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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HOMING ENDONUCLEASE I-CVUI IN COMPLEX WITH ITS TARGET (SRO1.3) IN THE PRESENCE OF 2 MM CA
 
Authors :  R. Molina, P. Redondo, B. Lopezmendez, M. Villate, N. Merino, F. J. Blan J. Valton, S. Grizot, P. Duchateau, J. Prieto, G. Montoya
Date :  02 Jul 15  (Deposition) - 23 Sep 15  (Release) - 09 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydrolase-Dna Complex, Gene Targeting, Genetics, Protein-Dna Interaction, Homing Endonucleases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Molina, P. Redondo, B. Lopez-Mendez, M. Villate, N. Merino, F. J. Blanco, J. Valton, S. Grizot, P. Duchateau, J. Prieto, G. Montoya
Crystal Structure Of The Homing Endonuclease I-Cvui Provides A New Template For Genome Modification
J. Biol. Chem. V. 290 28727 2015
PubMed-ID: 26363068  |  Reference-DOI: 10.1074/JBC.M115.678342

(-) Compounds

Molecule 1 - DNA ENDONUCLEASE I-CVUI
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA PLYSS
    Expression System Vector: PET24D
    Expression System Vector Type: PLASMID
    Organism Common: GREEN ALGAE
    Organism Scientific: CHLORELLA VULGARIS
    Organism Taxid: 3077
    Synonym: 23S RRNA INTRON PROTEIN, I-CVUI
 
Molecule 2 - 24MER DNA, 5'-D(*DTP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*AP *DCP*GP*AP*CP*GP*TP*TP*CP*TP*GP*A)-3'
    Chains: C, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 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
1AC1SOFTWAREASP A:23 , HOH A:2004 , HOH A:2041 , ALA B:22 , DC C:514 , DG D:615BINDING SITE FOR RESIDUE CA A1163
2AC2SOFTWAREALA A:22 , HOH A:2001 , HOH A:2002 , ASP B:23 , DG C:515 , DC D:614BINDING SITE FOR RESIDUE CA B1164

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A72)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A72)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A72)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A72)

(-) Exons   (0, 0)

(no "Exon" information available for 5A72)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeee....eeeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a72 A   6 NFHDQLKFAWLAGFVDADGCINAQIVSREDYLLKYQVRVSLTVFQSTTQHFILLDIQKILGCGTVRKRNDGMSEFCVVGGTSLQTTLEKLLPYLNLKRAQAKLVLQIIKKLPNTKDPSVLMEAALLADKVGLLTDGKKRTILAENVRECLKKLGHVV 162
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       


Chain B from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeee....eeeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a72 B   6 NFHDQLKFAWLAGFVDADGCINAQIVSREDYLLKYQVRVSLTVFQSTTQHFILLDIQKILGCGTVRKRNDGMSEFCVVGGTSLQTTLEKLLPYLNLKRAQAKLVLQIIKKLPNTKDPSVLMEAALLADKVGLLTDGKKRTILAENVRECLKKLGHVVS 163
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155        


Chain C from PDB  Type:DNA  Length:24
                                                        
                 5a72 C 501 TCAGAACGTCGTACGACGTTCTGA 524
                                   510       520    


Chain D from PDB  Type:DNA  Length:24
                                                        
                 5a72 D 601 TCAGAACGTCGTACGACGTTCTGA 624
                                   610       620
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  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 5A72)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A72)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A72)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  5a72
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  DNE1_CHLVU | P56347
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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_CHLVU | P56347: 5a74 5a77 5a78

(-) Related Entries Specified in the PDB File

5a73 CRYSTAL STRUCTURE OF THE HOMING ENDONUCLEASE I-CVUI IN COMPLEX WITH ITS TARGET (SRO1.3) IN THE PRESENCE OF 2 MM MG
5a74 CRYSTAL STRUCTURE OF THE HOMING ENDONUCLEASE I-CVUI IN COMPLEX WITH ITS TARGET (SRO1.3) IN THE PRESENCE OF 2 MM MN
5a75 CRYSTAL STRUCTURE OF THE HOMING ENDONUCLEASE I-CVUI IN COMPLEX WITH ITS TARGET (SRO1.3) IN THE PRESENCE OF 10 MM MG
5a77 CRYSTAL STRUCTURE OF THE HOMING ENDONUCLEASE I-CVUI IN COMPLEX WITH I-CREI TARGET (C1221) IN THE PRESENCE OF 2 MM MG REVEALING DNA CLEAVED
5a78 CRYSTAL STRUCTURE OF THE HOMING ENDONUCLEASE I-CVUI IN COMPLEX WITH I-CREI TARGET (C1221) IN THE PRESENCE OF 2 MM MG REVEALING DNA NOT CLEAVED