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(-) Description

Title :  RIBONUCLEASE FROM ESCHERICHIA COLI COMPLEXED WITH ITS INHIBTOR PROTEIN
 
Authors :  S. Yajima, K. Nakanishi, K. Takahashi, T. Ogawa, Y. Kezuka, M. Hidaka, T. Nonaka, K. Ohsawa, H. Masaki
Date :  27 May 04  (Deposition) - 01 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Protein Complex, Toxin/Toxin Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yajima, K. Nakanishi, K. Takahashi, T. Ogawa, M. Hidaka, Y. Kezuka, T. Nonaka, K. Ohsawa, H. Masaki
Relation Between Trnase Activity And The Structure Of Colicin D According To X-Ray Crystallography
Biochem. Biophys. Res. Commun. V. 322 966 2004
PubMed-ID: 15336558  |  Reference-DOI: 10.1016/J.BBRC.2004.07.206
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COLICIN D
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Gene: CDA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - COLICIN D IMMUNITY PROTEIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CDI
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: INHIBITOR PROTEIN
    Synonym: IMMD;
MICROCIN D IMMUNITY PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:651 , ASN A:672 , GLY A:673 , ASN A:687 , GLU B:50 , MET B:53 , ARG B:57 , LYS B:84 , HOH B:1002 , HOH B:1035BINDING SITE FOR RESIDUE MES B 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TFK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TFK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TFK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1TFK)

(-) Exons   (0, 0)

(no "Exon" information available for 1TFK)

(-) 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:94
 aligned with CEAD_ECOLX | P17998 from UniProtKB/Swiss-Prot  Length:697

    Alignment length:94
                                   613       623       633       643       653       663       673       683       693    
           CEAD_ECOLX   604 QLDKKYKHAGDFGISDTKKNRETLTKFRDAIEEHLSDKDTVEKGTYRREKGSKVYFNPNTMNVVIIKSNGEFLSGWKINPDADNGRIYLETGEL 697
               SCOP domains d1tfka_ A: Colicin D nuclease domain                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Colicin_D-1tfkA01 A:604-695                                                                 -- Pfam domains
         Sec.struct. author ....hhhhhhhhh......hhhhhhhhhhhhhhhhhh...ee..........eeee.....eeeee.....eeeeee....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 1tfk A 604 QLDKKYKHAGDFGISDTKKNRETLTKFRDAIEEHLSDKDTVEKGTYRREKGSKVYFNPNTMNVVIIKSNGEFLSGWKINPDADNGRIYLETGEL 697
                                   613       623       633       643       653       663       673       683       693    


Chain B from PDB  Type:PROTEIN  Length:86
 aligned with IMMD_ECOLX | P11899 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:86
                                                                                                               87 
                                    12        22        32        42        52        62        72        82    | 
           IMMD_ECOLX     3 KMAMIDLAKLFLASKITAIEFSERICVERRRLYGVKDLSPNILNCGEELFMAAERFEPDADRANYEIDDNGLKVEVRSILEKFKL-   -
               SCOP domains d1tfkb_ B: automated matches                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains Colicin_immun-1tfkB01 B:3-86                                                        -- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 1tfk B   3 KMAMIDLAKLFLASKITAIEFSERICVERRRLYGVKDLSPNILNCGEELFMAAERFEPDADRANYEIDDNGLKVEVRSILEKFKLH  88
                                    12        22        32        42        52        62        72        82
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1TFK)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Colicin_D] (3)
(-)
Clan: no clan defined [family: Colicin_immun] (3)

(-) Gene Ontology  (9, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CEAD_ECOLX | P17998)
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:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0005727    extrachromosomal circular DNA    Circular DNA structures that are not part of a chromosome.

Chain B   (IMMD_ECOLX | P11899)
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: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:0030153    bacteriocin immunity    A process that mediates resistance to a bacteriocin: any of a heterogeneous group of polypeptide antibiotics that are secreted by certain bacterial strains and are able to kill cells of other susceptible (frequently related) strains after adsorption at specific receptors on the cell surface. They include the colicins, and their mechanisms of action vary.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CEAD_ECOLX | P17998: 1tfo 1v74
        IMMD_ECOLX | P11899: 1tfo 1v74

(-) Related Entries Specified in the PDB File

1tfo SAME PROTEIN EXCEPT ADDITIONAL 10 RESIDUES AT THE N-TERMINAL