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(-) Description

Title :  RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD
 
Authors :  M. J. Van Der Woerd, J. J. Pelletier, S. -Y. Xu, A. M. Friedman
Date :  04 Nov 99  (Deposition) - 21 Feb 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,W
Keywords :  Protein-Dna Complex, Restriction Endonuclease, Thermophilic Enzyme, Degenerate Dna Recognition, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Van Der Woerd, J. J. Pelletier, S. Xu, A. M. Friedman
Restriction Enzyme Bsobi-Dna Complex: A Tunnel For Recognition Of Degenerate Dna Sequences And Potential Histidine Catalysis.
Structure V. 9 133 2001
PubMed-ID: 11250198  |  Reference-DOI: 10.1016/S0969-2126(01)00564-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*T*AP*TP*AP*CP*TP*CP*GP*AP*GP*TP*AP*T)- 3')
    Chains: W, C
    Engineered: YES
    Other Details: DNA SEQUENCE DESIGNED FOR CRYSTALLIZATION BASED ON THE CENTRAL RECOGNITION SEQUENCE OF BACILLUS STEAROTHERMOPHILUS
    Synthetic: YES
 
Molecule 2 - BSOBI RESTRICTION ENDONUCLEASE
    Chains: A, B
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Synonym: TYPE II RESTRICTION ENZYME, TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCW

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1DIO10Ligand/Ion1,4-DIETHYLENE DIOXIDE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:21 , SER A:269 , SER A:274 , DIO A:1004 , LYS B:84 , LEU B:86BINDING SITE FOR RESIDUE DIO A 1000
02AC2SOFTWAREGLN A:297 , SER A:298 , GLN B:69 , ASP B:70 , LEU B:73 , LYS B:91 , ILE B:95 , HOH B:1189BINDING SITE FOR RESIDUE DIO B 1001
03AC3SOFTWAREALA A:136 , GLN A:139 , GLN A:140 , SER A:162 , THR A:182 , ALA A:184 , HOH A:1027BINDING SITE FOR RESIDUE DIO A 1002
04AC4SOFTWAREALA B:136 , GLN B:139 , GLN B:140 , SER B:162 , THR B:182 , ALA B:184BINDING SITE FOR RESIDUE DIO B 1003
05AC5SOFTWARETYR A:21 , SER A:269 , GLY A:272 , LEU A:273 , SER A:274 , DIO A:1000 , HOH A:1205 , LYS B:84BINDING SITE FOR RESIDUE DIO A 1004
06AC6SOFTWAREILE A:29 , HOH A:1119 , ASP B:90 , SER B:94 , ASN B:97BINDING SITE FOR RESIDUE DIO B 1005
07AC7SOFTWAREGLN B:139 , ASN B:201 , ASP B:212 , LEU B:241 , HOH B:1118 , HOH B:1184 , DT W:5BINDING SITE FOR RESIDUE DIO B 1006
08AC8SOFTWARELYS A:84 , PHE A:85 , TYR B:21 , DIO B:1009BINDING SITE FOR RESIDUE DIO A 1007
09AC9SOFTWAREILE A:78 , ASP A:90 , SER A:94 , ASN A:97 , HOH A:1078 , LEU B:33BINDING SITE FOR RESIDUE DIO A 1008
10BC1SOFTWAREPHE A:85 , DIO A:1007 , TYR B:21 , TYR B:24 , PRO B:247 , GLU B:285BINDING SITE FOR RESIDUE DIO B 1009

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DC1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DC1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DC1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DC1)

(-) Exons   (0, 0)

(no "Exon" information available for 1DC1)

(-) 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:310
 aligned with T2B1_GEOSE | P70985 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:319
                                    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       294       304       314         
           T2B1_GEOSE     5 KPFENHLKSVDDLKTTYEEYRAGFIAFALEKNKRSTPYIERARALKVAASVAKTPKDLLYLEDIQDALLYASGISDKAKKFLTEDDKKESINNLIENFLEPAGEEFIDELIFRYLLFQGDSLGGTMRNIAGALAQQKLTRAIISALDIANIPYKWLDSRDKKYTNWMDKPEDDYELETFAKGISWTINGKHRTLMYNITVPLVKKNVDICLFNCEPEIYTPQKVHQQPEKYLLLGELKGGIDPAGADEHWKTANTALTRIRNKFSEKGLSPKTIFIGAAIEHSMAEEIWDQLQSGSLTNSANLTKTEQVGSLCRWIINI 323
               SCOP domains d1dc1a_ A: Restriction endonuclease BsobI                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1dc1A01 A:5-38,A:127-323          1dc1A02 A:39-126  [code=1.10.238.90, no name defined]                                   1dc1A01 A:5-38,A:127-323  [code=3.40.91.10, no name defined]                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........eee......hhhh.eeeeeeee..eeeeeeeeeee....eeeeeeeee...---------.hhh.eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dc1 A   5 KPFENHLKSVDDLKTTYEEYRAGFIAFALEKNKRSTPYIERARALKVAASVAKTPKDLLYLEDIQDALLYASGISDKAKKFLTEDDKKESINNLIENFLEPAGEEFIDELIFRYLLFQGDSLGGTMRNIAGALAQQKLTRAIISALDIANIPYKWLDSRDKKYTNWMDKPEDDYELETFAKGISWTINGKHRTLMYNITVSLVKKNVDICLFNCEP---------QQPEKYLLLGELKGGIDPAGADEHWKTANTALTRIRNKFSEKGLSPKTIFIGAAIEHSMAEEIWDQLQSGSLTNSANLTKTEQVGSLCRWIINI 323
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214     |   -     | 234       244       254       264       274       284       294       304       314         
                                                                                                                                                                                                                                                 220       230                                                                                             


Chain B from PDB  Type:PROTEIN  Length:311
 aligned with T2B1_GEOSE | P70985 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:320
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323
           T2B1_GEOSE     4 QKPFENHLKSVDDLKTTYEEYRAGFIAFALEKNKRSTPYIERARALKVAASVAKTPKDLLYLEDIQDALLYASGISDKAKKFLTEDDKKESINNLIENFLEPAGEEFIDELIFRYLLFQGDSLGGTMRNIAGALAQQKLTRAIISALDIANIPYKWLDSRDKKYTNWMDKPEDDYELETFAKGISWTINGKHRTLMYNITVPLVKKNVDICLFNCEPEIYTPQKVHQQPEKYLLLGELKGGIDPAGADEHWKTANTALTRIRNKFSEKGLSPKTIFIGAAIEHSMAEEIWDQLQSGSLTNSANLTKTEQVGSLCRWIINI 323
               SCOP domains d1dc1b_ B: Restriction endonuclease BsobI                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -1dc1B01 B:5-38,B:127-322          1dc1B02 B:39-126  [code=1.10.238.90, no name defined]                                   1dc1B01 B:5-38,B:127-322  [code=3.40.91.10, no name defined]                                                                                                                                        - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee........eee......hhhh.eeeeeeee..eeeeeeeeeee....eeeeeeeee...---------.hhh.eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dc1 B   4 QKPFENHLKSVDDLKTTYEEYRAGFIAFALEKNKRSTPYIERARALKVAASVAKTPKDLLYLEDIQDALLYASGISDKAKKFLTEDDKKESINNLIENFLEPAGEEFIDELIFRYLLFQGDSLGGTMRNIAGALAQQKLTRAIISALDIANIPYKWLDSRDKKYTNWMDKPEDDYELETFAKGISWTINGKHRTLMYNITVSLVKKNVDICLFNCEP---------QQPEKYLLLGELKGGIDPAGADEHWKTANTALTRIRNKFSEKGLSPKTIFIGAAIEHSMAEEIWDQLQSGSLTNSANLTKTEQVGSLCRWIINI 323
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213      |  -      |233       243       253       263       273       283       293       303       313       323
                                                                                                                                                                                                                                                  220       230                                                                                             


Chain C from PDB  Type:DNA  Length:13
                                             
                 1dc1 C   1 TATACTCGAGTAT  13
                                    10   


Chain W from PDB  Type:DNA  Length:12
                                            
                 1dc1 W   1 ATACTCGAGTAT  12
                                    10
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DC1)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (T2B1_GEOSE | P70985)
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.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
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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