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(-) Description

Title :  K28R MUTANT OF HOMING ENDONUCLEASE I-CREI
 
Authors :  D. Sussman, L. Rosen
Date :  20 Aug 06  (Deposition) - 05 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Homing Endonulease I-Crei, Dna, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. E. Rosen, H. A. Morrison, S. Masri, M. J. Brown, B. Springstubb, D. Sussman, B. L. Stoddard, L. M. Seligman
Homing Endonuclease I-Crei Derivatives With Novel Dna Target Specificities.
Nucleic Acids Res. V. 34 4791 2006
PubMed-ID: 16971456  |  Reference-DOI: 10.1093/NAR/GKL645
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*GP*CP*AP*AP*AP*TP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*AP *TP*TP*TP*CP*G)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'- D(*CP*GP*AP*AP*AP*TP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*AP *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 Plasmid: PI-CREI
    Expression System Strain: BL-21 RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    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  (1, 2)

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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:19 , ASP B:320 , DG C:515 , DC D:564BINDING SITE FOR RESIDUE CA B 1
2AC2SOFTWAREASP A:20 , HOH B:145 , GLY B:319 , DA C:514 , DG D:565BINDING SITE FOR RESIDUE CA A 154

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I3P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I3P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I3P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2I3P)

(-) Exons   (0, 0)

(no "Exon" information available for 2I3P)

(-) 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 d2i3pa_ A: automated matches                                                                                                                             SCOP domains
               CATH domains 2i3pA00 A:2-153 Homing endonucleases                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee...hhhhhhhhhhhh..eeee...eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i3p A   2 NTKYNKEFLLYLAGFVDGDGSIIAQIRPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLD 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 d2i3pb_ B: automated matches                                                                                                                             SCOP domains
               CATH domains 2i3pB00 B:302-453 Homing endonucleases                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeeee..eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i3p B 302 NTKYNKEFLLYLAGFVDGDGSIIAQIRPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLD 453
                                   311       321       331       341       351       361       371       381       391       401       411       421       431       441       451  


Chain C from PDB  Type:DNA  Length:24
                                                        
                 2i3p C 501 GCAAATCGTCGTGAGACAATTTCG 524
                                   510       520    


Chain D from PDB  Type:DNA  Length:24
                                                        
                 2i3p D 551 CGAAATTGTCTCACGACGATTTGC 574
                                   560       570
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "Pfam Domain" information available for 2I3P)

(-) 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 | P05725: 1af5 1bp7 1g9y 1g9z 1mow 1n3e 1n3f 1t9i 1t9j 1u0c 1u0d 2i3q 2o7m 2vbj 2vbl 2vbn 2vbo 4aab 4aad 4aae 4aaf 4aag 4aqu 4aqx

(-) Related Entries Specified in the PDB File

2i3q Q44V MUTANT OF HOMING ENDONUCLEASE I-CREI