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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, Israel Structural Proteomics Center (Ispc)
Date :  11 Mar 09  (Deposition) - 08 Sep 09  (Release) - 08 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Protein-Protein Complex, Structural Genomics, Israel Structural Proteomics Center, Ispc, Bacteriocin Immunity, Plasmid, Antibiotic, Antimicrobial, Bacteriocin, Endonuclease, Hydrolase, Metal-Binding, Nuclease, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Bernath, O. Dym, S. Albeck, S. Magdassi, A. Keeble, C. Kleanthous, D. S. Tawfik
Following Evolutionary Paths To High Affinity And Selectivity Protein-Protein Interactions
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COLICIN-E9 IMMUNITY PROTEIN
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET20
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 446-576
    Gene: COLE7, CEA
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - COLICIN-E7
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET20
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: IMM, CEIE9
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: IMME9, MICROCIN-E9 IMMUNITY PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B 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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:544 , HIS A:569 , HIS A:573BINDING SITE FOR RESIDUE ZN A 600
2AC2SOFTWAREHIS B:544 , ALA B:545 , HIS B:569 , HIS B:573BINDING SITE FOR RESIDUE ZN B 600

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GKL)

(-) 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: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 d3gkla_ A: automated matches                                                                                                    SCOP domains
               CATH domains 3gklA00 A:450-576 Colicin e7 immunity protein. Chain B                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee........hhhhhh.....ee.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..................eeee..-------.ee...eeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gkl A  450 PGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHAEK-------VYDMDNISVVTPKRHIDIHRGK  576
                                   459       469       479       489       499       509       519       529       539       | -     | 559       569       
                                                                                                                           547     555                     


Chain B 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 d3gklb_ B: automated matches                                                                                                    SCOP domains
               CATH domains 3gklB00 B: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
                3gkl B  450 PGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHAEK-------VYDMDNISVVTPKRHIDIHRGK  576
                                   459       469       479       489       499       509       519       529       539       | -     | 559       569       
                                                                                                                           547     555                     


Chain C 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 d3gklc_ C: ImmE9 protein (Im9)                                                     SCOP domains
               CATH domains 3gklC00 C:1004-1085  [code=1.10.1200.20, no name defined]                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhh.......hhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                3gkl C 1004 KHSISDYTEAEFLQLVATICDADATSEEELDKLITHFGEMTEHPSGSDLIYYPEEGDDDSPSGIVNTVKQWRAANGKSGFKQ 1085
                                  1013      1023      1033      1043      1053      1063      1073      1083  


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 d3gkld_ D: ImmE9 protein (Im9)                                                     SCOP domains
               CATH domains 3gklD00 D:1004-1085  [code=1.10.1200.20, no name defined]                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.......hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                3gkl D 1004 KHSISDYTEAEFLQLVATICDADATSEEELDKLITHFGEMTEHPSGSDLIYYPEEGDDDSPSGIVNTVKQWRAANGKSGFKQ 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
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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.

Chain C,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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CEA7_ECOLX | Q47112: 1m08 1mz8 1pt3 1ujz 1zns 1znv 2axc 2erh 2ivh 2jaz 2jb0 2jbg 3fbd 3gjn 3zfk 7cei
        IMM9_ECOLX | P13479: 1bxi 1e0h 1emv 1fr2 1imp 1imq 2gyk 2gze 2gzf 2gzg 2gzi 2gzj 2k5x 2vln 2vlo 2vlp 2vlq 3gjn 5ew5

(-) Related Entries Specified in the PDB File

3gjn THE SAME PROTEIN COMPLEX, DIFFERENT MUTATIONS