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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CARBOXY TERMINAL DOMAIN OF COLICIN E5 COMPLEXED WITH ITS INHIBITOR
 
Authors :  S. Yajima, S. Inoue, T. Ogawa, T. Nonaka, K. Ohsawa, H. Masaki
Date :  06 Mar 06  (Deposition) - 23 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  E,I
Keywords :  Alpha/Beta Protein, Protein-Inhibitor Protein Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yajima, S. Inoue, T. Ogawa, T. Nonaka, K. Ohsawa, H. Masaki
Structural Basis For Sequence-Dependent Recognition Of Colicin E5 Trnase By Mimicking The Mrna-Trna Interaction
Nucleic Acids Res. V. 34 6074 2006
PubMed-ID: 17099236  |  Reference-DOI: 10.1093/NAR/GKL729
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COLICIN-E5
    Chains: E
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBR328
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN, RESIDUES 2-116
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: FRAGMENT
 
Molecule 2 - COLICIN-E5 IMMUNITY PROTEIN
    Chains: I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBR328
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: IMME5, MICROCIN-E5 IMMUNITY PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : EI

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2DFX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro E:62 -Pro E:63
2Asn I:57 -Pro I:58

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DFX)

(-) 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 E from PDB  Type:PROTEIN  Length:92
 aligned with CEA5_ECOLX | P18000 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:92
                                    93       103       113       123       133       143       153       163       173  
           CEA5_ECOLX    84 LKIDQKIRGQMPERGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKYVVVNDRTGEVTQISDKTDPGWVDDSRIQWG 175
               SCOP domains d2dfxe_ E: automated matches                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.hhhhhhhhhhh...eeeeeeehhhhh......eeeeeeeeee..eeeeee.....eeee..............ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 2dfx E  20 LKIDQKIRGQMPERGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKYVVVNDRTGEVTQISDKTDPGWVDDSRIQWG 111
                                    29        39        49        59        69        79        89        99       109  


Chain I from PDB  Type:PROTEIN  Length:106
 aligned with IMM5_ECOLX | P13476 from UniProtKB/Swiss-Prot  Length:83

    Alignment length:106
                                                   1                                                                                  
                                     -         -   |     7        17        27        37        47        57        67        77      
           IMM5_ECOLX     - -----------------------MKLSPKAAIEVCNEAAKKGLWILGIDGGHWLNPGFRIDSSASWTYDMPEEYKSKIPENNRLAIENIKDDIENGYTAFIITLKM  83
               SCOP domains -----------------------d2dfxi1 I:26-108 Colicin E5 immunity protein ImmE5                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhh........hhhhhhhhhhhhhhhh..eeeeeeeee....eee.hhhhee......hhhhhhhhhhhhhhhhhhhhhh...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2dfx I   3 KLFEHTVLYDSGDAFFELKGNASMKLSPKAAIEVCNEAAKKGLWILGIDGGHWLNPGFRIDSSASWTYDMPEEYKSKIPENNRLAIENIKDDIENGYTAFIITLKM 108
                                    12        22        32        42        52        62        72        82        92       102
   Legend:   → Mismatch (orange background)
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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  (2, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (CEA5_ECOLX | P18000)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids 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.
    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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

Chain I   (IMM5_ECOLX | P13476)
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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    Asn I:57 - Pro I:58   [ RasMol ]  
    Pro E:62 - Pro E:63   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        CEA5_ECOLX | P18000: 2a8k 2djh 2fhz 3ao9 3vj7
        IMM5_ECOLX | P13476: 2fhz

(-) Related Entries Specified in the PDB File

2djh THE SAME PROTEIN WITHOUT INHIBITOR