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(-) Description

Title :  Y33H MUTANT OF HOMING ENDONUCLEASE I-CREI
 
Authors :  D. Sussman, M. Chadsey, S. Fauce, A. Engel, A. Bruett, R. Monnat, B. L. St L. M. Seligman
Date :  13 Jul 04  (Deposition) - 02 Nov 04  (Release) - 06 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D  (2x)
Biol. Unit 1:  A,B,C,D  (1x)
Keywords :  Dna Endonuclease I-Crei, Protein/Dna, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Sussman, M. Chadsey, S. Fauce, A. Engel, A. Bruett, R. Monnat, B. L. Stoddard, L. M. Seligman
Isolation And Characterization Of New Homing Endonuclease Specificities At Individual Target Site Positions.
J. Mol. Biol. V. 342 31 2004
PubMed-ID: 15313605  |  Reference-DOI: 10.1016/J.JMB.2004.07.031

(-) Compounds

Molecule 1 - 5'-D(*GP*CP*GP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP *GP*TP*TP*CP*CP*G)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP *TP*TP*TP*CP*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
    Organism Scientific: CHLAMYDOMONAS REINHARDTII
    Organism Taxid: 3055
    Synonym: 23S RRNA INTRON PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit (2x): ABCD
Biological Unit 1 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1U0D)

(-) Sites  (0, 0)

(no "Site" information available for 1U0D)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U0D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U0D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U0D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U0D)

(-) Exons   (0, 0)

(no "Exon" information available for 1U0D)

(-) 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: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 d1u0da_ A: DNA endonuclease I-CreI                                                                                                                       SCOP domains
               CATH domains 1u0dA00 A:2-153 Homing endonucleases                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhheeeeeeee.........eeeeeeeeeee..hhhhhhhhhhhhh..eeeee..eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u0d A   2 NTKYNKEFLLYLAGFVDGDGSIIAQIKPNQSHKFKHQLSLTFQVTEKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLD 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 d1u0db_ B: DNA endonuclease I-CreI                                                                                                                       SCOP domains
               CATH domains 1u0dB00 B:302-453 Homing endonucleases                                                                                                                   CATH domains
           Pfam domains (1) -----------LAGLIDADG_1-1u0dB01 B:313-409                                                                    -------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------LAGLIDADG_1-1u0dB02 B:313-409                                                                    -------------------------------------------- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeehhhhhhhhhhhhhhhh..eeee....eeeee.hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u0d B 302 NTKYNKEFLLYLAGFVDGDGSIIAQIKPNQSHKFKHQLSLTFQVTEKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLD 453
                                   311       321       331       341       351       361       371       381       391       401       411       421       431       441       451  


Chain C from PDB  Type:DNA  Length:24
                                                        
                 1u0d C 501 GCGAAACGTCGTGAGACAGTTCCG 524
                                   510       520    


Chain D from PDB  Type:DNA  Length:24
                                                        
                 1u0d D 551 CGGAACTGTCTCACGACGTTTCGC 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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Homing_endonuc (19)

(-) Gene Ontology  (8, 8)

Asymmetric 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 2i3p 2i3q 2o7m 2vbj 2vbl 2vbn 2vbo 4aab 4aad 4aae 4aaf 4aag 4aqu 4aqx

(-) Related Entries Specified in the PDB File

1u0c