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(-) Description

Title :  I-CREI(D20N)/DNA COMPLEX
 
Authors :  B. Chevalier, D. Sussman, C. Otis, D. Boudreau, M. Turmel, C. Lemieux, K. Stephens, R. J. Monnat Jr. , B. L. Stoddard
Date :  17 May 04  (Deposition) - 16 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein, Dna, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Chevalier, D. Sussman, C. Otis, A. J. Noel, M. Turmel, C. Lemieux, K. Stephens, R. J. Monnat Jr. , B. L. Stoddard
Metal-Dependent Dna Cleavage Mechanism Of The I-Crei Laglidadg Homing Endonuclease.
Biochemistry V. 43 14015 2004
PubMed-ID: 15518550  |  Reference-DOI: 10.1021/BI048970C
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP *TP*TP*TP*CP*G)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'- D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP *TP*TP*TP*GP*C)-3'
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA ENDONUCLEASE I-CREI
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CR.LSU INTRON OF CHOROPLAST 23S RRNA GENE
    Mutation: YES
    Organism Scientific: CHLAMYDOMONAS REINHARDTII
    Organism Taxid: 3055
    Synonym: 23S RRNA INTRON PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2NA4Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:20 , GLY B:319 , DA C:514 , HOH C:1004 , HOH C:1007 , DG D:565 , HOH D:1035BINDING SITE FOR RESIDUE CA C 801
2AC2SOFTWAREGLY A:19 , ASN B:320 , DG C:515 , HOH C:1008 , DC D:564 , HOH D:1013 , HOH D:1035BINDING SITE FOR RESIDUE CA C 802
3AC3SOFTWAREHOH A:1017 , ALA B:434 , ASN B:436 , HOH B:1090 , HOH B:1209 , HOH B:1218 , HOH B:1277 , HOH B:1610BINDING SITE FOR RESIDUE NA B 803
4AC4SOFTWAREALA A:134 , ASN A:136 , HOH A:1044 , HOH A:1273 , HOH A:1576 , HOH A:1618 , HOH B:1314BINDING SITE FOR RESIDUE NA A 804
5AC5SOFTWAREHOH C:1055 , HOH C:1464 , HOH C:1582 , HOH C:1622 , HOH D:1256 , HOH D:1563BINDING SITE FOR RESIDUE NA D 805
6AC6SOFTWAREHOH C:1178 , HOH C:1410 , HOH D:1164 , HOH D:1269 , HOH D:1282 , HOH D:1449BINDING SITE FOR RESIDUE NA C 806

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T9I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1T9I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T9I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T9I)

(-) Exons   (0, 0)

(no "Exon" information available for 1T9I)

(-) 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:153
 aligned with DNE1_CHLRE | P05725 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
           DNE1_CHLRE     2 NTKYNKEFLLYLAGFVDGDGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLDS 154
               SCOP domains d1t9ia_ A: DNA endonuclease I-CreI                                                                                                                        SCOP domains
               CATH domains 1t9iA00 A:2-154 Homing endonucleases                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhheeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeeee..eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t9i A   2 NTKYNKEFLLYLAGFVDGNGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLDS 154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   


Chain B from PDB  Type:PROTEIN  Length:155
 aligned with DNE1_CHLRE | P05725 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:155
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     
           DNE1_CHLRE     2 NTKYNKEFLLYLAGFVDGDGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLDSLS 156
               SCOP domains d1t9ib_ B: DNA endonuclease I-CreI                                                                                                                          SCOP domains
               CATH domains 1t9iB00 B:302-456 Homing endonucleases                                                                                                                      CATH domains
           Pfam domains (1) -----------LAGLIDADG_1-1t9iB01 B:313-409                                                                    ----------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------LAGLIDADG_1-1t9iB02 B:313-409                                                                    ----------------------------------------------- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhheeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeee...eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t9i B 302 NTKYNKEFLLYLAGFVDGNGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLDSLS 456
                                   311       321       331       341       351       361       371       381       391       401       411       421       431       441       451     


Chain C from PDB  Type:DNA  Length:24
                                                        
                 1t9i C 501 GCAAAACGTCGTGAGACAGTTTCG 524
                                   510       520    


Chain D from PDB  Type:DNA  Length:24
                                                        
                 1t9i D 551 CGAAACTGTCTCACGACGTTTTGC 574
                                   560       570
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Homing_endonuc (19)

(-) 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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  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 1t9j 1u0c 1u0d 2i3p 2i3q 2o7m 2vbj 2vbl 2vbn 2vbo 4aab 4aad 4aae 4aaf 4aag 4aqu 4aqx

(-) Related Entries Specified in the PDB File

1g9y I-CREI/DNA CALCIUM COMPLEX (PRE HYDROLYSIS)
1g9z I-CREI/DNA MAGNESIUM COMPLEX (POST HYDROLYSIS)
1t9j I-CREI(Q47E)/DNA COMPLEX