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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MUTANT N560A OF THE NUCLEASE DOMAIN OF COLE7 IN COMPLEX WITH IM7
 
Authors :  H. Huang, H. S. Yuan
Date :  07 Dec 06  (Deposition) - 03 Apr 07  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Hydrolase/Inhibitor, Hydrolase-Inhibitor Complex, Zinc, Toxin, Plasmid, Nuclease, Hydrolase, Antibiotic, H-N-H Motif, Bacteriocin, Endonuclease, Metal-Binding, Antimicrobial, Dna Hydrolysis, Bacteriocin Immunity, His Metal Finger Motif (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Huang, H. S. Yuan
The Conserved Asparagine In The Hnh Motif Serves An Important Structural Role In Metal Finger Endonucleases.
J. Mol. Biol. V. 368 812 2007
PubMed-ID: 17368670  |  Reference-DOI: 10.1016/J.JMB.2007.02.044

(-) Compounds

Molecule 1 - COLICIN-E7 IMMUNITY PROTEIN
    Chains: A, C
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE70
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 316407
    Strain: W3110
    Synonym: COLICIN E7 IMMUNITY PROTEIN, IMME7, MICROCIN-E7 IMMUNITY PROTEIN
 
Molecule 2 - COLICIN E7
    Chains: B, D
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE70
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: NUCLEASE DOMAIN, RESIDUES 446-576
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 316407
    Strain: W3110
    Synonym: COLICIN-E7

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:544 , HIS B:569 , HIS B:573 , SO4 B:1578BINDING SITE FOR RESIDUE ZN B 1577
2AC2SOFTWAREHIS B:544 , HIS B:545 , HIS B:569 , HIS B:573 , ZN B:1577BINDING SITE FOR RESIDUE SO4 B 1578
3AC3SOFTWAREHIS D:544 , HIS D:569 , HIS D:573 , SO4 D:1578BINDING SITE FOR RESIDUE ZN D 1577
4AC4SOFTWAREHIS D:544 , HIS D:545 , HIS D:569 , HIS D:573 , ZN D:1577BINDING SITE FOR RESIDUE SO4 D 1578

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2JBG)

(-) 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:87
 aligned with IMM7_ECOLX | Q03708 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
           IMM7_ECOLX     1 MELKNSISDYTEAEFVQLLKEIEKENVAATDDVLDVLLEHFVKITEHPDGTDLIYYPSDNRDDSPEGIVKEIKEWRAANGKPGFKQG  87
               SCOP domains d2jbga_ A: ImmE7 protein (Im7)                                                          SCOP domains
               CATH domains 2jbgA00 A:1-87  [code=1.10.1200.20, no name defined]                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhh.......hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 2jbg A   1 MELKNSISDYTEAEFVQLLKEIEKENVAATDDVLDVLLEHFVKITEHPDGTDLIYYPSDNRDDSPEGIVKEIKEWRAANGKPGFKQG  87
                                    10        20        30        40        50        60        70        80       


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with CEA7_ECOLX | Q47112 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:129
                                   457       467       477       487       497       507       517       527       537       547       557       567         
           CEA7_ECOLX   448 NKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHRGK 576
               SCOP domains d2jbgb1 B:448-576 DNase domain of colicin E7                                                                                      SCOP domains
               CATH domains 2jbgB00 B:448-576 Colicin e7 immunity protein. Chain B                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....................ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh.......eeee.--------......eeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jbg B 448 NKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHE--------VYDMDAISVVTPKRHIDIHRGK 576
                                   457       467       477       487       497       507       517       527       537        |-       557       567         
                                                                                                                            546      555                     


Chain C from PDB  Type:PROTEIN  Length:87
 aligned with IMM7_ECOLX | Q03708 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
           IMM7_ECOLX     1 MELKNSISDYTEAEFVQLLKEIEKENVAATDDVLDVLLEHFVKITEHPDGTDLIYYPSDNRDDSPEGIVKEIKEWRAANGKPGFKQG  87
               SCOP domains d2jbgc_ C: ImmE7 protein (Im7)                                                          SCOP domains
               CATH domains 2jbgC00 C:1-87  [code=1.10.1200.20, no name defined]                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhh.......hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 2jbg C   1 MELKNSISDYTEAEFVQLLKEIEKENVAATDDVLDVLLEHFVKITEHPDGTDLIYYPSDNRDDSPEGIVKEIKEWRAANGKPGFKQG  87
                                    10        20        30        40        50        60        70        80       


Chain D from PDB  Type:PROTEIN  Length:121
 aligned with CEA7_ECOLX | Q47112 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:129
                                   457       467       477       487       497       507       517       527       537       547       557       567         
           CEA7_ECOLX   448 NKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHRGK 576
               SCOP domains d2jbgd_ D: DNase domain of colicin E7                                                                                             SCOP domains
               CATH domains 2jbgD00 D:448-576 Colicin e7 immunity protein. Chain B                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..........hhhhhh.....ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh.......eeee.--------......eeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jbg D 448 NKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHE--------VYDMDAISVVTPKRHIDIHRGK 576
                                   457       467       477       487       497       507       517       527       537        |-       557       567         
                                                                                                                            546      555
   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 2JBG)

(-) Gene Ontology  (12, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (IMM7_ECOLX | Q03708)
molecular function
    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).
    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,D   (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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  CEA7_ECOLX | Q47112
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  IMM7_ECOLX | Q03708
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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 3fbd 3gjn 3gkl 3zfk 7cei
        IMM7_ECOLX | Q03708: 1ayi 1cei 1mz8 1ujz 1unk 1znv 2erh 2jaz 2jb0 2k0d 4f37 5ina 7cei

(-) Related Entries Specified in the PDB File

1ayi COLICIN E7 IMMUNITY PROTEIN IM7
1cei STRUCTURE DETERMINATION OF THE COLICIN E7 IMMUNITY PROTEIN(IMME7) THAT BINDS SPECIFICALLY TO THE DNASE-TYPE COLICINE7 AND INHIBITS ITS BACTERIOCIDAL ACTIVITY
1m08 CRYSTAL STRUCTURE OF THE UNBOUND NUCLEASE DOMAIN OF COLE7
1mz8 CRYSTAL STRUCTURES OF THE NUCLEASE DOMAIN OF COLE7/IM7 INCOMPLEX WITH A PHOSPHATE ION AND A ZINC ION
1pt3 CRYSTAL STRUCTURES OF NUCLEASE-COLE7 COMPLEXED WITH OCTAMERDNA
1ujz CRYSTAL STRUCTURE OF THE E7_C/IM7_C COMPLEX ; ACOMPUTATIONALLY DESIGNED INTERFACE BETWEEN THE COLICIN E7DNASE AND THE IM7 IMMUNITY PROTEIN
1unk STRUCTURE OF COLICIN E7 IMMUNITY PROTEIN
1zns CRYSTAL STRUCTURE OF N-COLE7/12-BP DNA/ ZN COMPLEX
1znv HOW A HIS-METAL FINGER ENDONUCLEASE COLE7 BINDS AND CLEAVESDNA WITH A TRANSITION METAL ION COFACTOR
2axc CRYSTAL STRUCTURE OF COLE7 TRANSLOCATION DOMAIN
2erh CRYSTAL STRUCTURE OF THE E7_G/IM7_G COMPLEX ; A DESIGNEDINTERFACE BETWEEN THE COLICIN E7 DNASE AND THE IM7IMMUNITY PROTEIN
2ivh CRYSTAL STRUCTURE OF THE NUCLEASE DOMAIN OF COLE7 (H545Q MUTANT) IN COMPLEX WITH AN 18-BP DUPLEX DNA
2jaz CRYSTAL STRUCTURE OF THE MUTANT N560D OF THE NUCLEASE DOMAIN OF COLE7 IN COMPLEX WITH IM7
2jb0 CRYSTAL STRUCTURE OF THE MUTANT H573A OF THE NUCLEASE DOMAIN OF COLE7 IN COMPLEX WITH IM7
7cei THE ENDONUCLEASE DOMAIN OF COLICIN E7 IN COMPLEX WITH ITSINHIBITOR IM7 PROTEIN