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(-) Description

Title :  DNA BINDING DOMAIN OF RESTRICTION ENDONUCLEASE BOUND TO DNA
 
Authors :  R. Sukackaite, S. Grazulis, V. Siksnys
Date :  08 Jul 11  (Deposition) - 23 May 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Dna Complex, Restriction Endonuclease, Base Flipping, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Sukackaite, S. Grazulis, G. Tamulaitis, V. Siksnys
The Recognition Domain Of The Methyl-Specific Endonuclease Mcrbc Flips Out 5-Methylcytosine.
Nucleic Acids Res. V. 40 7552 2012
PubMed-ID: 22570415  |  Reference-DOI: 10.1093/NAR/GKS332

(-) Compounds

Molecule 1 - 5-METHYLCYTOSINE-SPECIFIC RESTRICTION ENZYME B
    ChainsA, B
    EC Number3.1.21.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPBAD24
    Expression System StrainER2267
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DNA BINDING DOMAIN
    GeneMCRB
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK-12
    SynonymECOKMCRBC
 
Molecule 2 - DNA (5'-D(*T*GP*AP*GP*AP*CP*CP*GP*GP*TP*AP*GP*C)-3')
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 3 - DNA (5'-D(*A*GP*CP*TP*AP*CP*CP*GP*GP*TP*CP*TP*C)-3')
    ChainsD
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3SSE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser B:95 -Ser B:96

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3SSE)

(-) 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:153
 aligned with MCRB_ECOLI | P15005 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
           MCRB_ECOLI     2 ESIQPWIEKFIKQAQQQRSQSTKDYPTSYRNLRVKLSFGYGNFTSIPWFAFLGEGQEASNGIYPVILYYKDFDELVLAYGISDTNEPHAQWQFSSDIPKTIAEYFQATSGVYPKKYGQSYYACSQKVSQGIDYTRFASMLDNIINDYKLIFNS 154
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh..........eee.eeeeeee.........eeeeee........eeeeeeeee...eeeeeeeee..................hhhhhhhhhh.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sse A   2 ESIQPWIEKFIKQAQQQRSQSTKDYPTSYRNLRVKLSFGYGNFTSIPWFAFLGEGQEASNGIYPVILYYKDFDELVLAYGISDTNEPHAQWQFSSDIPKTIAEYFQATSGVYPKKYGQSYYACSQKVSQGIDYTRFASMLDNIINDYKLIFNS 154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   

Chain B from PDB  Type:PROTEIN  Length:148
 aligned with MCRB_ECOLI | P15005 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141        
           MCRB_ECOLI     2 ESIQPWIEKFIKQAQQQRSQSTKDYPTSYRNLRVKLSFGYGNFTSIPWFAFLGEGQEASNGIYPVILYYKDFDELVLAYGISDTNEPHAQWQFSSDIPKTIAEYFQATSGVYPKKYGQSYYACSQKVSQGIDYTRFASMLDNIINDYK 149
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh..........eee.eeeeeee.........eeeeee........eeeeeeeee...eeeeeeeee..................hhhhhhhhhh.........eeeeeeee..................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sse B   2 ESIQPWIEKFIKQAQQQRSQSTKDYPTSYRNLRVKLSFGYGNFTSIPWFAFLGEGQEASNGIYPVILYYKDFDELVLAYGISDTNEPHAQWQFSSDIPKTIAEYFQATSGVYPKKYGQSYYACSQKVSQGIDYTRFASMLDNIINDYK 149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141        

Chain C from PDB  Type:DNA  Length:12
                                            
                 3sse C   2 GAGACCGGTAGC  13
                                    11  

Chain D from PDB  Type:DNA  Length:12
                                            
                 3sse D   2 GCTACCGGTCTC  13
                                    11  

   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 3SSE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MCRB_ECOLI | P15005)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0015666    restriction endodeoxyribonuclease activity    Catalysis of endonucleolytic cleavage of DNA in a site-specific manner, resulting in double-strand breaks.
biological process
    GO:0006308    DNA catabolic process    The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0009307    DNA restriction-modification system    A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.
    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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    Ser B:95 - Ser B:96   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        MCRB_ECOLI | P150053ssc 3ssd

(-) Related Entries Specified in the PDB File

3ssc 3ssd