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(-) Description

Title :  I-MSOI RE-DESIGNED FOR ALTERED DNA CLEAVAGE SPECIFICITY (-7C)
 
Authors :  G. K. Taylor, B. L. Stoddard
Date :  13 Nov 09  (Deposition) - 19 May 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D,F,G,H,I
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  F,G,H,I  (1x)
Keywords :  Redesign, Protein-Dna Complex, Chloroplast, Endonuclease, Hydrolase- Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Ashworth, G. K. Taylor, J. J. Havranek, S. A. Quadri, B. L. Stoddard, D. Baker
Computational Reprogramming Of Homing Endonuclease Specificity At Multiple Adjacent Base Pairs.
Nucleic Acids Res. V. 38 5601 2010
PubMed-ID: 20435674  |  Reference-DOI: 10.1093/NAR/GKQ283

(-) Compounds

Molecule 1 - SITE-SPECIFIC DNA ENDONUCLEASE I-MSOI
    Chains: A, B, F, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24D
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: I-MSOI, ORF170
    Mutation: YES
    Organism Scientific: MONOMASTIX SP.
    Organism Taxid: 141716
    Strain: OKE-1
 
Molecule 2 - 5'-D(*GP*CP*AP*GP*AP*CP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP *GP*TP*TP*CP*CP*G)-3'
    Chains: C, H
    Engineered: YES
    Other Details: SYNTHETIC DNA
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP *GP*TP*CP*TP*GP*C)-3'
    Chains: D, I
    Engineered: YES
    Other Details: SYNTHETIC DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDFGHI
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     FGHI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:20 , GLY A:21 , HOH A:173 , ASP B:22 , DA C:14 , DG D:15BINDING SITE FOR RESIDUE CA A 171
2AC2SOFTWAREASP A:22 , GLY B:21 , DG C:15 , DC D:14BINDING SITE FOR RESIDUE CA A 172
3AC3SOFTWAREASP A:22 , GLY B:21 , ASP B:22 , DA C:14 , DG C:15 , DC D:14 , DG D:15BINDING SITE FOR RESIDUE CA C 25
4AC4SOFTWAREASP F:20 , GLY F:21 , ASP G:22 , GLN G:50 , DA H:14 , DG I:15BINDING SITE FOR RESIDUE CA F 171
5AC5SOFTWAREASP F:22 , GLY G:21 , DG H:15 , DC I:14BINDING SITE FOR RESIDUE CA F 172
6AC6SOFTWAREGLY F:21 , ASP F:22 , GLY G:21 , ASP G:22 , DA H:14 , DG H:15 , DC I:14 , DG I:15BINDING SITE FOR RESIDUE CA H 25

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KO2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KO2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KO2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KO2)

(-) Exons   (0, 0)

(no "Exon" information available for 3KO2)

(-) 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:161
 aligned with C0JWR6_MONSK | C0JWR6 from UniProtKB/TrEMBL  Length:170

    Alignment length:161
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165 
         C0JWR6_MONSK     6 TLQPTEAAYIAGFLDGDGSIYAKLIPRPDYKDIKYQVSLAISFIQRKDKFPYLQDIYDQLGKRGNLRKDRGDGIADYTIIGSTHLSIILPDLVPYLRIKKKQANRILHIINLYPQAQKNPSKFLDLVKIVDDVQNLNKRADELKSTNYDRLLEEFLKAGKI 166
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ko2A00 A:6-166 Homing endonucleases                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhheeeeeeeee........eeeeeeeeeeee..hhhhhhhhhhhh....eee......eeeeeeehhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ko2 A   6 TLQPTEAAYIAGFLDGDGSIYARLIPRPDYKDIKYQVELAISFIQRKDKFPYLQDIYDQLGKRGTLRKDRGDGIADYTIWGSTHLSIILPDLVPYLRIKKKQANRILHIINLYPQAQKNPSKFLDLVKIVDDVQNLNKRADELKSTNYDRLLEEFLKAGKI 166
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165 


Chain B from PDB  Type:PROTEIN  Length:161
 aligned with C0JWR6_MONSK | C0JWR6 from UniProtKB/TrEMBL  Length:170

    Alignment length:161
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165 
         C0JWR6_MONSK     6 TLQPTEAAYIAGFLDGDGSIYAKLIPRPDYKDIKYQVSLAISFIQRKDKFPYLQDIYDQLGKRGNLRKDRGDGIADYTIIGSTHLSIILPDLVPYLRIKKKQANRILHIINLYPQAQKNPSKFLDLVKIVDDVQNLNKRADELKSTNYDRLLEEFLKAGKI 166
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ko2B00 B:6-166 Homing endonucleases                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhheeeeeeeee........eeeeeeeeeeee..hhhhhhhhhhhh....eee......eeeeeeehhhhhh.hhhhh......hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ko2 B   6 TLQPTEAAYIAGFLDGDGSIYARLIPRPDYKDIKYQVELAISFIQRKDKFPYLQDIYDQLGKRGTLRKDRGDGIADYTIWGSTHLSIILPDLVPYLRIKKKQANRILHIINLYPQAQKNPSKFLDLVKIVDDVQNLNKRADELKSTNYDRLLEEFLKAGKI 166
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165 


Chain C from PDB  Type:DNA  Length:24
                                                        
                 3ko2 C   1 GCAGACCGTCGTGAGACAGTTCCG  24
                                    10        20    


Chain D from PDB  Type:DNA  Length:24
                                                        
                 3ko2 D   1 CGGAACTGTCTCACGACGGTCTGC  24
                                    10        20    


Chain F from PDB  Type:PROTEIN  Length:161
 aligned with C0JWR6_MONSK | C0JWR6 from UniProtKB/TrEMBL  Length:170

    Alignment length:161
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165 
         C0JWR6_MONSK     6 TLQPTEAAYIAGFLDGDGSIYAKLIPRPDYKDIKYQVSLAISFIQRKDKFPYLQDIYDQLGKRGNLRKDRGDGIADYTIIGSTHLSIILPDLVPYLRIKKKQANRILHIINLYPQAQKNPSKFLDLVKIVDDVQNLNKRADELKSTNYDRLLEEFLKAGKI 166
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ko2F00 F:6-166 Homing endonucleases                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhheeeeeeeee........eeeeeeeeeeee..hhhhhhhhhhhhh...eee......eeeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ko2 F   6 TLQPTEAAYIAGFLDGDGSIYARLIPRPDYKDIKYQVELAISFIQRKDKFPYLQDIYDQLGKRGTLRKDRGDGIADYTIWGSTHLSIILPDLVPYLRIKKKQANRILHIINLYPQAQKNPSKFLDLVKIVDDVQNLNKRADELKSTNYDRLLEEFLKAGKI 166
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165 


Chain G from PDB  Type:PROTEIN  Length:161
 aligned with C0JWR6_MONSK | C0JWR6 from UniProtKB/TrEMBL  Length:170

    Alignment length:161
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165 
         C0JWR6_MONSK     6 TLQPTEAAYIAGFLDGDGSIYAKLIPRPDYKDIKYQVSLAISFIQRKDKFPYLQDIYDQLGKRGNLRKDRGDGIADYTIIGSTHLSIILPDLVPYLRIKKKQANRILHIINLYPQAQKNPSKFLDLVKIVDDVQNLNKRADELKSTNYDRLLEEFLKAGKI 166
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ko2G00 G:6-166 Homing endonucleases                                                                                                                              CATH domains
           Pfam domains (1) ---------LAGLIDADG_1-3ko2G01 G:15-136                                                                                              ------------------------------ Pfam domains (1)
           Pfam domains (2) ---------LAGLIDADG_1-3ko2G02 G:15-136                                                                                              ------------------------------ Pfam domains (2)
           Pfam domains (3) ---------LAGLIDADG_1-3ko2G03 G:15-136                                                                                              ------------------------------ Pfam domains (3)
           Pfam domains (4) ---------LAGLIDADG_1-3ko2G04 G:15-136                                                                                              ------------------------------ Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhheeeeeeee..........eeeeeeeeeee..hhhhhhhhhhhh....eee......eeeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ko2 G   6 TLQPTEAAYIAGFLDGDGSIYARLIPRPDYKDIKYQVELAISFIQRKDKFPYLQDIYDQLGKRGTLRKDRGDGIADYTIWGSTHLSIILPDLVPYLRIKKKQANRILHIINLYPQAQKNPSKFLDLVKIVDDVQNLNKRADELKSTNYDRLLEEFLKAGKI 166
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165 


Chain H from PDB  Type:DNA  Length:24
                                                        
                 3ko2 H   1 GCAGACCGTCGTGAGACAGTTCCG  24
                                    10        20    


Chain I from PDB  Type:DNA  Length:24
                                                        
                 3ko2 I   1 CGGAACTGTCTCACGACGGTCTGC  24
                                    10        20
   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 3KO2)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Homing_endonuc (19)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,F,G   (C0JWR6_MONSK | C0JWR6)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
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.
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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  3ko2
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  C0JWR6_MONSK | C0JWR6
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        C0JWR6_MONSK | C0JWR6: 1m5x 2fld 3fd2

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