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(-) Description

Title :  R54A MUTANT OF E9 DNASE DOMAIN IN COMPLEX WITH IM9
 
Authors :  A. H. Keeble, L. A. Joachimiak, M. J. Mate, N. Meenan, N. Kirkpatrick, D. Baker, C. Kleanthous
Date :  15 Jan 08  (Deposition) - 20 May 08  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Binding, Protein-Protein Interaction, Metal-Binding, Antimicrobial, Bacteriocin Immunity, Hydrolase, Antibiotic, Bacteriocin, Endonuclease, Zinc, Colicin, Plasmid, Nuclease, Hth Motif (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. H. Keeble, L. A. Joachimiak, M. J. Mate, N. Meenan, N. Kirkpatrick, D. Baker, C. Kleanthous
Experimental And Computational Analyses Of The Energetic Basis For Dual Recognition Of Immunity Proteins By Colicin Endonucleases.
J. Mol. Biol. V. 379 745 2008
PubMed-ID: 18471830  |  Reference-DOI: 10.1016/J.JMB.2008.03.055

(-) Compounds

Molecule 1 - COLICIN-E9 IMMUNITY PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: IMME9, MICROCIN-E9 IMMUNITY PROTEIN
 
Molecule 2 - COLICIN E9
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: DNASE DOMAIN, RESIDUES 450-582
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1MLA3Ligand/IonMALONIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:102 , ASP B:104 , ARG B:120 , THR B:122 , HIS B:127 , HOH B:2134BINDING SITE FOR RESIDUE MLA B1135
2AC2SOFTWAREGLU B:2 , SER B:3 , LYS B:4 , ARG B:5 , ILE B:107 , HOH B:2135BINDING SITE FOR RESIDUE MLA B1136
3AC3SOFTWAREARG B:5 , HIS B:102 , HIS B:103BINDING SITE FOR RESIDUE MLA B1137

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VLP)

(-) 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: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 d2vlpa_ A: ImmE9 protein (Im9)                                                     SCOP domains
               CATH domains 2vlpA00 A:4-85  [code=1.10.1200.20, no name defined]                               CATH domains
               Pfam domains Colicin_Pyocin-2vlpA01 A:4-85                                                      Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhh.......hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 2vlp A   4 KHSISDYTEAEFLQLVTTICNADTSSEEELVKLVTHFEEMTEHPSGSDLIYYPKEGDDDSPSGIVNTVKQWRAANGKSGFKQ  85
                                    13        23        33        43        53        63        73        83  


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 d2vlpb_ B: automated matches                                                                                                           SCOP domains
               CATH domains 2vlpB00 B:1-134 Colicin e7 immunity protein. Chain B                                                                                   CATH domains
               Pfam domains --Colicin-DNase-2vlpB01 B:3-133                                                                                                      - Pfam domains
         Sec.struct. author ..hhhhh.ee..........hhhhhhhh...ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh.......eeee..hhhhh........eeeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vlp B   1 MESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFAKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRGK 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)

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  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: His-Me_finger (38)
(-)
Clan: no clan defined [family: Colicin_Pyocin] (11)

(-) 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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  2vlp
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  IMM9_ECOLX | P13479
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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 2k5x 2vln 2vlo 2vlq 2wpt 3o0e 4jml 5ew5
        IMM9_ECOLX | P13479: 1bxi 1e0h 1emv 1fr2 1imp 1imq 2gyk 2gze 2gzf 2gzg 2gzi 2gzj 2k5x 2vln 2vlo 2vlq 3gjn 3gkl 5ew5

(-) Related Entries Specified in the PDB File

1bxi CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI COLICIN E9 DNASEDOMAIN WITH ITS COGNATE IMMUNITY PROTEIN IM9
1e0h INHIBITOR PROTEIN IM9 BOUND TO ITS PARTNER E9 DNASE
1emv CRYSTAL STRUCTURE OF COLICIN E9 DNASE DOMAIN WITH ITSCOGNATE IMMUNITY PROTEIN IM9 (1.7 ANGSTROMS)
1fr2 CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN WITH A MUTANTIMMUNITY PROTEIN IM9(E41A)
1fsj CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN
1imp COLICIN E9 IMMUNITY PROTEIN IM9, NMR, 21 STRUCTURES
1imq COLICIN E9 IMMUNITY PROTEIN IM9, NMR, MINIMIZEDAVERAGE STRUCTURE
1v13 CRYSTAL STRUCTURE OF THE MUTANT HIS103ALA OF THE COLICIN E9 DNASE DOMAIN IN COMPLEX WITH ZN+2 (2.0 ANGSTROMS)
1v14 CRYSTAL STRUCTURE OF THE COLICIN E9, MUTANT HIS103ALA, IN COMPLEX WITH MG+2 AND DSDNA (RESOLUTION 2.9A)
1v15 CRYSTAL STRUCTURE OF THE COLICIN E9, MUTANT HIS103ALA, IN COMPLEX WITH ZN+2 AND DSDNA (RESOLUTION 2.4A)
2ivz STRUCTURE OF TOLB IN COMPLEX WITH A PEPTIDE OF THE COLICIN E9 T-DOMAIN
2vln N75A MUTANT OF E9 DNASE DOMAIN IN COMPLEX WITH IM9
2vlo K97A MUTANT OF E9 DNASE DOMAIN IN COMPLEX WITH IM9
2vlq F86A MUTANT OF E9 DNASE DOMAIN IN COMPLEX WITH IM9