Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  GROUP I INTRON-ENCODED HOMING ENDONUCLEASE I-CEUI COMPLEXED WITH DNA
 
Authors :  P. C. Spiegel, B. L. Stoddard
Date :  07 Nov 05  (Deposition) - 23 May 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,X,Y
Keywords :  Homing Endonuclease, Laglidadg, Homodimer, Protein/Dna Complex, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. C. Spiegel, B. Chevalier, D. Sussman, M. Turmel, C. Lemieux, B. L. Stoddard
The Structure Of I-Ceui Homing Endonuclease: Evolving Asymmetric Dna Recognition From A Symmetric Protein Scaffold.
Structure V. 14 869 2006
PubMed-ID: 16698548  |  Reference-DOI: 10.1016/J.STR.2006.03.009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - I-CEUI DNA TARGET SITE
    Chains: X
    Engineered: YES
    Other Details: SYNTHESIZED NUCLEIC ACID
    Synthetic: YES
 
Molecule 2 - I-CEUI DNA TARGET SITE, COMPLIMENTARY STRAND
    Chains: Y
    Engineered: YES
    Other Details: SYNTHESIZED NUCLEIC ACID
    Synthetic: YES
 
Molecule 3 - DNA ENDONUCLEASE I-CEUI
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET30A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: I-CEUI
    Mutation: YES
    Organism Scientific: CHLAMYDOMONAS EUGAMETOS
    Organism Taxid: 3053
    Synonym: 23S RRNA INTRON 1 PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABXY

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:86 , HOH A:1003 , HOH A:1077 , HOH A:1078 , HOH A:1137 , HOH X:1097BINDING SITE FOR RESIDUE CA A 801
2AC2SOFTWAREGLY A:65 , GLU A:66 , GLU B:66 , DA X:615 , DG X:616 , DG Y:715 , DG Y:716BINDING SITE FOR RESIDUE CA X 802
3AC3SOFTWAREASP B:86 , HOH B:1173 , HOH X:1175 , HOH Y:1096 , HOH Y:1103BINDING SITE FOR RESIDUE CA B 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EX5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EX5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EX5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EX5)

(-) Exons   (0, 0)

(no "Exon" information available for 2EX5)

(-) 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:207
 aligned with DNE1_CHLMO | P32761 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:207
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       
           DNE1_CHLMO     5 ILKPGEKLPQDKLEELKKINDAVKKTKNFSKYLIDLRKLFQIDEVQVTSESKLFLAGFLEGEASLNISTKKLATSKFGLVVDPEFNVTQHVNGVKVLYLALEVFKTGRIRHKSGSNATLVLTIDNRQSLEEKVIPFYEQYVVAFSSPEKVKRVANFKALLELFNNDAHQDLEQLVNKILPIWDQMRKQQGQSNEGFPNLEAAQDFAR 211
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeee......eeeeee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ex5 A   5 ILKPGEKLPQDKLEELKKINDAVKKTKNFSKYLIDLRKLFQIDEVQVTSESKLFLAGFLEGEASLNISTKKLATSKFGLVVDPEFNVTRHVNGVKVLYLALEVFKTGRIRHKSGSNATLVLTIDNRQSLEEKVIPFYEQYVVAFSSPEKVKRVANFKALLELFNNDAHQDLEQLVNKILPIWDQMRKQQGQSNEGFPNLEAAQDFAR 211
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       


Chain B from PDB  Type:PROTEIN  Length:207
 aligned with DNE1_CHLMO | P32761 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:207
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       
           DNE1_CHLMO     5 ILKPGEKLPQDKLEELKKINDAVKKTKNFSKYLIDLRKLFQIDEVQVTSESKLFLAGFLEGEASLNISTKKLATSKFGLVVDPEFNVTQHVNGVKVLYLALEVFKTGRIRHKSGSNATLVLTIDNRQSLEEKVIPFYEQYVVAFSSPEKVKRVANFKALLELFNNDAHQDLEQLVNKILPIWDQMRKQQGQSNEGFPNLEAAQDFAR 211
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeee......eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh............hhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ex5 B   5 ILKPGEKLPQDKLEELKKINDAVKKTKNFSKYLIDLRKLFQIDEVQVTSESKLFLAGFLEGEASLNISTKKLATSKFGLVVDPEFNVTRHVNGVKVLYLALEVFKTGRIRHKSGSNATLVLTIDNRQSLEEKVIPFYEQYVVAFSSPEKVKRVANFKALLELFNNDAHQDLEQLVNKILPIWDQMRKQQGQSNEGFPNLEAAQDFAR 211
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       


Chain X from PDB  Type:DNA  Length:26
                                                          
                 2ex5 X 601 CGATAACGGTCCTAAGGTAGCGAAGC 626
                                   610       620      


Chain Y from PDB  Type:DNA  Length:26
                                                          
                 2ex5 Y 701 GCTTCGCTACCTTAGGACCGTTATCG 726
                                   710       720
   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  (0, 0)

(no "SCOP Domain" information available for 2EX5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2EX5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EX5)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DNE1_CHLMO | P32761)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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.
biological process
    GO:0006314    intron homing    Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ex5)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2ex5
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DNE1_CHLMO | P32761
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.-.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  DNE1_CHLMO | P32761
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 2EX5)

(-) Related Entries Specified in the PDB File

1af5 LAGLIDADG HOMING ENDONUCLEASE
1bp7 LAGLIDADG HOMING ENDONUCLEASE
1g9y LAGLIDADG HOMING ENDONUCLEASEE
1g9z LAGLIDADG HOMING ENDONUCLEASE
1m5x LAGLIDADG HOMING ENDONUCLEASE
1mow LAGLIDADG HOMING ENDONUCLEASE