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(-) Description

Title :  CRYSTAL STRUCTURE OF I-CREI BOUND TO A PALINDROMIC DNA SEQUENCE II (PALINDROME OF RIGHT SIDE OF WILDTYPE DNA TARGET SEQUENCE)
 
Authors :  B. Chevalier, M. Turmel, C. Lemieux, R. J. Monnat, B. L. Stoddard
Date :  28 Oct 02  (Deposition) - 03 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C,D,E,F  (1x)
Biol. Unit 2:  G,H,I,J,K,L  (1x)
Keywords :  Homing, Endonuclease, Laglidadg, Dna Recognition, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Chevalier, M. Turmel, C. Lemieux, R. J. Monnat, B. L. Stoddard
Flexible Dna Target Site Recognition By Divergent Homing Endonuclease Isoschizomers I-Crei And I-Msoi
J. Mol. Biol. V. 329 253 2003
PubMed-ID: 12758074  |  Reference-DOI: 10.1016/S0022-2836(03)00447-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*GP*A)- 3'
    Chains: C, E, I, K
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(P*GP*AP*CP*AP*GP*TP*TP*TP*CP*G-3')
    Chains: D, F, J, L
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA ENDONUCLEASE I-CREI
    Chains: A, B, G, H
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PI-CREI
    Expression System Strain: BL21[DE3]
    Expression System Taxid: 562
    Expression System Vector: T7
    Expression System Vector Type: PLASMID
    Gene: CR.LSU INTRON OF CHOROPLAST 23S RDNA GENE
    Organism Scientific: CHLAMYDOMONAS REINHARDTII
    Organism Taxid: 3055
    Synonym: 23S RRNA INTRON PROTEIN

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): ABCDEF      
Biological Unit 2 (1x):       GHIJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:19 , HOH A:1007 , ASP B:220 , DA C:414 , DG F:465BINDING SITE FOR RESIDUE CA F 497
2AC2SOFTWAREASP A:20 , ASP B:220 , DA C:414 , DG D:415 , DA E:464 , DG F:465BINDING SITE FOR RESIDUE CA C 498
3AC3SOFTWAREASP A:20 , GLY B:219 , HOH B:1001 , DG D:415 , DA E:464BINDING SITE FOR RESIDUE CA D 499
4AC4SOFTWAREASP G:520 , GLY H:719 , HOH H:1020 , DG J:915 , DA K:964BINDING SITE FOR RESIDUE CA J 997
5AC5SOFTWAREASP G:520 , ASP H:720 , DA I:914 , DG J:915 , DA K:964 , DG L:965BINDING SITE FOR RESIDUE CA I 998
6AC6SOFTWAREGLY G:519 , ASP H:720 , HOH H:1011 , DA I:914 , DG L:965BINDING SITE FOR RESIDUE CA L 999

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N3F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N3F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N3F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N3F)

(-) Exons   (0, 0)

(no "Exon" information available for 1N3F)

(-) Sequences/Alignments

Asymmetric 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:149
 aligned with DNE1_CHLRE | P05725 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:149
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         
           DNE1_CHLRE     3 TKYNKEFLLYLAGFVDGDGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAV 151
               SCOP domains d1n3fa_ A: DNA endonuclease I-CreI                                                                                                                    SCOP domains
               CATH domains 1n3fA00 A:3-151 Homing endonucleases                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeeee..eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n3f A   3 TKYNKEFLLYLAGFVDGDGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAV 151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         


Chain B from PDB  Type:PROTEIN  Length:149
 aligned with DNE1_CHLRE | P05725 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:149
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         
           DNE1_CHLRE     3 TKYNKEFLLYLAGFVDGDGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAV 151
               SCOP domains d1n3fb_ B: DNA endonuclease I-CreI                                                                                                                    SCOP domains
               CATH domains 1n3fB00 B:203-351 Homing endonucleases                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeeee..eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n3f B 203 TKYNKEFLLYLAGFVDGDGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAV 351
                                   212       222       232       242       252       262       272       282       292       302       312       322       332       342         


Chain C from PDB  Type:DNA  Length:14
                                              
                 1n3f C 401 CGAAACTGTCTCGA 414
                                   410    


Chain D from PDB  Type:DNA  Length:10
                                          
                 1n3f D 415 GACAGTTTCG 424
                                   424


Chain E from PDB  Type:DNA  Length:14
                                              
                 1n3f E 451 CGAAACTGTCTCGA 464
                                   460    


Chain F from PDB  Type:DNA  Length:10
                                          
                 1n3f F 465 GACAGTTTCG 474
                                   474


Chain G from PDB  Type:PROTEIN  Length:149
 aligned with DNE1_CHLRE | P05725 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:149
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         
           DNE1_CHLRE     3 TKYNKEFLLYLAGFVDGDGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAV 151
               SCOP domains d1n3fg_ G: DNA endonuclease I-CreI                                                                                                                    SCOP domains
               CATH domains 1n3fG00 G:503-651 Homing endonucleases                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeeee..eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n3f G 503 TKYNKEFLLYLAGFVDGDGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAV 651
                                   512       522       532       542       552       562       572       582       592       602       612       622       632       642         


Chain H from PDB  Type:PROTEIN  Length:149
 aligned with DNE1_CHLRE | P05725 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:149
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         
           DNE1_CHLRE     3 TKYNKEFLLYLAGFVDGDGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAV 151
               SCOP domains d1n3fh_ H: DNA endonuclease I-CreI                                                                                                                    SCOP domains
               CATH domains 1n3fH00 H:703-851 Homing endonucleases                                                                                                                CATH domains
           Pfam domains (1) ----------LAGLIDADG_1-1n3fH01 H:713-809                                                                    ------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----------LAGLIDADG_1-1n3fH02 H:713-809                                                                    ------------------------------------------ Pfam domains (2)
           Pfam domains (3) ----------LAGLIDADG_1-1n3fH03 H:713-809                                                                    ------------------------------------------ Pfam domains (3)
           Pfam domains (4) ----------LAGLIDADG_1-1n3fH04 H:713-809                                                                    ------------------------------------------ Pfam domains (4)
         Sec.struct. author ...hhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeee...eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n3f H 703 TKYNKEFLLYLAGFVDGDGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAV 851
                                   712       722       732       742       752       762       772       782       792       802       812       822       832       842         


Chain I from PDB  Type:DNA  Length:14
                                              
                 1n3f I 901 CGAAACTGTCTCGA 914
                                   910    


Chain J from PDB  Type:DNA  Length:10
                                          
                 1n3f J 915 GACAGTTTCG 924
                                   924


Chain K from PDB  Type:DNA  Length:14
                                              
                 1n3f K 951 CGAAACTGTCTCGA 964
                                   960    


Chain L from PDB  Type:DNA  Length:10
                                          
                 1n3f L 965 GACAGTTTCG 974
                                   974
   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Homing_endonuc (19)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,G,H   (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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  1n3f
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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 1t9i 1t9j 1u0c 1u0d 2i3p 2i3q 2o7m 2vbj 2vbl 2vbn 2vbo 4aab 4aad 4aae 4aaf 4aag 4aqu 4aqx

(-) Related Entries Specified in the PDB File

1n3e CRYSTAL STRUCTURE OF I-CREI BOUND TO A PALINDROMIC DNA SEQUENCE I (PALINDROME OF LEFT SIDE OF WILDTYPE DNA TARGET SEQUENCE)