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(-) Description

Title :  CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN WITH A MUTANT IMMUNITY PROTEIN IM9 (Y55F)
 
Authors :  P. S. Santi, O. O. Kolade, U. C. Kuhlmann, C. Kleanthous, A. M. Hemmings
Date :  11 May 06  (Deposition) - 18 Mar 08  (Release) - 06 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Protein Complex, 4-Helix Bundle, Dnase Domain, Hnh-Motif, Antibiotic-Antibiotic Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. C. Kuhlmann, P. S. Santi, O. O. Kolade, C. Kleanthous, A. M. Hemmings
Crystal Structure Of The Complex Of The Colicin E9 Dnase Domain With A Mutant Immunity Protein, Im9 (Y55F)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COLICIN-E9 IMMUNITY PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: IMM9_ECOLI
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI K12
    Organism Taxid: 83333
    Strain: K-12
    Synonym: IMME9, MICROCIN-E9 IMMUNITY PROTEIN
 
Molecule 2 - COLICIN-E9
    Chains: B
    EC Number: 3.1.21.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99A
    Expression System Strain: JM105
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: COLICIN E9,C-TERMINAL DOMAIN,DNASE DOMAIN
    Gene: COL, CEI
    Organism Scientific: ESCHERICHIA COLI K12
    Organism Taxid: 83333
    Strain: K-12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:102 , HIS B:127 , HIS B:131BINDING SITE FOR RESIDUE ZN B 301
2AC2SOFTWARESER A:28 , ARG B:5 , LEU B:101 , HIS B:102 , HIS B:103 , HIS B:127 , HIS B:131 , HOH B:518BINDING SITE FOR RESIDUE PO4 B 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GZG)

(-) 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:83
 aligned with IMM9_ECOLX | P13479 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:83
                                    12        22        32        42        52        62        72        82   
           IMM9_ECOLX     3 LKHSISDYTEAEFLQLVTTICNADTSSEEELVKLVTHFEEMTEHPSGSDLIYYPKEGDDDSPSGIVNTVKQWRAANGKSGFKQ  85
               SCOP domains d2gzga_ A: ImmE9 protein (Im9)                                                      SCOP domains
               CATH domains 2gzgA00 A:3-85  [code=1.10.1200.20, no name defined]                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhh.......hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 2gzg A   3 LKHSISDYTEAEFLQLVTTICNADTSSEEELVKLVTHFEEMTEHPSGSDLIYFPKEGDDDSPSGIVNTVKQWRAANGKSGFKQ  85
                                    12        22        32        42        52        62        72        82   


Chain B from PDB  Type:PROTEIN  Length:132
 aligned with CEA9_ECOLX | P09883 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:132
                                   459       469       479       489       499       509       519       529       539       549       559       569       579  
           CEA9_ECOLX   450 ESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRG 581
               SCOP domains d2gzgb_ B: DNase domain of colicin E9                                                                                                SCOP domains
               CATH domains 2gzgB00 B:2-133 Colicin e7 immunity protein. Chain B                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.ee............hhhhhh...ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh.......eeee..hhhhh....hhh.eeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gzg B   2 ESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRG 133
                                    11        21        31        41        51        61        71        81        91       101       111       121       131
   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 alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GZG)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(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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  2gzg
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  CEA9_ECOLX | P09883
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  IMM9_ECOLX | P13479
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  3.1.21.1
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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 2gzi 2gzj 2ivz 2k5x 2vln 2vlo 2vlp 2vlq 2wpt 3o0e 4jml 5ew5
        IMM9_ECOLX | P13479: 1bxi 1e0h 1emv 1fr2 1imp 1imq 2gyk 2gze 2gzf 2gzi 2gzj 2k5x 2vln 2vlo 2vlp 2vlq 3gjn 3gkl 5ew5

(-) Related Entries Specified in the PDB File

1bxi CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI COLICIN E9 DNASE DOMAIN WITH ITS COGNATE IMMUNITY PROTEIN IM9
1emv CRYSTAL STRUCTURE OF COLICIN E9 DNASE DOMAIN WITH ITS COGNATE IMMUNITY PROTEIN IM9 (1.7 ANGSTROMS)
2gyk CRYSTAL STRUCTURES OF THE COMPLEXES OF THE COLICIN E9 DNASE DOMAIN WITH MUTANT IMMUNITY PROTEINS
2gze CRYSTAL STRUCTURE OF THE COMPLEX OF THE COLICIN E9 DNASE DOMAIN WITH A MUTANT IMMUNITY PROTEIN, IM9 (Y55A)
2gzf CRYSTAL STRUCTURE OF THE COMPLEX OF THE COLICIN E9 DNASE DOMAIN WITH A MUTANT IMMUNITY PROTEIN, IM9 (Y54F)
2gzi CRYSTAL STRUCTURE OF THE COMPLEX OF THE COLICIN E9 DNASE DOMAIN WITH A MUTANT IMMUNITY PROTEIN, IM9 (V34A)
2gzj CRYSTAL STRUCTURE OF THE COMPLEX OF THE COLICIN E9 DNASE DOMAIN WITH A MUTANT IMMUNITY PROTEIN, IM9 (D51A)