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(-) Description

Title :  CHEMICAL SHIFT STRUCTURE OF COLICIN E9 DNASE DOMAIN WITH ITS COGNATE IMMUNITY PROTEIN IM9
 
Authors :  R. W. Montalvao, A. Cavalli, M. Vendruscolo
Date :  01 Jul 08  (Deposition) - 09 Dec 08  (Release) - 09 Dec 08  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B
Keywords :  Colicin E9, Immunity Protein Im9, Bacteriocin Immunity, Plasmid, Antibiotic, Antimicrobial, Bacteriocin, Endonuclease, Hydrolase, Metal-Binding, Nuclease, Zinc, Immune System/Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. W. Montalvao, A. Cavalli, X. Salvatella, T. L. Blundell, M. Vendruscolo
Structure Determination Of Protein-Protein Complexes Using Nmr Chemical Shifts: Case Of An Endonuclease Colicin-Immunity Protein Complex
J. Am. Chem. Soc. V. 130 15990 2008
PubMed-ID: 18980319
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COLICIN-E9 IMMUNITY PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Gene: IMM, CEIE9
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: IMME9, MICROCIN-E9 IMMUNITY PROTEIN
 
Molecule 2 - COLICIN-E9
    Chains: B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Fragment: UNP RESIDUES 450-582
    Gene: COL, CEI
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2K5X)

(-) Sites  (0, 0)

(no "Site" information available for 2K5X)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2K5X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2K5X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2K5X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2K5X)

(-) Exons   (0, 0)

(no "Exon" information available for 2K5X)

(-) Sequences/Alignments

NMR Structure
   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 IMM9_ECOLX | P13479 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:86
                                    10        20        30        40        50        60        70        80      
           IMM9_ECOLX     1 MELKHSISDYTEAEFLQLVTTICNADTSSEEELVKLVTHFEEMTEHPSGSDLIYYPKEGDDDSPSGIVNTVKQWRAANGKSGFKQG  86
               SCOP domains d2k5xa_ A: ImmE9 protein (Im9)                                                         SCOP domains
               CATH domains 2k5xA00 A:1-86  [code=1.10.1200.20, no name defined]                                   CATH domains
               Pfam domains Colicin_Pyocin-2k5xA01 A:1-85                                                        - Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhh.......hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2k5x A   1 MELKHSISDYTEAEFLQLVTTICNADTSSEEELVKLVTHFEEMTEHPSGSDLIYYPKEGDDDSPSGIVNTVKQWRAANGKSGFKQG  86
                                    10        20        30        40        50        60        70        80      


Chain B from PDB  Type:PROTEIN  Length:134
 aligned with CEA9_ECOLX | P09883 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:134
                                   458       468       478       488       498       508       518       528       538       548       558       568       578    
           CEA9_ECOLX   449 KESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRGK 582
               SCOP domains d2k5xb_ B: DNase domain of colicin E9                                                                                                  SCOP domains
               CATH domains 2k5xB00 B:1-134 Colicin e7 immunity protein. Chain B                                                                                   CATH domains
               Pfam domains --Colicin-DNase-2k5xB01 B:3-133                                                                                                      - Pfam domains
         Sec.struct. author ........ee..........hhhhhh.....ee.hhhhhhh....ee.hhhhhhhhhhhhhhhh.......hhhhhhhhhh..................eeee..hhhhh....hhh.eeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2k5x B   1 MESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRGK 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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)

NMR Structure
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

NMR Structure
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

NMR Structure
(-)
Clan: His-Me_finger (38)
(-)
Clan: no clan defined [family: Colicin_Pyocin] (11)

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (IMM9_ECOLX | P13479)
molecular function
    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   (CEA9_ECOLX | P09883)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
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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  CEA9_ECOLX | P09883
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 Related Entries

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

UniProtKB/Swiss-Prot
        CEA9_ECOLX | P09883: 1bxi 1emv 1fr2 1fsj 1v13 1v14 1v15 2gyk 2gze 2gzf 2gzg 2gzi 2gzj 2ivz 2vln 2vlo 2vlp 2vlq 2wpt 3o0e 4jml 5ew5
        IMM9_ECOLX | P13479: 1bxi 1e0h 1emv 1fr2 1imp 1imq 2gyk 2gze 2gzf 2gzg 2gzi 2gzj 2vln 2vlo 2vlp 2vlq 3gjn 3gkl 5ew5

(-) Related Entries Specified in the PDB File

4115 IMMUNITY PROTEIN IM9 CHEMICAL SHIFTS
4352 COLICIN E9 CHEMICAL SHIFTS
1emv IMMUNITY PROTEIN IM9 & COLICIN E9 COMPLEX
1fsj COLICIN E9
1imq IMMUNITY PROTEIN IM9