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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COLICIN E2 DNASE-IM2 COMPLEX
 
Authors :  J. A. Wojdyla, C. Kleanthous
Date :  07 Oct 11  (Deposition) - 21 Mar 12  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Protein-Protein Complex, Dnase, High Affinity, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Wojdyla, S. J. Fleishman, D. Baker, C. Kleanthous
Structure Of The Ultra-High-Affinity Colicin E2 Dnase-Im2 Complex.
J. Mol. Biol. V. 417 79 2012
PubMed-ID: 22306467  |  Reference-DOI: 10.1016/J.JMB.2012.01.019

(-) Compounds

Molecule 1 - COLICIN-E2 IMMUNITY PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21D
    Expression System Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: IMM, CEIB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: IMME2, MICROCIN-E2 IMMUNITY PROTEIN
 
Molecule 2 - COLICIN-E2
    Chains: B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21D
    Expression System Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNASE DOMAIN (UNP RESIDUES 449-581)
    Gene: COL, CEAB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2ZN1Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:102 , HIS B:127 , HIS B:131 , HOH B:385 , HOH B:386 , HOH B:388 , HOH B:393BINDING SITE FOR RESIDUE ZN B 135
2AC2SOFTWAREARG B:54 , GLU B:100 , LEU B:101 , HOH B:221BINDING SITE FOR RESIDUE CA B 136

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U43)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3U43)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U43)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3U43)

(-) Exons   (0, 0)

(no "Exon" information available for 3U43)

(-) 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:92
 aligned with IMM2_ECOLX | P04482 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:92
                                                                                                              86        
                                    12        22        32        42        52        62        72        82   |     -  
           IMM2_ECOLX     3 LKHSISDYTEAEFLEFVKKICRAEGATEEDDNKLVREFERLTEHPDGSDLIYYPRDDREDSPEGIVKEIKEWRAANGKSGFKQG--------   -
               SCOP domains d3u43a_ A: automated matches                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhh.......hhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 3u43 A   3 LKHSISDYTEAEFLEFVKKICRAEGATEEDDNKLVREFERLTEHPDGSDLIYYPRDDREDSPEGIVKEIKEWRAANGKSGFKQGLEHHHHHH  94
                                    12        22        32        42        52        62        72        82        92  


Chain B from PDB  Type:PROTEIN  Length:132
 aligned with CEA2_ECOLX | P04419 from UniProtKB/Swiss-Prot  Length:581

    Alignment length:132
                                   459       469       479       489       499       509       519       529       539       549       559       569       579  
           CEA2_ECOLX   450 SKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKNFDDFRKKFWEEVSKDPDLSKQFKGSNKTNIQKGKAPFARKKDQVGGRERFELHHDKPISQDGGVYDMNNIRVTTPKRHIDIHRGK 581
               SCOP domains d3u43b_ B: automated matches                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh.ee..........hhhhhhhh...ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh.......eeee..hhhhh........eeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3u43 B   3 SKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKNFDDFRKKFWEEVSKDPDLSKQFKGSNKTNIQKGKAPFARKKDQVGGRERFELHHDKPISQDGGVYDMNNIRVTTPKRHIDIHRGK 134
                                    12        22        32        42        52        62        72        82        92       102       112       122       132
   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 Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U43)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U43)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (IMM2_ECOLX | P04482)
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   (CEA2_ECOLX | P04419)
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.
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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  3u43
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 Related Entries

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

UniProtKB/Swiss-Prot
        CEA2_ECOLX | P04419: 2ysu
        IMM2_ECOLX | P04482: 2no8 2wpt

(-) Related Entries Specified in the PDB File

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