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(-) Description

Title :  RIBONUCLEASE DOMAIN OF COLICIN E3 IN COMPLEX WITH ITS IMMUNITY PROTEIN
 
Authors :  S. Carr, D. Walker, R. James, C. Kleanthous, A. M. Hemmings
Date :  28 Jun 00  (Deposition) - 28 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ribonuclease, Inhibition, Protein-Protein Interactions, Ribosome Inactivation, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Carr, D. Walker, R. James, C. Kleanthous, A. M. Hemmings
Inhibition Of A Ribosome Inactivating Ribonuclease: The Crystal Structure Of The Cytotoxic Domain Of Colicin E3 In Complex With Its Immunity Protein
Structure V. 8 949 2000
PubMed-ID: 10986462  |  Reference-DOI: 10.1016/S0969-2126(00)00186-6

(-) Compounds

Molecule 1 - COLICIN E3
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cellular Location: CYTOPLASM
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: RIBONUCLEASE DOMAIN RESIDUES 456-551
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: CO-EXPRESSED WITH A HIS-TAGGED IMMUNITY PROTEIN
 
Molecule 2 - IMMUNITY PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 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
1EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:5 , GLU A:19 , THR B:15 , TRP B:43 , HOH B:2038 , HOH B:2054 , HOH B:2087BINDING SITE FOR RESIDUE EDO B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E44)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1E44)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E44)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1E44)

(-) Exons   (0, 0)

(no "Exon" information available for 1E44)

(-) 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:84
 aligned with IMM3_ECOLX | P02984 from UniProtKB/Swiss-Prot  Length:85

    Alignment length:84
                                    11        21        31        41        51        61        71        81    
           IMM3_ECOLX     2 GLKLDLTWFDKSTEDFKGEEYSKDFGDDGSVMESLGVPFKDNVNNGCFDVIAEWVPLLQPYFNHQIDISDNEYFVSFDYRDGDW  85
               SCOP domains d1e44a_ A: Colicin E3 immunity protein                                               SCOP domains
               CATH domains 1e44A00 A:1-84  [code=3.10.50.20, no name defined]                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee.....eeeeee.......hhhhhhhh..........eee...hhhhhhhhhh........eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 1e44 A   1 GLKLDLTWFDKSTEDFKGEEYSKDFGDDGSVMESLGVPFKDNVNNGCFDVIAEWVPLLQPYFNHQIDISDNEYFVSFDYRDGDW  84
                                    10        20        30        40        50        60        70        80    


Chain B from PDB  Type:PROTEIN  Length:96
 aligned with CEA3_ECOLX | P00646 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:96
                                   465       475       485       495       505       515       525       535       545      
           CEA3_ECOLX   456 GFKDYGHDYHPAPKTENIKGLGDLKPGIPKTPKQNGGGKRKRWTGDKGRKIYEWDSQHGELEGYRASDGQHLGSFDPKTGNQLKGPDPKRNIKKYL 551
               SCOP domains d1e44b_ B: Ribonuclease domain of colicin E3                                                     SCOP domains
               CATH domains 1e44B00 B:1-96 Ribonuclease domain of colicin e3 (Residues 456-551)                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhh......hhhhh.....eee...............eeee....eeeeee....eeeeee..........................hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 1e44 B   1 GFKDYGHDYHPAPKTENIKGLGDLKPGIPKTPKQNGGGKRKRWTGDKGRKIYEWDSQHGELEGYRASDGQHLGSFDPKTGNQLKGPDPKRNIKKYL  96
                                    10        20        30        40        50        60        70        80        90
   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 beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E44)

(-) Gene Ontology  (14, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IMM3_ECOLX | P02984)
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.

Chain B   (CEA3_ECOLX | P00646)
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: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:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    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:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
biological process
    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.
    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.

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  1e44
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 Related Entries

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

UniProtKB/Swiss-Prot
        CEA3_ECOLX | P00646: 1jch 1ujw 2b5u 4udm 4v5k
        IMM3_ECOLX | P02984: 1jch 2b5u 3eip 4udm

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1E44)