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(-) Description

Title :  NEW INSIGHTS INTO THE MECHANISM OF BACTERIAL TYPE III TOXIN-ANTITOXIN SYSTEMS: SELECTIVE TOXIN INHIBITION BY A NON-CODING RNA PSEUDOKNOT
 
Authors :  F. L. Short, X. Y. Pei, T. R. Blower, S. L. Ong, B. F. Luisi, G. P. C. Salmond
Date :  09 May 12  (Deposition) - 26 Dec 12  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,G
Biol. Unit 1:  A,G  (3x)
Keywords :  Toxin-Antitoxin Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. L. Short, X. Y. Pei, T. R. Blower, S. L. Ong, P. C. Fineran, B. F. Luisi, G. P. C. Salmond
Selectivity And Self-Assembly In The Control Of A Bacterial Toxin By An Antitoxic Noncoding Rna Pseudoknot.
Proc. Natl. Acad. Sci. Usa V. 110 E241 2013
PubMed-ID: 23267117  |  Reference-DOI: 10.1073/PNAS.1216039110

(-) Compounds

Molecule 1 - TOXN
    Atcc: 33679
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PFLS67
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector: PET21B
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS THURINGIENSIS
    Organism Taxid: 1428
    Other Details: ENVIRONMENT ISOLATED FROM SCOTLAND SOIL, U.K
    Plasmid: PAW63
    Strain: KURSTAKI HD-73
 
Molecule 2 - TOXI
    Atcc: 33679
    Chains: G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PFLS44
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector: PACYC184
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS THURINGIENSIS
    Organism Taxid: 1428
    Other Details: ENVIRONMENT ISOLATED FROM SCOTLAND SOIL, U.K
    Plasmid: PAW63
    Strain: KURSTAKI HD-73

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AG
Biological Unit 1 (3x): AG

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1A231Mod. NucleotideADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1A233Mod. NucleotideADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:72 , GLU A:76 , U G:15 , U G:16BINDING SITE FOR RESIDUE MPD A1173

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:142 -Gly A:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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    
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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:168
 aligned with TOXN_BACTK | Q3YN09 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:168
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164        
           TOXN_BACTK     5 DNPKFHTISTEYIDYLREADSKVPFNKDEQHSRPYVGVLEKINGHDYFVPLTSRNDKNFNSQVSVKLFDNDEKRIGVLLVNNMIPVPEKECKEIDIAEKTAADPQYGNLMLKQYLFLKENMDRVTNKVEKVYKDVTVQGKPSHKQKFLKGVCCDFPKLEEKCQEYKER 172
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeehhhhhhhhhhhh.............eeee.........eeeeee.......hhh.eeeee.....eeeeee.hhhee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ato A   5 DNPKFHTISTEYIDYLREADSKVPFNKDEQHSRPYVGVLEKINGHDYFVPLTSRNDKNFNSQVSVKLFDNDEKRIGVLLVNNMIPVPEKECKEIDIAEKTAADPQYGNLMLKQYLFLKENMDRVTNKVEKVYKDVTVQGKPSHKQKFLKGVCCDFPKLEEKCQEYKER 172
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164        


Chain G from PDB  Type:RNA  Length:34
                                                                  
                 4ato G   1 AAAUUGGUGUAACCUUACCGUAGUAGGUGCUAAa  34
                                    10        20        30   |
                                                            34-A23
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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 4ATO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (TOXN_BACTK | Q3YN09)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006276    plasmid maintenance    The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division.

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