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(-) Description

Title :  CRYSTAL STRUCTURE OF I-CREI COMPLEXED WITH ITS TARGET METHYLATED AT POSITION PLUS 2 (IN THE B STRAND) IN THE PRESENCE OF MAGNESIUM
 
Authors :  J. Valton, F. Daboussi, S. Leduc, P. Redondo, R. Macmaster, R. Molina, G P. Duchateau
Date :  19 Apr 12  (Deposition) - 04 Jul 12  (Release) - 12 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Hydrolase, Methylation, Gene Targeting, Genetics, Protein-Dna Interaction, Homing Endonucleases (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Valton, F. Daboussi, S. Leduc, R. Molina, P. Redondo, R. Macmaster, G. Montoya, P. Duchateau
5'-Cytosine-Phosphoguanine (Cpg) Methylation Impacts The Activity Of Natural And Engineered Meganucleases.
J. Biol. Chem. V. 287 30139 2012
PubMed-ID: 22740697  |  Reference-DOI: 10.1074/JBC.M112.379966

(-) Compounds

Molecule 1 - DNA ENDONUCLEASE I-CREI
    ChainsA, B
    EC Number3.1.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorCDFDUET1
    Expression System Vector TypePLASMID
    FragmentRESIDUES 2-153
    Organism ScientificCHLAMYDOMONAS REINHARDTII
    Organism Taxid3055
    SynonymI-CREI, 23S RRNA INTRON PROTEIN
 
Molecule 2 - 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP)-3'
    ChainsC
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 3 - 5'-D(*GP*AP*CP*AP*GP*TP*TP*TP*GP*GP)-3'
    ChainsD
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 4 - 5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*5CM)-3'
    ChainsE
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 5 - 5'-D(*GP*AP*CP*GP*TP*TP*TP*TP*GP*AP)-3'
    ChainsF
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
15CM1Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2GOL5Ligand/IonGLYCEROL
3MG3Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:54 , LYS A:57 , LEU A:58 , GLU A:61 , LYS B:96BINDING SITE FOR RESIDUE GOL A1154
2AC2SOFTWAREALA A:25 , GLN A:26 , ILE A:27 , VAL A:129 , ARG A:141 , THR A:143 , HOH A:2012 , DC D:517 , DA D:518BINDING SITE FOR RESIDUE GOL A1155
3AC3SOFTWARETYR B:5 , ASN B:6 , PHE B:9 , GLU B:61BINDING SITE FOR RESIDUE GOL B1354
4AC4SOFTWAREARG A:51 , LEU B:97 , LYS B:98 , GLN B:101 , LEU B:135 , ASN B:136 , ASP B:137 , HOH B:2030 , HOH B:2031 , HOH B:2038 , DA F:616BINDING SITE FOR RESIDUE GOL B1355
5AC5SOFTWAREGLN B:38 , SER B:40 , SER B:79 , ILE B:81 , HOH B:2011 , HOH B:2014 , HOH B:2016 , DA C:503 , DA C:504BINDING SITE FOR RESIDUE GOL C1515
6AC6SOFTWAREASP A:20 , ASP B:20 , DA C:514 , DG D:515 , 5CM E:614 , DG F:615BINDING SITE FOR RESIDUE MG D1525
7AC7SOFTWAREASP A:20 , HOH A:2006 , GLY B:19 , DA C:514 , DG F:615BINDING SITE FOR RESIDUE MG F1625

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AQX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AQX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AQX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AQX)

(-) Exons   (0, 0)

(no "Exon" information available for 4AQX)

(-) 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:152
 aligned with DNE1_CHLRE | P05725 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  
           DNE1_CHLRE     2 NTKYNKEFLLYLAGFVDGDGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLD 153
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeeee..eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aqx A   2 NTKYNKEFLLYLAGFVDGDGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLD 153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with DNE1_CHLRE | P05725 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  
           DNE1_CHLRE     2 NTKYNKEFLLYLAGFVDGDGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLD 153
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeeee..eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aqx B   2 NTKYNKEFLLYLAGFVDGDGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLD 153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  

Chain C from PDB  Type:DNA  Length:14
                                              
                 4aqx C 501 TCAAAACGTCGTGA 514
                                   510    

Chain D from PDB  Type:DNA  Length:10
                                          
                 4aqx D 515 GACAGTTTGG 524
                                   524

Chain E from PDB  Type:DNA  Length:14
                                              
                 4aqx E 601 CCAAACTGTCTCAc 614
                                   610   |
                                       614-5CM

Chain F from PDB  Type:DNA  Length:10
                                          
                 4aqx F 615 GACGTTTTGA 624
                                   624

   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 4AQX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AQX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AQX)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DNE1_CHLRE | P05725)
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.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DNE1_CHLRE | P057251af5 1bp7 1g9y 1g9z 1mow 1n3e 1n3f 1t9i 1t9j 1u0c 1u0d 2i3p 2i3q 2o7m 2vbj 2vbl 2vbn 2vbo 4aab 4aad 4aae 4aaf 4aag 4aqu

(-) Related Entries Specified in the PDB File

1af5 GROUP I MOBILE INTRON ENDONUCLEASE
1bp7 GROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED WITH HOMING SITE DEOXYRIBONUCLEIC ACID
1g9y HOMING ENDONUCLEASE I-CREI / DNA SUBSTRATE COMPLEX WITHCALCIUM
1g9z LAGLIDADG HOMING ENDONUCLEASE I-CREI / DNA PRODUCT COMPLEXWITH MAGNESIUM
1mow E-DREI
1n3e CRYSTAL STRUCTURE OF I-CREI BOUND TO A PALINDROMIC DNASEQUENCE I (PALINDROME OF LEFT SIDE OF WILDTYPE DNA TARGETSEQUENCE)
1n3f CRYSTAL STRUCTURE OF I-CREI BOUND TO A PALINDROMIC DNASEQUENCE II (PALINDROME OF RIGHT SIDE OF WILDTYPE DNATARGET SEQUENCE)
1t9i I-CREI(D20N)/DNA COMPLEX
1t9j I-CREI(Q47E)/DNA COMPLEX
1u0c Y33C MUTATANT OF HOMING ENDONUCLEASE I-CREI
1u0d Y33H MUTATANT OF HOMING ENDONUCLEASE I-CREI
2vbj MOLECULAR BASIS OF HUMAN XPC GENE RECOGNITION AND CLEAVAGE BY ENGINEERED HOMING ENDONUCLEASE HETERODIMERS
2vbl MOLECULAR BASIS OF HUMAN XPC GENE RECOGNITION AND CLEAVAGE BY ENGINEERED HOMING ENDONUCLEASE HETERODIMERS
2vbn MOLECULAR BASIS OF HUMAN XPC GENE RECOGNITION AND CLEAVAGE BY ENGINEERED HOMING ENDONUCLEASE HETERODIMERS
2vbo MOLECULAR BASIS OF HUMAN XPC GENE RECOGNITION AND CLEAVAGE BY ENGINEERED HOMING ENDONUCLEASE HETERODIMERS
4aab CRYSTAL STRUCTURE OF THE MUTANT D75N I-CREI IN COMPLEX WITH ITS WILD-TYPE TARGET (THE FOUR CENTRAL BASES, 2NN REGION, ARE COMPOSED BY GTAC FROM 5' TO 3')
4aad CRYSTAL STRUCTURE OF THE MUTANT D75N I-CREI IN COMPLEX WITH ITS WILD-TYPE TARGET IN ABSENCE OF METAL IONS AT THE ACTIVE SITE (THE FOUR CENTRAL BASES, 2NN REGION, ARE COMPOSED BY GTAC FROM 5' TO 3')
4aae CRYSTAL STRUCTURE OF THE MUTANT D75N I-CREI IN COMPLEX WITH AN ALTERED TARGET (THE FOUR CENTRAL BASES , 2NN REGION, ARE COMPOSED BY AGCG FROM 5' TO 3')
4aaf CRYSTAL STRUCTURE OF THE MUTANT D75N I-CREI IN COMPLEX WITH AN ALTERED TARGET (THE FOUR CENTRAL BASES , 2NN REGION, ARE COMPOSED BY TGCA FROM 5' TO 3')
4aag CRYSTAL STRUCTURE OF THE MUTANT D75N I-CREI IN COMPLEX WITH ITS WILD-TYPE TARGET IN PRESENCE OF CA AT THE ACTIVE SITE (THE FOUR CENTRAL BASES, 2NN REGION, ARE COMPOSED BY GTAC FROM 5' TO 3')
4aqu CRYSTAL STRUCTURE OF I-CREI COMPLEXED WITH ITS TARGET METHYLATED AT POSITION PLUS 2 (IN THE B STRAND) IN THE PRESENCE OF CALCIUM