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(-) Description

Title :  STRUCTURAL CHARACTERIZATION OF THE INTERACTION OF COLICIN A, COLICIN N, AND TOLB WITH THE TOLAIII TRANSLOCON
 
Authors :  C. Li
Date :  19 Jan 11  (Deposition) - 25 Jan 12  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cola, Tola, Complex, Translocation, Cola Binds To Tola, Methylation, Protein Transport-Toxin Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Li, Y. Zhang, M. Vankemmelbeke, O. Hecht, F. S. Aleanizy, C. Macdonald, G. R. Moore, R. James, C. N. Penfold
Structural Evidence That Colicin A Protein Binds To A Novel Binding Site Of Tola Protein In Escherichia Coli Periplasm.
J. Biol. Chem. V. 287 19048 2012
PubMed-ID: 22493500  |  Reference-DOI: 10.1074/JBC.M112.342246

(-) Compounds

Molecule 1 - PROTEIN TOLA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentTOLA DOMAIN III, RESIDUES 302-421
    GeneTOLA, CIM, EXCC, LKY, B0739, JW0729
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK-12
 
Molecule 2 - COLICIN-A
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentCOLA, RESIDUES 53-107
    GeneCAA, COLA
    Organism ScientificCITROBACTER FREUNDII
    Organism Taxid546

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1MLY1Mod. Amino AcidN-DIMETHYL-LYSINE
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:352 , TYR A:353 , ASP A:354 , SER A:356 , ARG A:366BINDING SITE FOR RESIDUE TRS A 501

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:363 -A:388

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QDR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QDR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QDR)

(-) Exons   (0, 0)

(no "Exon" information available for 3QDR)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:93
 aligned with TOLA_ECOLI | P19934 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:93
                                   338       348       358       368       378       388       398       408       418   
           TOLA_ECOLI   329 NNGASGADINNYAGQIKSAIESKFYDASSYAGKTCTLRIKLAPDGMLLDIKPEGGDPALCQAALAAAKLAKIPKPPSQAVYEVFKNAPLDFKP 421
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh...hhhhhh...eeeeeee.....eeeeeeeeehhhhhhhhhhhhh........hhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 3qdr A 329 NNGASGADINNYAGQIKSAIESkFYDASSYAGKTCTLRIKLAPDGMLLDIKPEGGDPALCQAALAAAKLAKIPKPPSQAVYEVFKNAPLDFKP 421
                                   338       348  |    358       368       378       388       398       408       418   
                                                351-MLY                                                                  

Chain B from PDB  Type:PROTEIN  Length:49
 aligned with CEA_CITFR | P04480 from UniProtKB/Swiss-Prot  Length:592

    Alignment length:49
                                    66        76        86        96         
            CEA_CITFR    57 SYNTPWGKVIINAAGQPTMNGTVMTADNSSMVPYGRGFTRVLNSLVNNP 105
               SCOP domains ------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eeee.......ee..ee......eeeee..eeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------- Transcript
                 3qdr B  57 SYNTPWGKVIINAAGQPTMNGTVMTADNSSMVPYGRGFTRVLNSLVNNP 105
                                    66        76        86        96         

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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 3QDR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QDR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QDR)

(-) Gene Ontology  (17, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TOLA_ECOLI | P19934)
molecular function
    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:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0043213    bacteriocin transport    The directed movement of a bacteriocin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Bacteriocins are a group of antibiotics produced by bacteria and are encoded by a group of naturally occurring plasmids, e.g. Col E1. Bacteriocins are toxic to bacteria closely related to the bacteriocin producing strain.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0071237    cellular response to bacteriocin    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a bacteriocin stimulus. A bacteriocin is a protein substance released by certain bacteria that kills but does not lyse closely related strains of bacteria. Specific bacteriocins attach to specific receptors on cell walls and induce specific metabolic block, e.g. cessation of nucleic acid or protein synthesis of oxidative phosphorylation.
    GO:0017038    protein import    The targeting and directed movement of proteins into a cell or organelle. Not all import involves an initial targeting event.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
cellular component
    GO:0032153    cell division site    The eventual plane of cell division (also known as cell cleavage or cytokinesis) in a dividing cell. In Eukaryotes, the cleavage apparatus, composed of septin structures and the actomyosin contractile ring, forms along this plane, and the mitotic, or meiotic, spindle is aligned perpendicular to the division plane. In bacteria, the cell division site is generally located at mid-cell and is the site at which the cytoskeletal structure, the Z-ring, assembles.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B   (CEA_CITFR | P04480)
molecular function
    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).
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0050829    defense response to Gram-negative bacterium    Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CEA_CITFR | P044803iax
        TOLA_ECOLI | P199341s62 1tol 3qdp

(-) Related Entries Specified in the PDB File

3qdp