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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NUCLEASE DOMAIN OF COLE7 (H545Q MUTANT) IN COMPLEX WITH AN 18-BP DUPLEX DNA
 
Authors :  Y. T. Wang, W. J. Yang, C. L. Li, L. G. Doudeva, H. S. Yuan
Date :  13 Jun 06  (Deposition) - 02 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Bacteriocin, Endonuclease, Antimicrobial, Metal-Binding, Hydrolase/Dna Complex, Zinc, Plasmid, Nuclease, Hydrolase, Antibiotic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. T. Wang, W. J. Yang, C. L. Li, L. G. Doudeva, H. S. Yuan
Structural Basis For Sequence-Dependent Dna Cleavage By Nonspecific Endonucleases.
Nucleic Acids Res. V. 35 584 2007
PubMed-ID: 17175542  |  Reference-DOI: 10.1093/NAR/GKL621

(-) Compounds

Molecule 1 - COLCIN-E7
    Chains: A
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector: PQE70
    Fragment: NUCLEASE DOMAIN, RESIDUES 449-576
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: W3110
 
Molecule 2 - 5'-D(*GP*GP*AP*AP*TP*TP*CP*GP*AP*TP *CP*GP*AP*AP*TP*TP*CP*C)-3'
    Chains: B, C
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:544 , HIS A:569 , HIS A:573 , DT B:10 , DC B:11BINDING SITE FOR RESIDUE ZN A1577

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2IVH)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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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:124
 aligned with CEA7_ECOLX | Q47112 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:128
                                   458       468       478       488       498       508       518       528       538       548       558       568        
           CEA7_ECOLX   449 KPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHRGK 576
               SCOP domains d2ivha_ A: automated matches                                                                                                     SCOP domains
               CATH domains 2ivhA00 A:449-576 Colicin e7 immunity protein. Chain B                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...................ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.......hhhhh.......eeee.....----.ee...eeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ivh A 449 KPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHQEKPIS----VYDMDNISVVTPKRHIDIHRGK 576
                                   458       468       478       488       498       508       518       528       538       548 |    |558       568        
                                                                                                                               550  555                     


Chain B from PDB  Type:DNA  Length:18
                                                  
                 2ivh B   1 GGAATTCGATCGAATTCC  18
                                    10        


Chain C from PDB  Type:DNA  Length:18
                                                  
                 2ivh C  19 GGAATTCGATCGAATTCC  36
                                    28
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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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 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 2jaz 2jb0 2jbg 3fbd 3gjn 3gkl 3zfk 7cei

(-) Related Entries Specified in the PDB File

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
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
7cei THE ENDONUCLEASE DOMAIN OF COLICIN E7 IN COMPLEX WITH ITSINHIBITOR IM7 PROTEIN