIEVDVAFQYNDQYSESILSFVNNVRTKDGGTHEVGFKTAMTRVFNDYARRINELKTKDKNLDGNDIREGLTAVVSVRIPEELLQFTKSKLGTSEARSAVDSVVADKLPFYLEEKGQLSKSLVKKAIKAQQAREAARKAREDAR 399
                                    29        39        49        59        69        79        89        99    || 123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333    || 346       356       366       376       386       396   
                                                                                                              104|                                                                                                                                                                                                                        338|                                                         
                                                                                                               119                                                                                                                                                                                                                         342
   Legend:   → Mismatch (orange background)
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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 4URL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4URL)

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(-) Related Entries Specified in the PDB File

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