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(-)Asym./Biol. Unit
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(-) Description

Title :  CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE ECORII N-TERMINAL EFFECTOR-BINDING DOMAIN IN COMPLEX WITH COGNATE DNA
 
Authors :  D. Golovenko, E. Manakova, S. Grazulis, G. Tamulaitiene, V. Siksnys
Date :  06 Jun 09  (Deposition) - 22 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.51
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Restriction Endonuclease, Ecorii, Dna-Binding Pseudobarrel Fold, Protein-Dna Complex, Dna Recognition, Endonuclease, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Golovenko, E. Manakova, G. Tamulaitiene, S. Grazulis, V. Siksnys
Structural Mechanisms For The 5'-Ccwgg Sequence Recognition By The N- And C-Terminal Domains Of Ecorii.
Nucleic Acids Res. V. 37 6613 2009
PubMed-ID: 19729506  |  Reference-DOI: 10.1093/NAR/GKP699
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RESTRICTION ENDONUCLEASE
    Chains: A
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL EFFECTOR-BINDING DOMAIN (UNP RESIDUES 2-170)
    Gene: ECORII
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: RESTRICTION ENDONUCLEASE TYPE IIE
 
Molecule 2 - 5'-D(*GP*CP*CP*CP*TP*GP*GP*CP*G)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*GP*CP*CP*AP*GP*GP*GP*C)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3HQF)

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(-) SS Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
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Chain A from PDB  Type:PROTEIN  Length:173
 aligned with O69414_ECOLX | O69414 from UniProtKB/TrEMBL  Length:402

    Alignment length:173
                               1                                                                                                                                                                         
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167   
         O69414_ECOLX     - ---MSVFHNWLLEIACENYFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRELNPSVFLTAHVSSHDCPDSEARAIYYNSRHFGKTRNEKRITRWGRGSPLQDPENTGALTLLAFKLDEQGGDCKEVNIWVCASTDEEDVIETAIGEVIPGALISGPAGQILGGL 170
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..eeeeeee.hhhhhh.......eeeehhhhhhhhhhhhh.......eeeeeeee.......eeeeeeee..........eeeee.....hhhhhhhhh..eeeeeee.........eeeeee..hhhhhhhhhhhhh.......eeeehhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hqf A   0 HHGSSVFHNWLLEIACENYFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRELNPSVFLTAHVSSHDCPDSEARAIYYNSRHFGKTRNEKRITRWGRGSPLQDPENTGALTLLAFKLDEQGGDCKEVNIWVCASTDEEDVIETAIGEVIPGALISGPAGQILGGL 172
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169   


Chain B from PDB  Type:DNA  Length:9
                                         
                 3hqf B  -4 GCCCTGGCG   4


Chain C from PDB  Type:DNA  Length:9
                                         
                 3hqf C  -4 CGCCAGGGC   4
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O69414_ECOLX | O69414)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0009036    Type II site-specific deoxyribonuclease activity    Catalysis of the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates and 3' hydroxyls. Cleavage is dependent on the presence in the DNA of a specific recognition site; cleavage occurs at or very near this recognition site.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
biological process
    GO:0009307    DNA restriction-modification system    A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1na6 R.ECORII-R88A
3hqg