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(-) Description

Title :  CRYSTAL STRUCTURE OF YEFM-YOEB COMPLEX
 
Authors :  K. Kamada, F. Hanaoka
Date :  04 Jul 05  (Deposition) - 23 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (1x)
Biol. Unit 3:  A,B,C,D,E,F  (1x)
Keywords :  Yoeb, Yefm, Toxin, Antitoxin, Addiction Modules, Rnase, Inhibitor, Toxin Inhibitor/Toxin Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Kamada, F. Hanaoka
Conformational Change In The Catalytic Site Of The Ribonuclease Yoeb Toxin By Yefm Antitoxin
Mol. Cell V. 19 497 2005
PubMed-ID: 16109374  |  Reference-DOI: 10.1016/J.MOLCEL.2005.07.004
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTITOXIN YEFM
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidMODIFIED PET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneYEFM
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
 
Molecule 2 - TOXIN YOEB
    ChainsE, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET11A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneYOEB
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB  E 
Biological Unit 2 (1x)  CD F
Biological Unit 3 (1x)ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2A6Q)

(-) Sites  (0, 0)

(no "Site" information available for 2A6Q)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A6Q)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly D:7 -Pro D:8

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A6Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A6Q)

(-) Exons   (0, 0)

(no "Exon" information available for 2A6Q)

(-) 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:86
 aligned with YEFM_ECOLI | P69346 from UniProtKB/Swiss-Prot  Length:83

    Alignment length:86
                               1                                                                                  
                               |     7        17        27        37        47        57        67        77      
            YEFM_ECOLI    - ---MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKDIIE 83
               SCOP domains ---d2a6qa1 A:10-92 Antitoxin YefM                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeehhhhhhhhhhhhhhhhhhh..eeee.....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  2a6q A  7 GPHMRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKDIIE 92
                                    16        26        36        46        56        66        76        86      

Chain B from PDB  Type:PROTEIN  Length:58
 aligned with YEFM_ECOLI | P69346 from UniProtKB/Swiss-Prot  Length:83

    Alignment length:58
                               1                                                      
                               |     7        17        27        37        47        
            YEFM_ECOLI    - ---MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLL 55
               SCOP domains ---d2a6qb1 B:10-64 Antitoxin YefM                          SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeehhhhhhhhhhhhhhhhhhh..eeee......eeeeehhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  2a6q B  7 GPHMRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLL 64
                                    16        26        36        46        56        

Chain C from PDB  Type:PROTEIN  Length:86
 aligned with YEFM_ECOLI | P69346 from UniProtKB/Swiss-Prot  Length:83

    Alignment length:86
                               1                                                                                  
                               |     7        17        27        37        47        57        67        77      
            YEFM_ECOLI    - ---MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKDIIE 83
               SCOP domains d2a6qc_ C: Antitoxin YefM                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeehhhhhhhhhhhhhhhhhhh..eeee......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  2a6q C  7 GPHMRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKDIIE 92
                                    16        26        36        46        56        66        76        86      

Chain D from PDB  Type:PROTEIN  Length:58
 aligned with YEFM_ECOLI | P69346 from UniProtKB/Swiss-Prot  Length:83

    Alignment length:58
                               1                                                      
                               |     7        17        27        37        47        
            YEFM_ECOLI    - ---MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLL 55
               SCOP domains d2a6qd_ D: Antitoxin YefM                                  SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeehhhhhhhhhhhhhhhhhh...eeee.....eeeeeehhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  2a6q D  7 GPHMRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLL 64
                                    16        26        36        46        56        

Chain E from PDB  Type:PROTEIN  Length:84
 aligned with YOEB_ECOLI | P69348 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:84
                                    10        20        30        40        50        60        70        80    
            YOEB_ECOLI    1 MKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAACRYHY 84
               SCOP domains d2a6qe1 E:1-84 Toxin YoeB                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh........ee.hhhhh.eeeee.....eeeeee...eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  2a6q E  1 MKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAACRYHY 84
                                    10        20        30        40        50        60        70        80    

Chain F from PDB  Type:PROTEIN  Length:84
 aligned with YOEB_ECOLI | P69348 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:84
                                    10        20        30        40        50        60        70        80    
            YOEB_ECOLI    1 MKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAACRYHY 84
               SCOP domains d2a6qf_ F: Toxin YoeB                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh........ee.hhhhh..eeee.....eeeeee...eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  2a6q F  1 MKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAACRYHY 84
                                    10        20        30        40        50        60        70        80    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (2, 6)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2A6Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A6Q)

(-) Gene Ontology  (22, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (YEFM_ECOLI | P69346)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0015643    toxic substance binding    Interacting selectively and non-covalently with a toxic substance, a poisonous substance that causes damage to biological systems.
biological process
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0044010    single-species biofilm formation    A process in which planktonically growing microorganisms of the same species grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

Chain E,F   (YOEB_ECOLI | P69348)
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:0016892    endoribonuclease activity, producing 3'-phosphomonoesters    Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 3'-phosphomonoesters.
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043024    ribosomal small subunit binding    Interacting selectively and non-covalently with any part of the small ribosomal subunit.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
biological process
    GO:0006401    RNA catabolic process    The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
    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:0006402    mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
    GO:0098795    mRNA cleavage involved in gene silencing    Cleavage of an mRNA occurring as part of the mechanism of gene silencing.
    GO:1903507    negative regulation of nucleic acid-templated transcription    Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription.
    GO:0045947    negative regulation of translational initiation    Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0044010    single-species biofilm formation    A process in which planktonically growing microorganisms of the same species grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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 Related Entries

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

UniProtKB/Swiss-Prot
        YOEB_ECOLI | P693482a6r 2a6s 4v8x

(-) Related Entries Specified in the PDB File

2a6r YOEB UNDER PEG CONDITION
2a6s YOEB UNDER ISOPROPANOL CONDITION