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(-) Description

Title :  CRYSTAL STRUCTURE OF N-COLE7/12-BP DNA/ZN COMPLEX
 
Authors :  L. G. Doudeva, H. Huang, K. C. Hsia, Z. Shi, C. L. Li, Y. Shen, H. S. Yuan
Date :  12 May 05  (Deposition) - 14 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  H-N-H Motif, Endonuclease, Colicin, Protein-Dna Complex, His-Metal Finger, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. G. Doudeva, H. Huang, K. C. Hsia, Z. Shi, C. L. Li, Y. Shen, Y. S. Cheng, H. S. Yuan
Crystal Structural Analysis And Metal-Dependent Stability And Activity Studies Of The Cole7 Endonuclease Domain In Complex With Dna/Zn2+ Or Inhibitor/Ni2+
Protein Sci. V. 15 269 2006
PubMed-ID: 16434744  |  Reference-DOI: 10.1110/PS.051903406

(-) Compounds

Molecule 1 - 5'-D(*CP*GP*GP*GP*AP*TP*AP*TP*CP*CP*CP*G)-3'
    Chains: B, C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - COLICIN E7
    Chains: A
    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
    Gene: CEA7
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI STR. K12 SUBSTR.
    Organism Taxid: 316407
    Strain: W3110

 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 , DG B:4 , DA B:5BINDING SITE FOR RESIDUE ZN A 1500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZNS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZNS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZNS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZNS)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZNS)

(-) 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:118
 aligned with CEA7_ECOLX | Q47112 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:125
                                   459       469       479       489       499       509       519       529       539       549       559       569     
           CEA7_ECOLX   450 PGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHR 574
               SCOP domains d1znsa_ A: DNase domain of colicin E7                                                                                         SCOP domains
               CATH domains 1znsA00 A:450-574 Colicin e7 immunity protein. Chain B                                                                        CATH domains
               Pfam domains Colicin-DNase-1znsA01 A:450-574                                                                                               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
                 1zns A 450 PGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHEEK-------VYDMDNISVVTPKRHIDIHR 574
                                   459       469       479       489       499       509       519       529       539       | -     | 559       569     
                                                                                                                           547     555                   


Chain B from PDB  Type:DNA  Length:12
                                            
                 1zns B   1 CGGGATATCCCG  12
                                    10  


Chain C from PDB  Type:DNA  Length:12
                                            
                 1zns C  13 CGGGATATCCCG  24
                                    22
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: His-Me_finger (38)

(-) 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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  CEA7_ECOLX | Q47112
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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 1znv 2axc 2erh 2ivh 2jaz 2jb0 2jbg 3fbd 3gjn 3gkl 3zfk 7cei

(-) Related Entries Specified in the PDB File

1m08 UNBOUNDED NUCLEASE DOMAIN OF COLE7
1mz8 THE NUCLEASE DOMAIN OF COLE7/IM7 IN COMPLEX WITH A PHOSPHATE ION AND DIFFERENT DIVALENT METAL IONS
1pt3 CRYSTAL STRUCTURES OF NUCLEASE-COLE7 COMPLEXED WITH OCTAMER DNA
7cei THE DNASE DOMAIN OF COLE7 IN COMPLEX WITH IM7