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(-) Description

Title :  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')
 
Authors :  R. Molina, P. Redondo, S. Stella, M. Marenchino, M. D'Abramo, F. L. Gerv J. C. Epinat, J. Valton, S. Grizot, P. Duchateau, J. Prieto, G. Montoya
Date :  01 Dec 11  (Deposition) - 02 May 12  (Release) - 22 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,E,F
Keywords :  Hydrolase-Dna Complex, Gene Targeting, Protein-Dna Interaction, Homing Endonucleases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Molina, P. Redondo, S. Stella, M. Marenchino, M. D'Abramo, F. L. Gervasio, J. Charles Epinat, J. Valton, S. Grizot, P. Duchateau J. Prieto, G. Montoya
Non-Specific Protein-Dna Interactions Control I-Crei Target Binding And Cleavage.
Nucleic Acids Res. V. 40 6936 2012
PubMed-ID: 22495931  |  Reference-DOI: 10.1093/NAR/GKS320

(-) Compounds

Molecule 1 - DNA ENDONUCLEASE I-CREI
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: CDFDUET1, PET24D
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: CHLAMYDOMONAS REINHARDTII
    Organism Taxid: 3055
    Synonym: I-CREI, 23S RRNA INTRON PROTEIN
 
Molecule 2 - 24MER DNA
    Chains: E, F
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:28 , THR A:42 , ARG A:68 , SER A:79 , DG E:518 , DA F:606 , DC F:607BINDING SITE FOR RESIDUE GOL F1625
2AC2SOFTWARELYS B:82BINDING SITE FOR RESIDUE GOL B1154
3AC3SOFTWAREGLN B:26 , LYS B:28 , THR B:42 , SER B:79 , HOH B:2011 , DA E:505 , DA E:506 , DC E:507 , DG F:618BINDING SITE FOR RESIDUE GOL B1155
4AC4SOFTWAREASP B:20 , THR B:46 , HOH B:2001 , DC F:614 , DG F:615BINDING SITE FOR RESIDUE GOL B1156
5AC5SOFTWAREASP A:20 , THR A:46 , GOL B:1157 , DC E:514 , DG E:515BINDING SITE FOR RESIDUE GOL A1153
6AC6SOFTWAREDA E:513BINDING SITE FOR RESIDUE GOL E1525
7AC7SOFTWAREGOL A:1153 , GLY B:19 , GLY B:21 , SER B:22 , LYS B:98 , DA F:616BINDING SITE FOR RESIDUE GOL B1157
8AC8SOFTWARELYS B:107 , GLU B:110BINDING SITE FOR RESIDUE GOL B1158

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4AAD)

(-) 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:151
 aligned with DNE1_CHLRE | P05725 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151 
           DNE1_CHLRE     2 NTKYNKEFLLYLAGFVDGDGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVL 152
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhheeeeeeee.........eeeeeeeeeee..hhhhhhhhhhhhh..eeee...eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aad A   2 NTKYNKEFLLYLAGFVDGDGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSNYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVL 152
                                    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 ....hhhhhhhhhhhhhhhheeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeee...eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aad B   2 NTKYNKEFLLYLAGFVDGDGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSNYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLD 153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  


Chain E from PDB  Type:DNA  Length:24
                                                        
                 4aad E 501 TCAAAACGTCGTACGACGTTTTGA 524
                                   510       520    


Chain F from PDB  Type:DNA  Length:24
                                                        
                 4aad F 601 TCAAAACGTCGTACGACGTTTTGA 624
                                   610       620
   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 4AAD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  4aad
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  DNE1_CHLRE | P05725
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  3.1.-.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        DNE1_CHLRE | P05725: 1af5 1bp7 1g9y 1g9z 1mow 1n3e 1n3f 1t9i 1t9j 1u0c 1u0d 2i3p 2i3q 2o7m 2vbj 2vbl 2vbn 2vbo 4aab 4aae 4aaf 4aag 4aqu 4aqx

(-) 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')
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')