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(-) Description

Title :  STREPTOGRAMIN B LYASE STRUCTURE
 
Authors :  M. Lipka, M. Bochtler
Date :  19 Jun 07  (Deposition) - 14 Oct 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Propeller, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Lipka, R. Filipek, M. Bochtler
Crystal Structure And Mechanism Of The Staphylococcus Cohnii Virginiamycin B Lyase (Vgb).
Biochemistry V. 47 4257 2008
PubMed-ID: 18341294  |  Reference-DOI: 10.1021/BI7015266
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - STREPTOGRAMIN B LACTONASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX5T-VGBB
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: VGBB
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS COHNII
    Organism Taxid: 29382

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1IOD2Ligand/IonIODIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:19BINDING SITE FOR RESIDUE IOD A 557
2AC2SOFTWARETHR A:264 , HOH A:482BINDING SITE FOR RESIDUE IOD A 558

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QC5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QC5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QC5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QC5)

(-) Exons   (0, 0)

(no "Exon" information available for 2QC5)

(-) Sequences/Alignments

Asymmetric/Biological 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:298
 aligned with O87275_9STAP | O87275 from UniProtKB/TrEMBL  Length:295

    Alignment length:298
                                1                                                                                                                                                                                                                                                                                                     
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286        
         O87275_9STAP     - ----MNFYLEEFNLSIPDSGPYGITSSEDGKVWFTQHKANKISSLDQSGRIKEFEVPTPDAKVMCLIVSSLGDIWFTENGANKIGKLSKKGGFTEYPLPQPDSGPYGITEGLNGDIWFTQLNGDRIGKLTADGTIYEYDLPNKGSYPAFITLGSDNALWFTENQNNSIGRITNTGKLEEYPLPTNAAAPVGITSGNDGALWFVEIMGNKIGRITTTGEISEYDIPTPNARPHAITAGKNSEIWFTEWGANQIGRITNDKTIQEYQLQTENAEPHGITFGKDGSVWFALKCKIGKLNLN 294
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh..eeeee........eeeeee.....eeeee....eeeee.....eeeee.......eeeeee.....eeeee....eeeee.....eeeee.......eeeeee.....eeeee....eeeee.....eeeee.......eeeeee.....eeeee....eeeee.....eeeee.......eeeeee.....eeeee....eeeee.....eeeee.......eeeeee.....eeeee....eeeee.....eeeee..........eee.....eeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qc5 A  -3 SEAWMNFYLEEFNLSIPDSGPYGITSSEDGKVWFTQHKANKISSLDQSGRIKEFEVPTPDAKVMCLIVSSLGDIWFTENGANKIGKLSKKGGFTEYPLPQPDSGPYGITEGLNGDIWFTQLNGDRIGKLTADGTIYEYDLPNKGSYPAFITLGSDNALWFTENQNNSIGRITNTGKLEEYPLPTNAAAPVGITSGNDGALWFVEIMGNKIGRITTTGEISEYDIPTPNARPHAITAGKNSEIWFTEWGANQIGRITNDNTIQEYQLQTENAEPHGITFGKDGSVWFALKCKIGKLNLN 294
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286
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  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 2QC5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QC5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2QC5)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O87275_9STAP | O87275)
molecular function
    GO:0016835    carbon-oxygen lyase activity    Catalysis of the breakage of a carbon-oxygen bond.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
biological process
    GO:0017001    antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    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.

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