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(-) Description

Title :  CRYSTAL STRUCTURE OF TYPE IIF RESTRICTION ENDONUCLEASE BSE634I WITH COGNATE DNA
 
Authors :  E. N. Manakova, S. Grazulis, D. Golovenko, G. Tamulaitiene
Date :  11 Dec 11  (Deposition) - 25 Apr 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Restriction Endonuclease, Protein-Dna Complex, Hydrolase, Dna Binding Protein, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Manakova, S. Grazulis, M. Zaremba, G. Tamulaitiene, D. Golovenko, V. Siksnys
Structural Mechanisms Of The Degenerate Sequence Recognitio By Bse634I Restriction Endonuclease.
Nucleic Acids Res. V. 40 6741 2012
PubMed-ID: 22495930  |  Reference-DOI: 10.1093/NAR/GKS300

(-) Compounds

Molecule 1 - ENDONUCLEASE BSE634IR
    ChainsA, B
    EC Number3.1.21.4
    EngineeredYES
    Expression System PlasmidPUC18
    Expression System StrainER2267
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneBSE634IR
    MutationYES
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422
    Strain1422
 
Molecule 2 - DNA (5'-D(*TP*CP*GP*CP*AP*CP*CP*GP*GP*TP*GP*CP*G)-3')
    ChainsC, D
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
17PE1Ligand/Ion2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL
2CA2Ligand/IonCALCIUM ION
3CL1Ligand/IonCHLORIDE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:146 , LEU A:197 , HOH A:409 , DC C:6BINDING SITE FOR RESIDUE CA A 302
2AC2SOFTWAREGLU A:80 , LYS A:103 , MET A:104 , PRO A:105 , ASN A:106 , ASP A:146 , LEU A:176 , PHE A:179 , DC C:4 , DA C:5 , DC C:6BINDING SITE FOR RESIDUE 7PE A 303
3AC3SOFTWAREASP B:146 , LEU B:197 , HOH B:401 , DC D:6BINDING SITE FOR RESIDUE CA B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V20)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3V20)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V20)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V20)

(-) Exons   (0, 0)

(no "Exon" information available for 3V20)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:290
 aligned with Q8RT53_GEOSE | Q8RT53 from UniProtKB/TrEMBL  Length:293

    Alignment length:290
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
         Q8RT53_GEOSE     3 TNLTNSNCVEEYKENGKTKIRIKPFNALIELYHHQTPTGSIKENLDKLENYVKDVVKAKGLAIPTSGAFSNTRGTWFEVMIAIQSWNYRVKRELNDYLIIKMPNVKTLHFRKIFDNETREKLHQLEKTLLTHKQQVRLITSNPDLLIIRQKDLIKSEYNLPINKLTHENIDVALTLFKDIEGKCKWDSLVAGVGLKTSLRPDRRLQLVHEGNILKSLFAHLKMRYWNPKAEFKYYGASSEPVSKADDDALQTAATHTIVNVNSTPERAVDDIFSLTSFEDIDKMLDQIIK 292
               SCOP domains d3v20a_ A: Restriction endonuclease Bse634I                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..eeeee....eeeeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhhhhhhhhhh.............eeeee.hhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhh.eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh.......eeeeee....hhhhhhhhh..hhhhh............eeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v20 A   3 TNLTNSNCVEEYKENGKTKIRIKPFNALIELYHHQTPTGSIKENLDKLENYVKDVVKAKGLAIPTSGAFSNTRGTWFEVMIAIQSWNYRVKRELNDYLIIKMPNVKTFDFRKIFDNETREKLHQLEKSLLTHKQQVRLITSNPDLLIIRQKDLIKSEYNLPINKLTHENIDVALTLFKDIEGKCKWDSLVAGVGLKTSLRPDRRLQLVHEGNILKSLFAHLKMAYWNPKAEFKYYGASSEPVSKADDDALQTAATHTIVNVNSTPERAVDDIFSLTSFEDIDKMLDQIIK 292
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292

Chain B from PDB  Type:PROTEIN  Length:288
 aligned with Q8RT53_GEOSE | Q8RT53 from UniProtKB/TrEMBL  Length:293

    Alignment length:288
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284        
         Q8RT53_GEOSE     5 LTNSNCVEEYKENGKTKIRIKPFNALIELYHHQTPTGSIKENLDKLENYVKDVVKAKGLAIPTSGAFSNTRGTWFEVMIAIQSWNYRVKRELNDYLIIKMPNVKTLHFRKIFDNETREKLHQLEKTLLTHKQQVRLITSNPDLLIIRQKDLIKSEYNLPINKLTHENIDVALTLFKDIEGKCKWDSLVAGVGLKTSLRPDRRLQLVHEGNILKSLFAHLKMRYWNPKAEFKYYGASSEPVSKADDDALQTAATHTIVNVNSTPERAVDDIFSLTSFEDIDKMLDQIIK 292
               SCOP domains d3v20b_ B: Restriction endonuclease Bse634I                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeee..eeeeeehhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhhhhhhhh...............eeeee.hhhhhhhhhh.....hhhhhhhhhhhhhhhh.......eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh.......eeeeee....hhhhhhhh...hhhhh............eeee..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v20 B   5 LTNSNCVEEYKENGKTKIRIKPFNALIELYHHQTPTGSIKENLDKLENYVKDVVKAKGLAIPTSGAFSNTRGTWFEVMIAIQSWNYRVKRELNDYLIIKMPNVKTFDFRKIFDNETREKLHQLEKSLLTHKQQVRLITSNPDLLIIRQKDLIKSEYNLPINKLTHENIDVALTLFKDIEGKCKWDSLVAGVGLKTSLRPDRRLQLVHEGNILKSLFAHLKMAYWNPKAEFKYYGASSEPVSKADDDALQTAATHTIVNVNSTPERAVDDIFSLTSFEDIDKMLDQIIK 292
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284        

Chain C from PDB  Type:DNA  Length:13
                                             
                 3v20 C   1 TCGCACCGGTGCG  13
                                    10   

Chain D from PDB  Type:DNA  Length:13
                                             
                 3v20 D   1 TCGCACCGGTGCG  13
                                    10   

   Legend:   → Mismatch (orange background)
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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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V20)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V20)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8RT53_GEOSE | Q8RT53)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0009036    Type II site-specific deoxyribonuclease activity    Catalysis of the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates and 3' hydroxyls. Cleavage is dependent on the presence in the DNA of a specific recognition site; cleavage occurs at or very near this recognition site.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
biological process
    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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 Related Entries

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

UniProtKB/TrEMBL
        Q8RT53_GEOSE | Q8RT531knv 3v1z 3v21

(-) Related Entries Specified in the PDB File

3v1z THE SAME PROTEIN WITH THE OTHER VARIANT OF COGNATE DNA
3v21