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(-) Description

Title :  ALTERNATIVE BINDING MODE OF RESTRICTION ENDONUCLEASE BCNI TO COGNATE DNA
 
Authors :  M. Sokolowska, M. Kaus-Drobek, H. Czapinska, G. Tamulaitis, R. H. Szczepanowski, V. Siksnys, M. Bochtler
Date :  10 Aug 09  (Deposition) - 11 Aug 10  (Release) - 11 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,E,F  (1x)
Biol. Unit 2:  B,G,H  (1x)
Biol. Unit 3:  C,I,J  (1x)
Biol. Unit 4:  D,K,L  (1x)
Keywords :  Endonuclease-Dna Complex, Restriction Enzyme, Bcni, Pseudopalindromic Sequence Recognition, Pseudosymmetry, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sokolowska, M. Kaus-Drobek, H. Czapinska, G. Tamulaitis, R. H. Szczepanowski, V. Siksnys, M. Bochtler
How Bcni And Mvai Distinguish W From S
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - R.BCNI
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD24
    Expression System Strain: ER2267
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BCNIR
    Organism Scientific: BREVIBACILLUS CENTROSPORUS
    Organism Taxid: 54910
 
Molecule 2 - 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3'
    Chains: E, G, I, K
    Engineered: YES
    Other Details: G STRAND
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3'
    Chains: F, H, J, L
    Engineered: YES
    Other Details: C STRAND
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): A   EF      
Biological Unit 2 (1x):  B    GH    
Biological Unit 3 (1x):   C     IJ  
Biological Unit 4 (1x):    D      KL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3IMB)

(-) Sites  (0, 0)

(no "Site" information available for 3IMB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3IMB)

(-) 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:238
 aligned with Q8RNV8_9BACL | Q8RNV8 from UniProtKB/TrEMBL  Length:238

    Alignment length:238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
         Q8RNV8_9BACL     1 MKIWSKEEVVNKLHEIKNKGYLSVPTDMFRTDDGVVGQILERQFGVQENNITLGDLGEFELKGMRNRKAKSNLTLFHKKPVAGQTVIQIFNRFGYVKPSSRNPEVMKKKLFTTIKGGRLNNLGLTLNAKHASEINLYYQDEYLSTWDLNLSKIEKLVLVFAETIGRANSPEEQFHFTKAYMLTEINDITSLINDGVLVMDLCIDQDLSKSKGPHDRGPHLRIPISKLDKLYRNIERLL 238
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh..ee..........hhhhhhhhhhh...............eeeeee.......eeeee....ee.hhhhhhhhhheeee.......eeeeeeeee.........eeeeeee..eeeeee..eeeeee...hhhhh.eeeeeeeee........eeeeeeeeeeeee..hhhhhhh...eeeeeeeee.......ee...eeeehhhhhhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3imb A   1 MKIWSKEEVVNKLHEIKNKGYLSVPTDMFRTDDGVVGQILERQFGVQENNITLGDLGEFELKGMRNRKAKSNLTLFHKKPVAGQTVIQIFNRFGYVKPSSRNPEVMKKKLFTTIKGGRLNNLGLTLNAKHASEINLYYQDEYLSTWDLNLSKIEKLVLVFAETIGRANSPEEQFHFTKAYMLTEINDITSLINDGVLVMDLCIDQDLSKSKGPHDRGPHLRIPISKLDKLYRNIERLL 238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        


Chain B from PDB  Type:PROTEIN  Length:238
 aligned with Q8RNV8_9BACL | Q8RNV8 from UniProtKB/TrEMBL  Length:238

    Alignment length:238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
         Q8RNV8_9BACL     1 MKIWSKEEVVNKLHEIKNKGYLSVPTDMFRTDDGVVGQILERQFGVQENNITLGDLGEFELKGMRNRKAKSNLTLFHKKPVAGQTVIQIFNRFGYVKPSSRNPEVMKKKLFTTIKGGRLNNLGLTLNAKHASEINLYYQDEYLSTWDLNLSKIEKLVLVFAETIGRANSPEEQFHFTKAYMLTEINDITSLINDGVLVMDLCIDQDLSKSKGPHDRGPHLRIPISKLDKLYRNIERLL 238
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh..ee..........hhhhhhhhhhhh..............eeeeee.......eeeee....ee.hhhhhhhhhheeee.......eeeeeeeee.........eeeeeee..eeeeee..eeeeee..hhhhhh.eeeeeeeee........eeeeeeeeeeeee..hhhhhhh...eeeeeeeee.......ee...eeeehhhhhhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3imb B   1 MKIWSKEEVVNKLHEIKNKGYLSVPTDMFRTDDGVVGQILERQFGVQENNITLGDLGEFELKGMRNRKAKSNLTLFHKKPVAGQTVIQIFNRFGYVKPSSRNPEVMKKKLFTTIKGGRLNNLGLTLNAKHASEINLYYQDEYLSTWDLNLSKIEKLVLVFAETIGRANSPEEQFHFTKAYMLTEINDITSLINDGVLVMDLCIDQDLSKSKGPHDRGPHLRIPISKLDKLYRNIERLL 238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        


Chain C from PDB  Type:PROTEIN  Length:238
 aligned with Q8RNV8_9BACL | Q8RNV8 from UniProtKB/TrEMBL  Length:238

    Alignment length:238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
         Q8RNV8_9BACL     1 MKIWSKEEVVNKLHEIKNKGYLSVPTDMFRTDDGVVGQILERQFGVQENNITLGDLGEFELKGMRNRKAKSNLTLFHKKPVAGQTVIQIFNRFGYVKPSSRNPEVMKKKLFTTIKGGRLNNLGLTLNAKHASEINLYYQDEYLSTWDLNLSKIEKLVLVFAETIGRANSPEEQFHFTKAYMLTEINDITSLINDGVLVMDLCIDQDLSKSKGPHDRGPHLRIPISKLDKLYRNIERLL 238
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh...ee..........hhhhhhhhhhh...............eeeeee.......eeeee....ee.hhhhhhhhhheeee.......eeeeeeeee.........eeeeeee..eeeeee..eeeeee...hhhhh.eeeeeeeee........eeeeeeeeeeeee..hhhhhhh...eeeeeeeee.......ee...eeeehhhhhhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3imb C   1 MKIWSKEEVVNKLHEIKNKGYLSVPTDMFRTDDGVVGQILERQFGVQENNITLGDLGEFELKGMRNRKAKSNLTLFHKKPVAGQTVIQIFNRFGYVKPSSRNPEVMKKKLFTTIKGGRLNNLGLTLNAKHASEINLYYQDEYLSTWDLNLSKIEKLVLVFAETIGRANSPEEQFHFTKAYMLTEINDITSLINDGVLVMDLCIDQDLSKSKGPHDRGPHLRIPISKLDKLYRNIERLL 238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        


Chain D from PDB  Type:PROTEIN  Length:238
 aligned with Q8RNV8_9BACL | Q8RNV8 from UniProtKB/TrEMBL  Length:238

    Alignment length:238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
         Q8RNV8_9BACL     1 MKIWSKEEVVNKLHEIKNKGYLSVPTDMFRTDDGVVGQILERQFGVQENNITLGDLGEFELKGMRNRKAKSNLTLFHKKPVAGQTVIQIFNRFGYVKPSSRNPEVMKKKLFTTIKGGRLNNLGLTLNAKHASEINLYYQDEYLSTWDLNLSKIEKLVLVFAETIGRANSPEEQFHFTKAYMLTEINDITSLINDGVLVMDLCIDQDLSKSKGPHDRGPHLRIPISKLDKLYRNIERLL 238
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh..ee..........hhhhhhhhhhh...............eeeeee.......eeeee....ee.hhhhhhhhhheeee.......eeeeeeeee.........eeeeeee..eeeeee..eeeeee.........eeeeeeeee........eeeeeeeeeeeee..hhhhhhh...eeeeeeeee.......ee...eeeehhhhhhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3imb D   1 MKIWSKEEVVNKLHEIKNKGYLSVPTDMFRTDDGVVGQILERQFGVQENNITLGDLGEFELKGMRNRKAKSNLTLFHKKPVAGQTVIQIFNRFGYVKPSSRNPEVMKKKLFTTIKGGRLNNLGLTLNAKHASEINLYYQDEYLSTWDLNLSKIEKLVLVFAETIGRANSPEEQFHFTKAYMLTEINDITSLINDGVLVMDLCIDQDLSKSKGPHDRGPHLRIPISKLDKLYRNIERLL 238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        


Chain E from PDB  Type:DNA  Length:9
                                         
                 3imb E  -4 GTCCGGGCG   4


Chain F from PDB  Type:DNA  Length:9
                                         
                 3imb F  -4 CGCCCGGAC   4


Chain G from PDB  Type:DNA  Length:9
                                         
                 3imb G  -4 GTCCGGGCG   4


Chain H from PDB  Type:DNA  Length:9
                                         
                 3imb H  -4 CGCCCGGAC   4


Chain I from PDB  Type:DNA  Length:9
                                         
                 3imb I  -4 GTCCGGGCG   4


Chain J from PDB  Type:DNA  Length:9
                                         
                 3imb J  -4 CGCCCGGAC   4


Chain K from PDB  Type:DNA  Length:9
                                         
                 3imb K  -4 GTCCGGGCG   4


Chain L from PDB  Type:DNA  Length:9
                                         
                 3imb L  -4 CGCCCGGAC   4
   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 3IMB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IMB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IMB)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8RNV8_9BACL | Q8RNV8)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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

UniProtKB/TrEMBL
        Q8RNV8_9BACL | Q8RNV8: 2odh 2odi 2q10

(-) Related Entries Specified in the PDB File

2aor CRYSTAL STRUCTURE OF MUTH-HEMIMETHYLATED DNA COMPLEX
2azo DNA MISMATCH REPAIR PROTEIN MUTH FROM E. COLI
2oa9 RESTRICTION ENDONUCLEASE MVAI IN THE ABSENCE OF DNA
2oaa RESTRICTION ENDONUCLEASE MVAI-COGNATE DNA SUBSTRATE COMPLEX
2odh RESTRICTION ENDONUCLEASE BCNI IN THE ABSENCE OF DNA
2odi RESTRICTION ENDONUCLEASE BCNI-COGNATE DNA SUBSTRATE COMPLEX