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(-) Description

Title :  THE STRUCTURE OF A BACTERIAL HOMING ENDONUCLEASE : I-SSP6803I
 
Authors :  L. Zhao, R. P. Bonocora, D. A. Shub, B. L. Stoddard
Date :  06 Feb 07  (Deposition) - 20 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,C,D,Y,Z
Keywords :  Protein-Dna Complex, Restriction Enzyme Fold, Pd-(D/E)-Xk Motif, Homing Endonuclease, Group I Intron, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Zhao, R. P. Bonocora, D. A. Shub, B. L. Stoddard
The Restriction Fold Turns To The Dark Side: A Bacterial Homing Endonuclease With A Pd-(D/E)-Xk Motif.
Embo J. V. 26 2432 2007
PubMed-ID: 17410205  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601672

(-) Compounds

Molecule 1 - SYNTHETIC DNA 29 MER
    Chains: Y
    Engineered: YES
    Other Details: SYNTHETIC CONSTRUCT CONTAINING NATURAL HOMING SITE OF I-SSPI6803I
    Synthetic: YES
 
Molecule 2 - SYNTHETIC DNA 29 MER
    Chains: Z
    Engineered: YES
    Other Details: SYNTHETIC CONSTRUCT CONTAINING NATURAL HOMING SITE OF I-SSPI6803I
    Synthetic: YES
 
Molecule 3 - PUTATIVE ENDONUCLEASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET15B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PASMID
    Mutation: YES
    Organism Scientific: SYNECHOCYSTIS SP.
    Organism Taxid: 1148
    Strain: PCC 6803

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDYZ

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:36 , GLN A:49 , VAL A:50 , DA Y:18BINDING SITE FOR RESIDUE CA A 501
2AC2SOFTWAREASP B:36 , GLN B:49 , VAL B:50 , HOH B:506 , DA Z:47BINDING SITE FOR RESIDUE CA B 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys C:58 -Thr C:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OST)

(-) 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:148
 aligned with Q57253_SYNY3 | Q57253 from UniProtKB/TrEMBL  Length:150

    Alignment length:148
                            1 2                                                                                                                                                 
                            | |      9        19        29        39        49        59        69        79        89        99       109       119       129       139        
         Q57253_SYNY3     1 M-STKLKGDIAEQAAILRALKLGWGVLKPLGDRLSYDLVFDVEGILLKVQVKSSWFSEKTGNYVVDNRRTRTNRRNIVRSPYRGNDFDFAVAYVEELELFYVFPVDVFISYGSEIHLVETDKRQRKPRSFGYREAWHLILQKGAAQKE 147
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh..eeeee........eeeee..eeeeeeeee.eee....eeeee..eee......eee........eeeeee....eeeeeehhhhhh...eeee...........hhhhh..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ost A   0 MGSTKLKGDIAQQAAIMRALKMGWGVLKPLGDRLSYDLVFDVEGILLKVQVKSSWKSEKTGNYVVDNRRTRTNRRNIVRSPYRGNDFDFAVAYVEELELFYVFPVDVFISYGSEIHLVETDKRQRKPRSFGYREAWHLILQKGAAQKE 147
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139        


Chain B from PDB  Type:PROTEIN  Length:148
 aligned with Q57253_SYNY3 | Q57253 from UniProtKB/TrEMBL  Length:150

    Alignment length:148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        
         Q57253_SYNY3     1 MSTKLKGDIAEQAAILRALKLGWGVLKPLGDRLSYDLVFDVEGILLKVQVKSSWFSEKTGNYVVDNRRTRTNRRNIVRSPYRGNDFDFAVAYVEELELFYVFPVDVFISYGSEIHLVETDKRQRKPRSFGYREAWHLILQKGAAQKET 148
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh..eeeee........eeeee..eeeeeeeee.ee......eeee.eeeee....eeeee.hhhhh.eeeeee....eeeeeehhhhhh...eeee.........hhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ost B   1 GSTKLKGDIAQQAAIMRALKMGWGVLKPLGDRLSYDLVFDVEGILLKVQVKSSWKSEKTGNYVVDNRRTRTNRRNIVRSPYRGNDFDFAVAYVEELELFYVFPVDVFISYGSEIHLVETDKRQRKPRSFGYREAWHLILQKGAAQKET 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        


Chain C from PDB  Type:PROTEIN  Length:138
 aligned with Q57253_SYNY3 | Q57253 from UniProtKB/TrEMBL  Length:150

    Alignment length:150
                            1 2                                                                                                                                                   
                            | |      9        19        29        39        49        59        69        79        89        99       109       119       129       139       149
         Q57253_SYNY3     1 M-STKLKGDIAEQAAILRALKLGWGVLKPLGDRLSYDLVFDVEGILLKVQVKSSWFSEKTGNYVVDNRRTRTNRRNIVRSPYRGNDFDFAVAYVEELELFYVFPVDVFISYGSEIHLVETDKRQRKPRSFGYREAWHLILQKGAAQKETS 149
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh..eeeee........eeeee..eeeeeeeee.........eee......------------.....eeeeee....eeeeeehhhhhh....eee.........hhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ost C   0 MGSTKLKGDIAQQAAIMRALKMGWGVLKPLGDRLSYDLVFDVEGILLKVQVKSSWKSEKTGNYVVDNRRTR------------GNDFDFAVAYVEELELFYVFPVDVFISYGSEIHLVETDKRQRKPRSFGYREAWHLILQKGAAQKETS 149
                                     9        19        29        39        49        59        69|        -   |    89        99       109       119       129       139       149
                                                                                                 70           83                                                                  


Chain D from PDB  Type:PROTEIN  Length:133
 aligned with Q57253_SYNY3 | Q57253 from UniProtKB/TrEMBL  Length:150

    Alignment length:148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141        
         Q57253_SYNY3     2 STKLKGDIAEQAAILRALKLGWGVLKPLGDRLSYDLVFDVEGILLKVQVKSSWFSEKTGNYVVDNRRTRTNRRNIVRSPYRGNDFDFAVAYVEELELFYVFPVDVFISYGSEIHLVETDKRQRKPRSFGYREAWHLILQKGAAQKETS 149
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) DUF3257-2ostD01 D:2-149                                                                                                                              Pfam domains (1)
           Pfam domains (2) DUF3257-2ostD02 D:2-149                                                                                                                              Pfam domains (2)
           Pfam domains (3) DUF3257-2ostD03 D:2-149                                                                                                                              Pfam domains (3)
           Pfam domains (4) DUF3257-2ostD04 D:2-149                                                                                                                              Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..eeeee........eeeee..eeeeeeeee.ee......eeee..---------------.....eeeeee....eeeeeehhhhhh...eeee.........hhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ost D   2 STKLKGDIAQQAAIMRALKMGWGVLKPLGDRLSYDLVFDVEGILLKVQVKSSWKSEKTGNYVVDNR---------------GNDFDFAVAYVEELELFYVFPVDVFISYGSEIHLVETDKRQRKPRSFGYREAWHLILQKGAAQKETS 149
                                    11        21        31        41        51        61     |   -         - |      91       101       111       121       131       141        
                                                                                            67              83                                                                  


Chain Y from PDB  Type:DNA  Length:29
                                                             
                 2ost Y   1 GAGGCCTTCGGGCTCATAACCCGAAGGGA  29
                                    10        20         


Chain Z from PDB  Type:DNA  Length:29
                                                             
                 2ost Z  30 TCTCCCTTCGGGTTATGAGCCCGAAGGCC  58
                                    39        49
   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  (0, 0)

(no "SCOP Domain" information available for 2OST)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OST)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: DUF3257] (1)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q57253_SYNY3 | Q57253)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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