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(-) Description

Title :  FOLLOWING EVOLUTIONARY PATHS TO HIGH AFFINITY AND SELECTIVITY PROTEIN-PROTEIN INTERACTIONS USING COLICIN7 AND IMMUNITY PROTEINS
 
Authors :  O. Dym, D. S. Tawfik
Date :  09 Mar 09  (Deposition) - 15 Sep 09  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.48
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Protein-Protein Complex, Bacteriocin Immunity, Antibiotic, Antimicrobial, Bacteriocin, Endonuclease, Hydrolase, Metal-Binding, Nuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. B. Levin, O. Dym, S. Albeck, S. Magdassi, A. H. Keeble, C. Kleanthous D. S. Tawfik
Following Evolutionary Paths To Protein-Protein Interaction With High Affinity And Selectivity
Nat. Struct. Mol. Biol. V. 16 1049 2009
PubMed-ID: 19749752  |  Reference-DOI: 10.1038/NSMB.1670

(-) Compounds

Molecule 1 - COLICIN-E9 IMMUNITY PROTEIN
    ChainsA, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET20
    Expression System StrainBL21 DE3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneIMM, CEIE9
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymIMME9, MICROCIN-E9 IMMUNITY PROTEIN
 
Molecule 2 - COLICIN-E7
    ChainsB, C
    EC Number3.1.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET20
    Expression System StrainBL21 DE3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 446-576
    GeneCOLE7, CEA
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B D
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:544 , HIS B:569 , HIS B:573 , HOH B:601BINDING SITE FOR RESIDUE ZN B 600
2AC2SOFTWAREHIS C:544 , HIS C:569 , HIS C:573 , HOH C:601BINDING SITE FOR RESIDUE ZN C 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GJN)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GJN)

(-) Sequences/Alignments

Asymmetric 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:82
 aligned with IMM9_ECOLX | P13479 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:82
                                    13        23        33        43        53        63        73        83  
          IMM9_ECOLX      4 KHSISDYTEAEFLQLVTTICNADTSSEEELVKLVTHFEEMTEHPSGSDLIYYPKEGDDDSPSGIVNTVKQWRAANGKSGFKQ   85
               SCOP domains d3gjna_ A: ImmE9 protein (Im9)                                                     SCOP domains
               CATH domains 3gjnA00 A:1004-1085  [code=1.10.1200.20, no name defined]                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhh.......hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                3gjn A 1004 KHSISDYTEAEFLQLVTTICDAEATSEEELDKLITHFEEMTEHPSGSDLIYWPKEGDDDSPSGIVNTVKQWRAANGKSGFKQ 1085
                                  1013      1023      1033      1043      1053      1063      1073      1083  

Chain B from PDB  Type:PROTEIN  Length:119
 aligned with CEA7_ECOLX | Q47112 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:125
                                   461       471       481       491       501       511       521       531       541       551       561       571     
          CEA7_ECOLX    452 KATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHRGK  576
               SCOP domains d3gjnb_ B: automated matches                                                                                                  SCOP domains
               CATH domains 3gjnB00 B:452-576 Colicin e7 immunity protein. Chain B                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee........hhhhhh.....ee.hhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhh......hhhhh.......eeee...------.ee...eeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                3gjn B  452 KATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHAEKP------VYDMDNISVVTPKRHIDIHRGK  576
                                   461       471       481       491       501       511       521       531       541      |  -   |   561       571     
                                                                                                                          548    555                     

Chain C from PDB  Type:PROTEIN  Length:120
 aligned with CEA7_ECOLX | Q47112 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:127
                                   459       469       479       489       499       509       519       529       539       549       559       569       
          CEA7_ECOLX    450 PGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHRGK  576
               SCOP domains d3gjnc_ C: automated matches                                                                                                    SCOP domains
               CATH domains 3gjnC00 C:450-576 Colicin e7 immunity protein. Chain B                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee........hhhhhhhh...ee.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh.......eeee..-------.ee...eeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gjn C  450 PGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHAEK-------VYDMDNISVVTPKRHIDIHRGK  576
                                   459       469       479       489       499       509       519       529       539       | -     | 559       569       
                                                                                                                           547     555                     

Chain D from PDB  Type:PROTEIN  Length:82
 aligned with IMM9_ECOLX | P13479 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:82
                                    13        23        33        43        53        63        73        83  
          IMM9_ECOLX      4 KHSISDYTEAEFLQLVTTICNADTSSEEELVKLVTHFEEMTEHPSGSDLIYYPKEGDDDSPSGIVNTVKQWRAANGKSGFKQ   85
               SCOP domains d3gjnd_ D: ImmE9 protein (Im9)                                                     SCOP domains
               CATH domains 3gjnD00 D:1004-1085  [code=1.10.1200.20, no name defined]                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhh.......hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                3gjn D 1004 KHSISDYTEAEFLQLVTTICDAEATSEEELDKLITHFEEMTEHPSGSDLIYWPKEGDDDSPSGIVNTVKQWRAANGKSGFKQ 1085
                                  1013      1023      1033      1043      1053      1063      1073      1083  

   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, 4)

Asymmetric Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,D   (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,C   (CEA7_ECOLX | Q47112)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        CEA7_ECOLX | Q471121m08 1mz8 1pt3 1ujz 1zns 1znv 2axc 2erh 2ivh 2jaz 2jb0 2jbg 3fbd 3gkl 3zfk 7cei
        IMM9_ECOLX | P134791bxi 1e0h 1emv 1fr2 1imp 1imq 2gyk 2gze 2gzf 2gzg 2gzi 2gzj 2k5x 2vln 2vlo 2vlp 2vlq 3gkl 5ew5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3GJN)